name: File
-description: Abstract class for various kinds of files. Subclasses will be defined
+description: Abstract class for various kinds of files. Subclasses may be defined
for specific file types.
comments:
- This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD)
@@ -388,14 +430,20 @@
Direct
from_schema: https://w3id.org/nhlbidatastage/bdchm
rank: 1000
range: integer
- uri:
- name: uri
+ file_location:
+ name: file_location
description: A unique identifier or url for identifying or locating the file.
- comments:
- - Not included in the Gen3 Core Metadata or Dublin Core.
from_schema: https://w3id.org/nhlbidatastage/bdchm
rank: 1000
+ multivalued: true
range: uriorcurie
+ md5sum:
+ name: md5sum
+ description: The 128-bit hash value expressed as a 32 digit hexadecimal number
+ used as a file's digital fingerprint.
+ from_schema: https://w3id.org/nhlbidatastage/bdchm
+ rank: 1000
+ range: string
data_type:
name: data_type
description: The nature or genre of the resource. Recommended best practice is
@@ -434,13 +482,21 @@
Direct
description: A reference to the Participant to which this file relates.
from_schema: https://w3id.org/nhlbidatastage/bdchm
range: Participant
+ derived_from:
+ name: derived_from
+ description: A File from which this File is derived. A derivation is a transformation
+ of an entity into another, an update of an entity resulting in a new one, or
+ the construction of a new entity based on a pre-existing entity.
+ from_schema: https://w3id.org/nhlbidatastage/bdchm
+ rank: 1000
+ range: File
Induced
name: File
-description: Abstract class for various kinds of files. Subclasses will be defined
+description: Abstract class for various kinds of files. Subclasses may be defined
for specific file types.
comments:
- This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD)
@@ -480,18 +536,28 @@
Induced
domain_of:
- File
range: integer
- uri:
- name: uri
+ file_location:
+ name: file_location
description: A unique identifier or url for identifying or locating the file.
- comments:
- - Not included in the Gen3 Core Metadata or Dublin Core.
from_schema: https://w3id.org/nhlbidatastage/bdchm
rank: 1000
- alias: uri
+ multivalued: true
+ alias: file_location
owner: File
domain_of:
- File
range: uriorcurie
+ md5sum:
+ name: md5sum
+ description: The 128-bit hash value expressed as a 32 digit hexadecimal number
+ used as a file's digital fingerprint.
+ from_schema: https://w3id.org/nhlbidatastage/bdchm
+ rank: 1000
+ alias: md5sum
+ owner: File
+ domain_of:
+ - File
+ range: string
data_type:
name: data_type
description: The nature or genre of the resource. Recommended best practice is
@@ -564,6 +630,18 @@
Induced
- ObservationSet
- Observation
range: Participant
+ derived_from:
+ name: derived_from
+ description: A File from which this File is derived. A derivation is a transformation
+ of an entity into another, an update of an entity resulting in a new one, or
+ the construction of a new entity based on a pre-existing entity.
+ from_schema: https://w3id.org/nhlbidatastage/bdchm
+ rank: 1000
+ alias: derived_from
+ owner: File
+ domain_of:
+ - File
+ range: File
identity:
name: identity
description: A 'business' identifier or accession number for the entity, typically
diff --git a/derived_from/index.html b/derived_from/index.html
new file mode 100644
index 0000000..9e04a2e
--- /dev/null
+++ b/derived_from/index.html
@@ -0,0 +1,415 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Slot: derived_from - BioData Catalyst Harmonized Model
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity.
from schema: https://w3id.org/nhlbidatastage/bdchm
+
+
LinkML Source
+
+
+
name: derived_from
+description: A File from which this File is derived. A derivation is a transformation
+ of an entity into another, an update of an entity resulting in a new one, or the
+ construction of a new entity based on a pre-existing entity.
+from_schema: https://w3id.org/nhlbidatastage/bdchm
+rank: 1000
+alias: derived_from
+owner: File
+domain_of:
+- File
+range: File
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/uri/index.html b/file_location/index.html
similarity index 94%
rename from uri/index.html
rename to file_location/index.html
index 3ca459f..308793b 100644
--- a/uri/index.html
+++ b/file_location/index.html
@@ -8,14 +8,14 @@
-
+
- Slot: uri - BioData Catalyst Harmonized Model
+ Slot: file_location - BioData Catalyst Harmonized Model
@@ -64,7 +64,7 @@
name: file_location
description: A unique identifier or url for identifying or locating the file.
-comments:
-- Not included in the Gen3 Core Metadata or Dublin Core.
from_schema: https://w3id.org/nhlbidatastage/bdchm
rank: 1000
-alias: uri
+multivalued: true
+alias: file_location
owner: File
domain_of:
- File
diff --git a/index.html b/index.html
index 59b2d5f..7356ec3 100644
--- a/index.html
+++ b/index.html
@@ -430,7 +430,7 @@
from schema: https://w3id.org/nhlbidatastage/bdchm
+
+
LinkML Source
+
+
+
name: md5sum
+description: The 128-bit hash value expressed as a 32 digit hexadecimal number used
+ as a file's digital fingerprint.
+from_schema: https://w3id.org/nhlbidatastage/bdchm
+rank: 1000
+alias: md5sum
+owner: File
+domain_of:
+- File
+range: string
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/search/search_index.json b/search/search_index.json
index 2de17ed..a17f3e6 100644
--- a/search/search_index.json
+++ b/search/search_index.json
@@ -1 +1 @@
-{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"BioData Catalyst Harmonized Model (bdchm) This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm Name: bdchm Classes Class Description Entity Any resource that has its own identifier BiologicProduct A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. BodySite A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. Condition Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. Consent An entity that can be used to capture consent code and other relevant data about consent for a study. Demography Demographics about an individual or animal receiving care or other health-related services. DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. Document A collection of information intented to be understood together as a whole, and codified in human-readable form. DrugExposure DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. File Abstract class for various kinds of files. Subclasses will be defined for specific file types. Observation A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. DimensionalObservation A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. ObservationSet A structured object to hold related Observations in a set. DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). Organization A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. Participant A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. Person Administrative information about an individual or animal receiving care or other health-related services. Procedure Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] Quantity A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. Questionnaire A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) ResearchStudy A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. Specimen Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) SpecimenCreationActivity The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. SpecimenTransportActivity An activity through which a specimen is transported between locations or organizations. Substance A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. TimePoint A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. Visit Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) ObservationValue Single-valued observation valueholiding slot ObservationValueBoolean Single-valued boolean observation ObservationValueDecimal Single-valued decimal observation ObservationValueInteger Single-valued integer observation ObservationValueQuantity Single-valued Quantity observation ObservationValueString Single-valued string observation QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) QuestionnaireResponseValue Single-valued answer to the question. (FHIR) QuestionnaireResponseValueBoolean Single-valued boolean answer to the question QuestionnaireResponseValueDecimal Single-valued decimal answer to the question QuestionnaireResponseValueInteger Single-valued integer answer to the question QuestionnaireResponseValueString Single-valued string answer to the question QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question ResearchStudyCollection A holder for ResearchStudy objects TimePeriod A period of time between a start and end time point. Slots Slot Description activity_type The high-level type of creation activity additive A material substance added to the container (typically to support the primary... age_at_condition_end The Participant's age (expressed in days) when the condition was recorded as ... age_at_condition_start The Participant's age (expressed in days) when the condition was first record... age_at_death The age of an individual at the time of death, expressed in days since birth age_at_enrollment The age in days when the Participant enrolled on the ResearchStudy age_at_exposure_end The Participant's age (expressed in days) at the exposure end date, if availa... age_at_exposure_start The Participant's age (expressed in days) at the exposure start date age_at_observation The Participant's age (expressed in days) when the Observation was made age_at_procedure The Participant's age (expressed in days) when the procedure was performed age_at_response The age (in days) of the Participant when the QuestionnaireResponse was captu... age_at_visit_end The age of the Participant (in days) at the end of the Visit age_at_visit_start The age of the Participant (in days) at the start of the Visit alias A secondary name for the organization such as a short name or abbreviation (e analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... associated_participant A reference to the Participant that is associated with this record associated_person A reference to the Person that is associated with this record associated_timepoint A collection of timepoint observations that are relevant to research projects... associated_visit A reference to the Visit during which this QuestionnaireResponse was captured breed A label given to a group of animals homogeneous in appearance and other chara... category The general category of observation set described cause_of_death Coded value indicating the circumstance or condition that results in the deat... cellular_composition_type A term describing the type of cell or cellular material comprising a specimen code Corresponding concept for this item in a terminology collection_method_type The type of method applied in collecting a sample from its original source collection_site The anatomic site from which a specimen was collected condition_concept The coded value for the presence of a disease or medical condition stated as ... condition_provenance A value representing the provenance of the Condition record condition_status A value indicating whether the medical condition described in this record is ... consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ... consents Data Use Restrictions that are used to indicate permissions/restrictions for ... contained_in A physical container in which a specimen is presently held or attached - as ... container A container in which the specimen is held or affixed during its storage container_number Informal number by which the container is referenced or identified (e container_type The kind of the container copyright Textual description of any use and/or publishing restrictions copyright_label Copyright holder and year(s) creation_activity The activity through which a specimen was created, by removing material from ... data_category A broad categorization of the contents of the data file data_type The nature or genre of the resource date_ended The date when the research project ended date_started The date when the research project began date_time An explicitly specified timepoint described in terms of a date and optionally... days_supply The number of days of supply of the medication as recorded in the original pr... derivation_method_type The type of method applied to derive a new specimen from an existing one derived_product A 'living' biologically active product that was derived from the specimen (e description A free text field to capture additional info/explanation about the research s... description_shortened An abbreviated description of a research program, project, or study device_concept The coded value for a device dimensional_measures Observations about the current physical dimensions of an object (e document_type The high-level type of the document (e drug_concept The coded value for a drug duration The length of time over which the activity was performed entries ethnicity An individual's self-described social and cultural grouping, specifically whe... event_type An event that occurred at the point in time specified by this TimePoint exposure_provenance A value representing the provenance of the DrugExposure record file_name The name (or part of a name) of a file (of any type) file_size The size of the data file (object) in bytes focus The entity that the report is primarily about format The file format, physical medium, or dimensions of the resource growth_rate When the specimen an actively growing model system, such as a cell or tissue ... has_questionnaire_item A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... id The 'logical' identifier of the entity within the system of record identity A 'business' identifier or accession number for the entity, typically as prov... index_time_point Another TimePoint from which this point is offset index_timepoint The text term used to describe the reference or anchor date used for date obf... items A collection of QuestionnaireItem objects which encapsulate the question bein... language The language(s) in which questions are presented member_of_research_study A reference to the Study(s) of which this Participant is a member method_type A specific type of method or procedure performed to process the specimen name An unabridged name of a research program, project, or study name_shortened An abbreviated name of a research program, project, or study observation_type The type of Observation being represented (e observations A set of one or more observations offset_from_index A quantity of time that, together with the index date or event, can be used t... organization_type The type of the organization (e originating_site The Organization through which a subject was enrolled on a ResearchStudy parent_container A larger container of which this container is a part (e parent_specimen An existing specimen from which the specimen of interest was directly derived... part_of A reference to a parent ResearchStudy (e passage_number When the specimen an actively growing model system, such as a cell or tissue ... performed_by The organization or group that performed the activity period_end When a period of time ended period_start When a period of time started principal_investigator The investigator or investigators leading a project procedure_concept The coded value that describes the procedure, derived from OMOP codes procedure_provenance A value representing the provenance of the Procedure record processing_activity An activity that modifies the physical structure, composition, or state of a ... product_type The high level type of model system (e publisher Name of the publisher/steward (organization or individual) of this Questionna... qualifier A qualifier that further refines or specifies the location of the body site -... quality_measure An observation about characteristics of a specimen that are indicative of its... quantity The quantity of procedures ordered or administered quantity_collected The quantity of material in the specimen as originally collected from its ori... quantity_measure An observation related to the present quantity of a specimen - e race An arbitrary classification of a taxonomic group that is a division of a spec... refills Intended refills at time of the prescription related_document A reference to an external document that is about or related to the specimen ... relationship_to_participant A value indicating the relationship between the Participant to which the Cond... research_project_type The 'type' of ResearchStudy represented (e response_value role A role played by the substance in a particular application (e route_concept Route of drug administration section_location The location in a parent specimen from which a section/portion was excised (e sex The biologic character or quality that distinguishes male and female from one... sig This is the verbatim instruction for the drug as written by the provider site A term describing any site in the body source_material_type The general kind of material from which the specimen was derived source_participant A specific Subject from which the specimen was directly or indirectly derived species The scientific binomial name for the species of the Person (e specimen_order A numeric value that represents the sequential order of this creation activit... specimen_type The high-level type of the specimen, based on its derivation provenance (i sponsor An entity that is responsible for the initiation, management, and/or financin... storage_activity An activity that results in the storage or maintenance of a specimen in a par... study_arm The arm(s) of the study on which the Participant is enrolled substance_quantity The quantity of substance this instance stands for substance_type The specific type of the substance - at as granular a level as possible text Name for group or question text title Name for this Questionnaire (human friendly) transport_activity An activity through which the specimen is transported between locations transport_destination An organization (facility, site, lab, etc) to which the specimen is delivered... transport_origin An organization (facility, site, lab, etc) from which the specimen was transp... type unit A coded or free text (in the uri A unique identifier or url for identifying or locating the file url A URL address for a resource that provides information about a research progr... valid_from The point in time from which the consent record is valid valid_to The point in time after which the consent record is invalid value A general slot to hold a value value_concept A coded value representing a quantity (e value_decimal An amount, in the given units (if specified) version The identifier that is used to identify this version of the questionnaire whe... visit_category A value representing the kind (or category) of visit, like inpatient or outpa... visit_provenance A value representing the provenance of the visit record, or where the record ... vital_status Coded value indicating the state or condition of being living or deceased; al... year_of_birth Numeric value to represent the calendar year in which an individual was born year_of_death Numeric value to represent the calendar year in which an individual died Enumerations Enumeration Description AnalyteTypeEnum CellularOrganismSpeciesEnum A constrained set of enumerative values containing the NCBITaxon values for c... ConditionConceptEnum A constrained set of enumerative values containing both the MONDO values for ... ConditionStatusEnum A constrained set of enumerative values indicating whether a Condition is pre... DataUseEnum A constrained set of enumerative values drawn from the Data Use Ontology (DUO... DeviceExposureConceptEnum Device codes from SNOMED DeviceExposureProvenanceEnum Source of device exposure record DrugExposureConceptEnum Drug codes from RxNorm DrugExposureProvenanceEnum Source of drug exposure record DrugRouteEnum Routes of drug administration EthnicityEnum A constrained set of enumerative values containing the United States Office o... HpoPhenotypicAbnormalityEnum A constrained set of enumerative values containing the HPO values for phenoty... MondoHumanDiseaseEnum A constrained set of enumerative values containing the MONDO values for human... ProcedureConceptEnum Procedure codes from OMOP ProvenanceEnum A constrained set of enumerative values containing the OMOP values for proven... RaceEnum A constrained set of enumerative values containing the United States Office o... SectionLocationEnum The location in a parent specimen from which a section/portion was excised SexEnum A constrained set of enumerative values containing the OMOP values for sex SourceMaterialTypeEnum SpecimenCollectionMethodType SpecimenCreationActivityTypeEnum The high-level type of activity through which the specimen was generated (i SpecimenProcessingActivityTypeEnum The high-level type of processing activity performed SpecimenQualityObservationMethodEnum A type of method used in determining the quantity of a specimen SpecimenQualityObservationTypeEnum Types of measurements that reflect the quality of a specimen or its suitabili... SpecimenQuantityObservationTypeEnum Measures related to the quantity of a specimen or analyte it currently contai... SpecimenTypeEnum A high-level type of specimen, based on its derivation provenance (i UnitOfMeasurementEnum Standard units of measurement from the [Units of Measurement (UOM) ontology](... VertebrateBreedEnum A constrained set of enumerative values containing the VBO values for vertebr... VisitCategoryEnum A constrained set of enumerative values containing the OMOP values for visit ... VisitProvenanceEnum A constrained set of enumerative values containing the OMOP values for visit ... VitalStatusEnum A constrained set of enumerative values containing the OMOP values for vital ... Types Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE Subsets Subset Description","title":"Index"},{"location":"#biodata-catalyst-harmonized-model-bdchm","text":"This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm Name: bdchm","title":"BioData Catalyst Harmonized Model (bdchm)"},{"location":"#classes","text":"Class Description Entity Any resource that has its own identifier BiologicProduct A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. BodySite A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. Condition Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. Consent An entity that can be used to capture consent code and other relevant data about consent for a study. Demography Demographics about an individual or animal receiving care or other health-related services. DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. Document A collection of information intented to be understood together as a whole, and codified in human-readable form. DrugExposure DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. File Abstract class for various kinds of files. Subclasses will be defined for specific file types. Observation A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. DimensionalObservation A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. ObservationSet A structured object to hold related Observations in a set. DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). Organization A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. Participant A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. Person Administrative information about an individual or animal receiving care or other health-related services. Procedure Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] Quantity A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. Questionnaire A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) ResearchStudy A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. Specimen Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) SpecimenCreationActivity The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. SpecimenTransportActivity An activity through which a specimen is transported between locations or organizations. Substance A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. TimePoint A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. Visit Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) ObservationValue Single-valued observation valueholiding slot ObservationValueBoolean Single-valued boolean observation ObservationValueDecimal Single-valued decimal observation ObservationValueInteger Single-valued integer observation ObservationValueQuantity Single-valued Quantity observation ObservationValueString Single-valued string observation QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) QuestionnaireResponseValue Single-valued answer to the question. (FHIR) QuestionnaireResponseValueBoolean Single-valued boolean answer to the question QuestionnaireResponseValueDecimal Single-valued decimal answer to the question QuestionnaireResponseValueInteger Single-valued integer answer to the question QuestionnaireResponseValueString Single-valued string answer to the question QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question ResearchStudyCollection A holder for ResearchStudy objects TimePeriod A period of time between a start and end time point.","title":"Classes"},{"location":"#slots","text":"Slot Description activity_type The high-level type of creation activity additive A material substance added to the container (typically to support the primary... age_at_condition_end The Participant's age (expressed in days) when the condition was recorded as ... age_at_condition_start The Participant's age (expressed in days) when the condition was first record... age_at_death The age of an individual at the time of death, expressed in days since birth age_at_enrollment The age in days when the Participant enrolled on the ResearchStudy age_at_exposure_end The Participant's age (expressed in days) at the exposure end date, if availa... age_at_exposure_start The Participant's age (expressed in days) at the exposure start date age_at_observation The Participant's age (expressed in days) when the Observation was made age_at_procedure The Participant's age (expressed in days) when the procedure was performed age_at_response The age (in days) of the Participant when the QuestionnaireResponse was captu... age_at_visit_end The age of the Participant (in days) at the end of the Visit age_at_visit_start The age of the Participant (in days) at the start of the Visit alias A secondary name for the organization such as a short name or abbreviation (e analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... associated_participant A reference to the Participant that is associated with this record associated_person A reference to the Person that is associated with this record associated_timepoint A collection of timepoint observations that are relevant to research projects... associated_visit A reference to the Visit during which this QuestionnaireResponse was captured breed A label given to a group of animals homogeneous in appearance and other chara... category The general category of observation set described cause_of_death Coded value indicating the circumstance or condition that results in the deat... cellular_composition_type A term describing the type of cell or cellular material comprising a specimen code Corresponding concept for this item in a terminology collection_method_type The type of method applied in collecting a sample from its original source collection_site The anatomic site from which a specimen was collected condition_concept The coded value for the presence of a disease or medical condition stated as ... condition_provenance A value representing the provenance of the Condition record condition_status A value indicating whether the medical condition described in this record is ... consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ... consents Data Use Restrictions that are used to indicate permissions/restrictions for ... contained_in A physical container in which a specimen is presently held or attached - as ... container A container in which the specimen is held or affixed during its storage container_number Informal number by which the container is referenced or identified (e container_type The kind of the container copyright Textual description of any use and/or publishing restrictions copyright_label Copyright holder and year(s) creation_activity The activity through which a specimen was created, by removing material from ... data_category A broad categorization of the contents of the data file data_type The nature or genre of the resource date_ended The date when the research project ended date_started The date when the research project began date_time An explicitly specified timepoint described in terms of a date and optionally... days_supply The number of days of supply of the medication as recorded in the original pr... derivation_method_type The type of method applied to derive a new specimen from an existing one derived_product A 'living' biologically active product that was derived from the specimen (e description A free text field to capture additional info/explanation about the research s... description_shortened An abbreviated description of a research program, project, or study device_concept The coded value for a device dimensional_measures Observations about the current physical dimensions of an object (e document_type The high-level type of the document (e drug_concept The coded value for a drug duration The length of time over which the activity was performed entries ethnicity An individual's self-described social and cultural grouping, specifically whe... event_type An event that occurred at the point in time specified by this TimePoint exposure_provenance A value representing the provenance of the DrugExposure record file_name The name (or part of a name) of a file (of any type) file_size The size of the data file (object) in bytes focus The entity that the report is primarily about format The file format, physical medium, or dimensions of the resource growth_rate When the specimen an actively growing model system, such as a cell or tissue ... has_questionnaire_item A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... id The 'logical' identifier of the entity within the system of record identity A 'business' identifier or accession number for the entity, typically as prov... index_time_point Another TimePoint from which this point is offset index_timepoint The text term used to describe the reference or anchor date used for date obf... items A collection of QuestionnaireItem objects which encapsulate the question bein... language The language(s) in which questions are presented member_of_research_study A reference to the Study(s) of which this Participant is a member method_type A specific type of method or procedure performed to process the specimen name An unabridged name of a research program, project, or study name_shortened An abbreviated name of a research program, project, or study observation_type The type of Observation being represented (e observations A set of one or more observations offset_from_index A quantity of time that, together with the index date or event, can be used t... organization_type The type of the organization (e originating_site The Organization through which a subject was enrolled on a ResearchStudy parent_container A larger container of which this container is a part (e parent_specimen An existing specimen from which the specimen of interest was directly derived... part_of A reference to a parent ResearchStudy (e passage_number When the specimen an actively growing model system, such as a cell or tissue ... performed_by The organization or group that performed the activity period_end When a period of time ended period_start When a period of time started principal_investigator The investigator or investigators leading a project procedure_concept The coded value that describes the procedure, derived from OMOP codes procedure_provenance A value representing the provenance of the Procedure record processing_activity An activity that modifies the physical structure, composition, or state of a ... product_type The high level type of model system (e publisher Name of the publisher/steward (organization or individual) of this Questionna... qualifier A qualifier that further refines or specifies the location of the body site -... quality_measure An observation about characteristics of a specimen that are indicative of its... quantity The quantity of procedures ordered or administered quantity_collected The quantity of material in the specimen as originally collected from its ori... quantity_measure An observation related to the present quantity of a specimen - e race An arbitrary classification of a taxonomic group that is a division of a spec... refills Intended refills at time of the prescription related_document A reference to an external document that is about or related to the specimen ... relationship_to_participant A value indicating the relationship between the Participant to which the Cond... research_project_type The 'type' of ResearchStudy represented (e response_value role A role played by the substance in a particular application (e route_concept Route of drug administration section_location The location in a parent specimen from which a section/portion was excised (e sex The biologic character or quality that distinguishes male and female from one... sig This is the verbatim instruction for the drug as written by the provider site A term describing any site in the body source_material_type The general kind of material from which the specimen was derived source_participant A specific Subject from which the specimen was directly or indirectly derived species The scientific binomial name for the species of the Person (e specimen_order A numeric value that represents the sequential order of this creation activit... specimen_type The high-level type of the specimen, based on its derivation provenance (i sponsor An entity that is responsible for the initiation, management, and/or financin... storage_activity An activity that results in the storage or maintenance of a specimen in a par... study_arm The arm(s) of the study on which the Participant is enrolled substance_quantity The quantity of substance this instance stands for substance_type The specific type of the substance - at as granular a level as possible text Name for group or question text title Name for this Questionnaire (human friendly) transport_activity An activity through which the specimen is transported between locations transport_destination An organization (facility, site, lab, etc) to which the specimen is delivered... transport_origin An organization (facility, site, lab, etc) from which the specimen was transp... type unit A coded or free text (in the uri A unique identifier or url for identifying or locating the file url A URL address for a resource that provides information about a research progr... valid_from The point in time from which the consent record is valid valid_to The point in time after which the consent record is invalid value A general slot to hold a value value_concept A coded value representing a quantity (e value_decimal An amount, in the given units (if specified) version The identifier that is used to identify this version of the questionnaire whe... visit_category A value representing the kind (or category) of visit, like inpatient or outpa... visit_provenance A value representing the provenance of the visit record, or where the record ... vital_status Coded value indicating the state or condition of being living or deceased; al... year_of_birth Numeric value to represent the calendar year in which an individual was born year_of_death Numeric value to represent the calendar year in which an individual died","title":"Slots"},{"location":"#enumerations","text":"Enumeration Description AnalyteTypeEnum CellularOrganismSpeciesEnum A constrained set of enumerative values containing the NCBITaxon values for c... ConditionConceptEnum A constrained set of enumerative values containing both the MONDO values for ... ConditionStatusEnum A constrained set of enumerative values indicating whether a Condition is pre... DataUseEnum A constrained set of enumerative values drawn from the Data Use Ontology (DUO... DeviceExposureConceptEnum Device codes from SNOMED DeviceExposureProvenanceEnum Source of device exposure record DrugExposureConceptEnum Drug codes from RxNorm DrugExposureProvenanceEnum Source of drug exposure record DrugRouteEnum Routes of drug administration EthnicityEnum A constrained set of enumerative values containing the United States Office o... HpoPhenotypicAbnormalityEnum A constrained set of enumerative values containing the HPO values for phenoty... MondoHumanDiseaseEnum A constrained set of enumerative values containing the MONDO values for human... ProcedureConceptEnum Procedure codes from OMOP ProvenanceEnum A constrained set of enumerative values containing the OMOP values for proven... RaceEnum A constrained set of enumerative values containing the United States Office o... SectionLocationEnum The location in a parent specimen from which a section/portion was excised SexEnum A constrained set of enumerative values containing the OMOP values for sex SourceMaterialTypeEnum SpecimenCollectionMethodType SpecimenCreationActivityTypeEnum The high-level type of activity through which the specimen was generated (i SpecimenProcessingActivityTypeEnum The high-level type of processing activity performed SpecimenQualityObservationMethodEnum A type of method used in determining the quantity of a specimen SpecimenQualityObservationTypeEnum Types of measurements that reflect the quality of a specimen or its suitabili... SpecimenQuantityObservationTypeEnum Measures related to the quantity of a specimen or analyte it currently contai... SpecimenTypeEnum A high-level type of specimen, based on its derivation provenance (i UnitOfMeasurementEnum Standard units of measurement from the [Units of Measurement (UOM) ontology](... VertebrateBreedEnum A constrained set of enumerative values containing the VBO values for vertebr... VisitCategoryEnum A constrained set of enumerative values containing the OMOP values for visit ... VisitProvenanceEnum A constrained set of enumerative values containing the OMOP values for visit ... VitalStatusEnum A constrained set of enumerative values containing the OMOP values for vital ...","title":"Enumerations"},{"location":"#types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE","title":"Types"},{"location":"#subsets","text":"Subset Description","title":"Subsets"},{"location":"AnalyteTypeEnum/","text":"Enum: AnalyteTypeEnum URI: AnalyteTypeEnum Permissible Values Value Meaning Description FFPE DNA None Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA None Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA None Total RNA None Total Ribonucleic Acid Repli-G X (Qiagen) DNA None Repli-G X (Qiagen) DNA RNA None Ribonucleic Acid Repli-G Pooled (Qiagen) DNA None REPLI-g Pooled DNA DNA None DNA EBV Immortalized Normal None Normal Epstein-Barr Virus Immortalization FFPE RNA None Formalin-Fixed Paraffin-Embedded RNA Protein None Protein Nuclei RNA None cfDNA None Slots Name Description analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: AnalyteTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FFPE DNA: text: FFPE DNA description: Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA: text: Repli-G (Qiagen) DNA description: Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA: text: GenomePlex (Rubicon) Amplified DNA Total RNA: text: Total RNA description: Total Ribonucleic Acid Repli-G X (Qiagen) DNA: text: Repli-G X (Qiagen) DNA description: Repli-G X (Qiagen) DNA RNA: text: RNA description: Ribonucleic Acid Repli-G Pooled (Qiagen) DNA: text: Repli-G Pooled (Qiagen) DNA description: REPLI-g Pooled DNA DNA: text: DNA description: DNA EBV Immortalized Normal: text: EBV Immortalized Normal description: Normal Epstein-Barr Virus Immortalization FFPE RNA: text: FFPE RNA description: Formalin-Fixed Paraffin-Embedded RNA Protein: text: Protein description: Protein Nuclei RNA: text: Nuclei RNA cfDNA: text: cfDNA","title":"Enum: AnalyteTypeEnum"},{"location":"AnalyteTypeEnum/#enum-analytetypeenum","text":"URI: AnalyteTypeEnum","title":"Enum: AnalyteTypeEnum"},{"location":"AnalyteTypeEnum/#permissible-values","text":"Value Meaning Description FFPE DNA None Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA None Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA None Total RNA None Total Ribonucleic Acid Repli-G X (Qiagen) DNA None Repli-G X (Qiagen) DNA RNA None Ribonucleic Acid Repli-G Pooled (Qiagen) DNA None REPLI-g Pooled DNA DNA None DNA EBV Immortalized Normal None Normal Epstein-Barr Virus Immortalization FFPE RNA None Formalin-Fixed Paraffin-Embedded RNA Protein None Protein Nuclei RNA None cfDNA None","title":"Permissible Values"},{"location":"AnalyteTypeEnum/#slots","text":"Name Description analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th...","title":"Slots"},{"location":"AnalyteTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"AnalyteTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"AnalyteTypeEnum/#linkml-source","text":"name: AnalyteTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FFPE DNA: text: FFPE DNA description: Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA: text: Repli-G (Qiagen) DNA description: Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA: text: GenomePlex (Rubicon) Amplified DNA Total RNA: text: Total RNA description: Total Ribonucleic Acid Repli-G X (Qiagen) DNA: text: Repli-G X (Qiagen) DNA description: Repli-G X (Qiagen) DNA RNA: text: RNA description: Ribonucleic Acid Repli-G Pooled (Qiagen) DNA: text: Repli-G Pooled (Qiagen) DNA description: REPLI-g Pooled DNA DNA: text: DNA description: DNA EBV Immortalized Normal: text: EBV Immortalized Normal description: Normal Epstein-Barr Virus Immortalization FFPE RNA: text: FFPE RNA description: Formalin-Fixed Paraffin-Embedded RNA Protein: text: Protein description: Protein Nuclei RNA: text: Nuclei RNA cfDNA: text: cfDNA","title":"LinkML Source"},{"location":"BiologicProduct/","text":"Class: BiologicProduct A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. URI: bdchm:BiologicProduct classDiagram class BiologicProduct Entity <|-- BiologicProduct BiologicProduct : description BiologicProduct : growth_rate BiologicProduct : id BiologicProduct : identity BiologicProduct : passage_number BiologicProduct : product_type Inheritance Entity BiologicProduct Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the model syst... direct product_type 0..1 String The high level type of model system (e direct passage_number 0..* Integer When the specimen an actively growing model system, such as a cell or tissue ... direct growth_rate 0..* String When the specimen an actively growing model system, such as a cell or tissue ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen derived_product range BiologicProduct Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:BiologicProduct native bdchm:BiologicProduct LinkML Source Direct name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string required: false Induced name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: BiologicProduct domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false alias: product_type owner: BiologicProduct domain_of: - BiologicProduct range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: passage_number owner: BiologicProduct domain_of: - BiologicProduct range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: BiologicProduct domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BiologicProduct domain_of: - Entity range: uriorcurie required: true","title":"Class: BiologicProduct"},{"location":"BiologicProduct/#class-biologicproduct","text":"A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. URI: bdchm:BiologicProduct classDiagram class BiologicProduct Entity <|-- BiologicProduct BiologicProduct : description BiologicProduct : growth_rate BiologicProduct : id BiologicProduct : identity BiologicProduct : passage_number BiologicProduct : product_type","title":"Class: BiologicProduct"},{"location":"BiologicProduct/#inheritance","text":"Entity BiologicProduct","title":"Inheritance"},{"location":"BiologicProduct/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the model syst... direct product_type 0..1 String The high level type of model system (e direct passage_number 0..* Integer When the specimen an actively growing model system, such as a cell or tissue ... direct growth_rate 0..* String When the specimen an actively growing model system, such as a cell or tissue ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"BiologicProduct/#usages","text":"used by used in type used Specimen derived_product range BiologicProduct","title":"Usages"},{"location":"BiologicProduct/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"BiologicProduct/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"BiologicProduct/#mappings","text":"Mapping Type Mapped Value self bdchm:BiologicProduct native bdchm:BiologicProduct","title":"Mappings"},{"location":"BiologicProduct/#linkml-source","text":"","title":"LinkML Source"},{"location":"BiologicProduct/#direct","text":"name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string required: false","title":"Direct"},{"location":"BiologicProduct/#induced","text":"name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: BiologicProduct domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false alias: product_type owner: BiologicProduct domain_of: - BiologicProduct range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: passage_number owner: BiologicProduct domain_of: - BiologicProduct range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: BiologicProduct domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BiologicProduct domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"BodySite/","text":"Class: BodySite A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. URI: bdchm:BodySite classDiagram class BodySite Entity <|-- BodySite BodySite : id BodySite : qualifier BodySite : site Inheritance Entity BodySite Slots Name Cardinality and Range Description Inheritance site 1..1 String A term describing any site in the body direct qualifier 0..* String A qualifier that further refines or specifies the location of the body site -... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used SpecimenCreationActivity collection_site range BodySite Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:BodySite native bdchm:BodySite LinkML Source Direct name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true range: string required: false Induced name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false alias: site owner: BodySite domain_of: - BodySite range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true alias: qualifier owner: BodySite domain_of: - BodySite range: string required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BodySite domain_of: - Entity range: uriorcurie required: true","title":"Class: BodySite"},{"location":"BodySite/#class-bodysite","text":"A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. URI: bdchm:BodySite classDiagram class BodySite Entity <|-- BodySite BodySite : id BodySite : qualifier BodySite : site","title":"Class: BodySite"},{"location":"BodySite/#inheritance","text":"Entity BodySite","title":"Inheritance"},{"location":"BodySite/#slots","text":"Name Cardinality and Range Description Inheritance site 1..1 String A term describing any site in the body direct qualifier 0..* String A qualifier that further refines or specifies the location of the body site -... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"BodySite/#usages","text":"used by used in type used SpecimenCreationActivity collection_site range BodySite","title":"Usages"},{"location":"BodySite/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"BodySite/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"BodySite/#mappings","text":"Mapping Type Mapped Value self bdchm:BodySite native bdchm:BodySite","title":"Mappings"},{"location":"BodySite/#linkml-source","text":"","title":"LinkML Source"},{"location":"BodySite/#direct","text":"name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true range: string required: false","title":"Direct"},{"location":"BodySite/#induced","text":"name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false alias: site owner: BodySite domain_of: - BodySite range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true alias: qualifier owner: BodySite domain_of: - BodySite range: string required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BodySite domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Boolean/","text":"Type: Boolean A binary (true or false) value URI: xsd:boolean base : Bool uri : xsd:boolean repr : bool Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Boolean"},{"location":"Boolean/#type-boolean","text":"A binary (true or false) value URI: xsd:boolean base : Bool uri : xsd:boolean repr : bool","title":"Type: Boolean"},{"location":"Boolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Boolean/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"CellularOrganismSpeciesEnum/","text":"Enum: CellularOrganismSpeciesEnum A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. URI: CellularOrganismSpeciesEnum This is a dynamic enum Slots Name Description species The scientific binomial name for the species of the Person (e Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: CellularOrganismSpeciesEnum description: A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:ncbitaxon source_nodes: - ncbitaxon:131567 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: CellularOrganismSpeciesEnum"},{"location":"CellularOrganismSpeciesEnum/#enum-cellularorganismspeciesenum","text":"A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. URI: CellularOrganismSpeciesEnum This is a dynamic enum","title":"Enum: CellularOrganismSpeciesEnum"},{"location":"CellularOrganismSpeciesEnum/#slots","text":"Name Description species The scientific binomial name for the species of the Person (e","title":"Slots"},{"location":"CellularOrganismSpeciesEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"CellularOrganismSpeciesEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"CellularOrganismSpeciesEnum/#linkml-source","text":"name: CellularOrganismSpeciesEnum description: A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:ncbitaxon source_nodes: - ncbitaxon:131567 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Condition/","text":"Class: Condition _Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. _ URI: bdchm:Condition classDiagram class Condition Entity <|-- Condition Condition : age_at_condition_end Condition : age_at_condition_start Condition : associated_participant Condition --> Participant : associated_participant Condition : associated_visit Condition --> Visit : associated_visit Condition : condition_concept Condition --> ConditionConceptEnum : condition_concept Condition : condition_provenance Condition --> ProvenanceEnum : condition_provenance Condition : condition_status Condition --> ConditionStatusEnum : condition_status Condition : id Condition : identity Condition : relationship_to_participant Inheritance Entity Condition Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct condition_concept 0..1 ConditionConceptEnum The coded value for the presence of a disease or medical condition stated as ... direct age_at_condition_start 0..1 Integer The Participant's age (expressed in days) when the condition was first record... direct age_at_condition_end 0..1 Integer The Participant's age (expressed in days) when the condition was recorded as ... direct condition_provenance 0..1 ProvenanceEnum A value representing the provenance of the Condition record direct condition_status 0..1 ConditionStatusEnum A value indicating whether the medical condition described in this record is ... direct relationship_to_participant 0..1 String A value indicating the relationship between the Participant to which the Cond... direct associated_participant 0..1 Participant A reference to the Participant to which the Condition is attributed direct associated_visit 0..1 Visit A reference to the Visit during which this Condition was recorded direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Condition native bdchm:Condition LinkML Source Direct name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit Induced name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_start owner: Condition domain_of: - Condition range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_end owner: Condition domain_of: - Condition range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Condition domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Condition domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Condition domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Condition domain_of: - Entity range: uriorcurie required: true","title":"Class: Condition"},{"location":"Condition/#class-condition","text":"_Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. _ URI: bdchm:Condition classDiagram class Condition Entity <|-- Condition Condition : age_at_condition_end Condition : age_at_condition_start Condition : associated_participant Condition --> Participant : associated_participant Condition : associated_visit Condition --> Visit : associated_visit Condition : condition_concept Condition --> ConditionConceptEnum : condition_concept Condition : condition_provenance Condition --> ProvenanceEnum : condition_provenance Condition : condition_status Condition --> ConditionStatusEnum : condition_status Condition : id Condition : identity Condition : relationship_to_participant","title":"Class: Condition"},{"location":"Condition/#inheritance","text":"Entity Condition","title":"Inheritance"},{"location":"Condition/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct condition_concept 0..1 ConditionConceptEnum The coded value for the presence of a disease or medical condition stated as ... direct age_at_condition_start 0..1 Integer The Participant's age (expressed in days) when the condition was first record... direct age_at_condition_end 0..1 Integer The Participant's age (expressed in days) when the condition was recorded as ... direct condition_provenance 0..1 ProvenanceEnum A value representing the provenance of the Condition record direct condition_status 0..1 ConditionStatusEnum A value indicating whether the medical condition described in this record is ... direct relationship_to_participant 0..1 String A value indicating the relationship between the Participant to which the Cond... direct associated_participant 0..1 Participant A reference to the Participant to which the Condition is attributed direct associated_visit 0..1 Visit A reference to the Visit during which this Condition was recorded direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Condition/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Condition/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Condition/#mappings","text":"Mapping Type Mapped Value self bdchm:Condition native bdchm:Condition","title":"Mappings"},{"location":"Condition/#linkml-source","text":"","title":"LinkML Source"},{"location":"Condition/#direct","text":"name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit","title":"Direct"},{"location":"Condition/#induced","text":"name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_start owner: Condition domain_of: - Condition range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_end owner: Condition domain_of: - Condition range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Condition domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Condition domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Condition domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Condition domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ConditionConceptEnum/","text":"Enum: ConditionConceptEnum A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. URI: ConditionConceptEnum This is a dynamic enum Slots Name Description condition_concept The coded value for the presence of a disease or medical condition stated as ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ConditionConceptEnum description: A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 inherits: - MondoHumanDiseaseEnum - HpoPhenotypicAbnormalityEnum","title":"Enum: ConditionConceptEnum"},{"location":"ConditionConceptEnum/#enum-conditionconceptenum","text":"A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. URI: ConditionConceptEnum This is a dynamic enum","title":"Enum: ConditionConceptEnum"},{"location":"ConditionConceptEnum/#slots","text":"Name Description condition_concept The coded value for the presence of a disease or medical condition stated as ...","title":"Slots"},{"location":"ConditionConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ConditionConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ConditionConceptEnum/#linkml-source","text":"name: ConditionConceptEnum description: A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 inherits: - MondoHumanDiseaseEnum - HpoPhenotypicAbnormalityEnum","title":"LinkML Source"},{"location":"ConditionStatusEnum/","text":"Enum: ConditionStatusEnum A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. URI: ConditionStatusEnum Permissible Values Value Meaning Description PRESENT None The condition is/was present in the patient ABSENT None The condition is/was absent in the patient UNKNOWN None The condition is/was of unknown status in the patient Slots Name Description condition_status A value indicating whether the medical condition described in this record is ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ConditionStatusEnum description: A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: PRESENT: text: PRESENT description: The condition is/was present in the patient. ABSENT: text: ABSENT description: The condition is/was absent in the patient. UNKNOWN: text: UNKNOWN description: The condition is/was of unknown status in the patient.","title":"Enum: ConditionStatusEnum"},{"location":"ConditionStatusEnum/#enum-conditionstatusenum","text":"A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. URI: ConditionStatusEnum","title":"Enum: ConditionStatusEnum"},{"location":"ConditionStatusEnum/#permissible-values","text":"Value Meaning Description PRESENT None The condition is/was present in the patient ABSENT None The condition is/was absent in the patient UNKNOWN None The condition is/was of unknown status in the patient","title":"Permissible Values"},{"location":"ConditionStatusEnum/#slots","text":"Name Description condition_status A value indicating whether the medical condition described in this record is ...","title":"Slots"},{"location":"ConditionStatusEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ConditionStatusEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ConditionStatusEnum/#linkml-source","text":"name: ConditionStatusEnum description: A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: PRESENT: text: PRESENT description: The condition is/was present in the patient. ABSENT: text: ABSENT description: The condition is/was absent in the patient. UNKNOWN: text: UNKNOWN description: The condition is/was of unknown status in the patient.","title":"LinkML Source"},{"location":"Consent/","text":"Class: Consent An entity that can be used to capture consent code and other relevant data about consent for a study. URI: bdchm:Consent classDiagram class Consent Entity <|-- Consent Consent : consent_code Consent --> DataUseEnum : consent_code Consent : id Consent : valid_from Consent --> TimePoint : valid_from Consent : valid_to Consent --> TimePoint : valid_to Inheritance Entity Consent Slots Name Cardinality and Range Description Inheritance consent_code 0..1 DataUseEnum Data Use Restrictions that are used to indicate permissions/restrictions for ... direct valid_from 0..1 TimePoint The point in time from which the consent record is valid direct valid_to 0..1 TimePoint The point in time after which the consent record is invalid direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant consents range Consent ResearchStudy consents range Consent Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Consent native bdchm:Consent LinkML Source Direct name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint Induced name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Consent domain_of: - Entity range: uriorcurie required: true","title":"Class: Consent"},{"location":"Consent/#class-consent","text":"An entity that can be used to capture consent code and other relevant data about consent for a study. URI: bdchm:Consent classDiagram class Consent Entity <|-- Consent Consent : consent_code Consent --> DataUseEnum : consent_code Consent : id Consent : valid_from Consent --> TimePoint : valid_from Consent : valid_to Consent --> TimePoint : valid_to","title":"Class: Consent"},{"location":"Consent/#inheritance","text":"Entity Consent","title":"Inheritance"},{"location":"Consent/#slots","text":"Name Cardinality and Range Description Inheritance consent_code 0..1 DataUseEnum Data Use Restrictions that are used to indicate permissions/restrictions for ... direct valid_from 0..1 TimePoint The point in time from which the consent record is valid direct valid_to 0..1 TimePoint The point in time after which the consent record is invalid direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Consent/#usages","text":"used by used in type used Participant consents range Consent ResearchStudy consents range Consent","title":"Usages"},{"location":"Consent/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Consent/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Consent/#mappings","text":"Mapping Type Mapped Value self bdchm:Consent native bdchm:Consent","title":"Mappings"},{"location":"Consent/#linkml-source","text":"","title":"LinkML Source"},{"location":"Consent/#direct","text":"name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint","title":"Direct"},{"location":"Consent/#induced","text":"name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Consent domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Curie/","text":"Type: Curie a compact URI URI: xsd:string base : Curie uri : xsd:string repr : str Comments in RDF serializations this MUST be expanded to a URI in non-RDF serializations MAY be serialized as the compact representation Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Curie"},{"location":"Curie/#type-curie","text":"a compact URI URI: xsd:string base : Curie uri : xsd:string repr : str","title":"Type: Curie"},{"location":"Curie/#comments","text":"in RDF serializations this MUST be expanded to a URI in non-RDF serializations MAY be serialized as the compact representation","title":"Comments"},{"location":"Curie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Curie/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DataUseEnum/","text":"Enum: DataUseEnum A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. URI: DataUseEnum Permissible Values Value Meaning Description GRU DUO:0000042 This data use permission indicates that use is allowed for general research u... HMB DUO:0000006 This data use permission indicates that use is allowed for health/medical/bio... DS DUO:0000007 This data use permission indicates that use is allowed provided it is related... NPUNCU DUO:0000018 This data use modifier indicates that use of the data is limited to not-for-p... IRB DUO:0000021 This data use modifier indicates that the requestor must provide documentatio... Slots Name Description consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DataUseEnum description: A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: GRU: text: GRU description: 'This data use permission indicates that use is allowed for general research use for any research purpose. This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.' meaning: DUO:0000042 HMB: text: HMB description: This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. meaning: DUO:0000006 DS: text: DS description: This data use permission indicates that use is allowed provided it is related to the specified disease. This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms. meaning: DUO:0000007 NPUNCU: text: NPUNCU description: This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. meaning: DUO:0000018 IRB: text: IRB description: This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. meaning: DUO:0000021","title":"Enum: DataUseEnum"},{"location":"DataUseEnum/#enum-datauseenum","text":"A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. URI: DataUseEnum","title":"Enum: DataUseEnum"},{"location":"DataUseEnum/#permissible-values","text":"Value Meaning Description GRU DUO:0000042 This data use permission indicates that use is allowed for general research u... HMB DUO:0000006 This data use permission indicates that use is allowed for health/medical/bio... DS DUO:0000007 This data use permission indicates that use is allowed provided it is related... NPUNCU DUO:0000018 This data use modifier indicates that use of the data is limited to not-for-p... IRB DUO:0000021 This data use modifier indicates that the requestor must provide documentatio...","title":"Permissible Values"},{"location":"DataUseEnum/#slots","text":"Name Description consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ...","title":"Slots"},{"location":"DataUseEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DataUseEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DataUseEnum/#linkml-source","text":"name: DataUseEnum description: A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: GRU: text: GRU description: 'This data use permission indicates that use is allowed for general research use for any research purpose. This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.' meaning: DUO:0000042 HMB: text: HMB description: This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. meaning: DUO:0000006 DS: text: DS description: This data use permission indicates that use is allowed provided it is related to the specified disease. This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms. meaning: DUO:0000007 NPUNCU: text: NPUNCU description: This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. meaning: DUO:0000018 IRB: text: IRB description: This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. meaning: DUO:0000021","title":"LinkML Source"},{"location":"Date/","text":"Type: Date a date (year, month and day) in an idealized calendar URI: xsd:date base : XSDDate uri : xsd:date repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Date"},{"location":"Date/#type-date","text":"a date (year, month and day) in an idealized calendar URI: xsd:date base : XSDDate uri : xsd:date repr : str","title":"Type: Date"},{"location":"Date/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Date/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DateOrDatetime/","text":"Type: DateOrDatetime Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#type-dateordatetime","text":"Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DateOrDatetime/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Datetime/","text":"Type: Datetime The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Datetime"},{"location":"Datetime/#type-datetime","text":"The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str","title":"Type: Datetime"},{"location":"Datetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Datetime/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Decimal/","text":"Type: Decimal A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Decimal"},{"location":"Decimal/#type-decimal","text":"A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal","title":"Type: Decimal"},{"location":"Decimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Decimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Demography/","text":"Class: Demography Demographics about an individual or animal receiving care or other health-related services. URI: bdchm:Demography classDiagram class Demography Entity <|-- Demography Demography : associated_participant Demography --> Participant : associated_participant Demography : ethnicity Demography --> EthnicityEnum : ethnicity Demography : id Demography : identity Demography : race Demography --> RaceEnum : race Demography : sex Demography --> SexEnum : sex Inheritance Entity Demography Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct associated_participant 0..1 Participant A reference to the Participant that is associated with this record direct sex 0..1 SexEnum The biologic character or quality that distinguishes male and female from one... direct ethnicity 0..1 EthnicityEnum An individual's self-described social and cultural grouping, specifically whe... direct race 0..1 RaceEnum An arbitrary classification of a taxonomic group that is a division of a spec... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Demography native bdchm:Demography LinkML Source Direct name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity - associated_participant attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: RaceEnum Induced name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sex owner: Demography domain_of: - Demography range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: race owner: Demography domain_of: - Demography range: RaceEnum identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Demography domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie associated_participant: name: associated_participant description: A reference to the Participant that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_participant owner: Demography domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Demography domain_of: - Entity range: uriorcurie required: true","title":"Class: Demography"},{"location":"Demography/#class-demography","text":"Demographics about an individual or animal receiving care or other health-related services. URI: bdchm:Demography classDiagram class Demography Entity <|-- Demography Demography : associated_participant Demography --> Participant : associated_participant Demography : ethnicity Demography --> EthnicityEnum : ethnicity Demography : id Demography : identity Demography : race Demography --> RaceEnum : race Demography : sex Demography --> SexEnum : sex","title":"Class: Demography"},{"location":"Demography/#inheritance","text":"Entity Demography","title":"Inheritance"},{"location":"Demography/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct associated_participant 0..1 Participant A reference to the Participant that is associated with this record direct sex 0..1 SexEnum The biologic character or quality that distinguishes male and female from one... direct ethnicity 0..1 EthnicityEnum An individual's self-described social and cultural grouping, specifically whe... direct race 0..1 RaceEnum An arbitrary classification of a taxonomic group that is a division of a spec... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Demography/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Demography/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Demography/#mappings","text":"Mapping Type Mapped Value self bdchm:Demography native bdchm:Demography","title":"Mappings"},{"location":"Demography/#linkml-source","text":"","title":"LinkML Source"},{"location":"Demography/#direct","text":"name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity - associated_participant attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: RaceEnum","title":"Direct"},{"location":"Demography/#induced","text":"name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sex owner: Demography domain_of: - Demography range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: race owner: Demography domain_of: - Demography range: RaceEnum identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Demography domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie associated_participant: name: associated_participant description: A reference to the Participant that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_participant owner: Demography domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Demography domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DeviceExposure/","text":"Class: DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. URI: bdchm:DeviceExposure classDiagram class DeviceExposure Entity <|-- DeviceExposure DeviceExposure : age_at_exposure_end DeviceExposure : age_at_exposure_start DeviceExposure : associated_participant DeviceExposure --> Participant : associated_participant DeviceExposure : associated_visit DeviceExposure --> Visit : associated_visit DeviceExposure : device_concept DeviceExposure --> DeviceExposureConceptEnum : device_concept DeviceExposure : exposure_provenance DeviceExposure --> DeviceExposureProvenanceEnum : exposure_provenance DeviceExposure : id DeviceExposure : identity DeviceExposure : quantity Inheritance Entity DeviceExposure Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct device_concept 0..1 DeviceExposureConceptEnum The coded value for a device direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DeviceExposureProvenanceEnum A value representing the provenance of the DeviceExposure record direct quantity 0..1 Float Amount of device used direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DeviceExposure native bdchm:DeviceExposure LinkML Source Direct name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false Induced name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_start owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_end owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: exposure_provenance owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DeviceExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DeviceExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DeviceExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DeviceExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DeviceExposure domain_of: - Entity range: uriorcurie required: true","title":"Class: DeviceExposure"},{"location":"DeviceExposure/#class-deviceexposure","text":"DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. URI: bdchm:DeviceExposure classDiagram class DeviceExposure Entity <|-- DeviceExposure DeviceExposure : age_at_exposure_end DeviceExposure : age_at_exposure_start DeviceExposure : associated_participant DeviceExposure --> Participant : associated_participant DeviceExposure : associated_visit DeviceExposure --> Visit : associated_visit DeviceExposure : device_concept DeviceExposure --> DeviceExposureConceptEnum : device_concept DeviceExposure : exposure_provenance DeviceExposure --> DeviceExposureProvenanceEnum : exposure_provenance DeviceExposure : id DeviceExposure : identity DeviceExposure : quantity","title":"Class: DeviceExposure"},{"location":"DeviceExposure/#inheritance","text":"Entity DeviceExposure","title":"Inheritance"},{"location":"DeviceExposure/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct device_concept 0..1 DeviceExposureConceptEnum The coded value for a device direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DeviceExposureProvenanceEnum A value representing the provenance of the DeviceExposure record direct quantity 0..1 Float Amount of device used direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DeviceExposure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DeviceExposure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DeviceExposure/#mappings","text":"Mapping Type Mapped Value self bdchm:DeviceExposure native bdchm:DeviceExposure","title":"Mappings"},{"location":"DeviceExposure/#linkml-source","text":"","title":"LinkML Source"},{"location":"DeviceExposure/#direct","text":"name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false","title":"Direct"},{"location":"DeviceExposure/#induced","text":"name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_start owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_end owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: exposure_provenance owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DeviceExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DeviceExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DeviceExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DeviceExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DeviceExposure domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DeviceExposureConceptEnum/","text":"Enum: DeviceExposureConceptEnum Device codes from SNOMED. URI: DeviceExposureConceptEnum This is a dynamic enum Slots Name Description device_concept The coded value for a device See Also https://bioregistry.io/registry/snomedct https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html https://www.nlm.nih.gov/healthit/snomedct/index.html urn:oid:2.16.840.1.113883.6.96 Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DeviceExposureConceptEnum description: Device codes from SNOMED. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/snomedct - https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html - https://www.nlm.nih.gov/healthit/snomedct/index.html - urn:oid:2.16.840.1.113883.6.96 rank: 1000 reachable_from: source_ontology: bioregistry:snomedct","title":"Enum: DeviceExposureConceptEnum"},{"location":"DeviceExposureConceptEnum/#enum-deviceexposureconceptenum","text":"Device codes from SNOMED. URI: DeviceExposureConceptEnum This is a dynamic enum","title":"Enum: DeviceExposureConceptEnum"},{"location":"DeviceExposureConceptEnum/#slots","text":"Name Description device_concept The coded value for a device","title":"Slots"},{"location":"DeviceExposureConceptEnum/#see-also","text":"https://bioregistry.io/registry/snomedct https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html https://www.nlm.nih.gov/healthit/snomedct/index.html urn:oid:2.16.840.1.113883.6.96","title":"See Also"},{"location":"DeviceExposureConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DeviceExposureConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DeviceExposureConceptEnum/#linkml-source","text":"name: DeviceExposureConceptEnum description: Device codes from SNOMED. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/snomedct - https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html - https://www.nlm.nih.gov/healthit/snomedct/index.html - urn:oid:2.16.840.1.113883.6.96 rank: 1000 reachable_from: source_ontology: bioregistry:snomedct","title":"LinkML Source"},{"location":"DeviceExposureProvenanceEnum/","text":"Enum: DeviceExposureProvenanceEnum Source of device exposure record URI: DeviceExposureProvenanceEnum Permissible Values Value Meaning Description CASE REPORT FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM AUTHORIZATION OMOP:32811 Claim authorization CLAIM DISCHARGE RECORD OMOP:32812 Claim discharge record CLAIM ENROLMENT RECORD OMOP:32813 Claim enrolment record COST RECORD OMOP:32814 Cost record DEATH CERTIFICATE OMOP:32815 Death Certificate DENTAL CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR ADMINISTRATION RECORD OMOP:32818 EHR administration record EHR ADMISSION NOTE OMOP:32819 EHR admission note EHR ANCILLARY REPORT OMOP:32820 EHR ancillary report EHR BILLING RECORD OMOP:32821 EHR billing record EHR CHIEF COMPLAINT OMOP:32822 EHR chief complaint EHR DISCHARGE RECORD OMOP:32823 EHR discharge record EHR DISCHARGE SUMMARY OMOP:32824 EHR discharge summary EHR DISPENSING RECORD OMOP:32825 EHR dispensing record EHR EMERGENCY ROOM NOTE OMOP:32826 EHR emergency room note EHR ENCOUNTER RECORD OMOP:32827 EHR encounter record EHR EPISODE RECORD OMOP:32828 EHR episode record EHR INPATIENT NOTE OMOP:32829 EHR inpatient note EHR MEDICATION LIST OMOP:32830 EHR medication list EHR NOTE OMOP:32831 EHR note EHR NURSING REPORT OMOP:32832 EHR nursing report EHR ORDER OMOP:32833 EHR order EHR OUTPATIENT NOTE OMOP:32834 EHR outpatient note EHR PATHOLOGY REPORT OMOP:32835 EHR Pathology report EHR PHYSICAL EXAMINATION OMOP:32836 EHR physical examination EHR PLANNED DISPENSING RECORD OMOP:32837 EHR planned dispensing record EHR PERSCRIPTION OMOP:32838 EHR prescription EHR PERSCRIPTION ISSUE RECORD OMOP:32839 EHR prescription issue record EHR PROBLEM LIST OMOP:32840 EHR problem list EHR RADIOLOGY REPORT OMOP:32841 EHR radiology report EHR REFERRAL RECORD OMOP:32842 EHR referral record EXTERNAL CDM INSTANCE OMOP:32843 External CDM instance FACILITY CLAIM OMOP:32844 Facility claim FACILITY CLAIM DETAIL OMOP:32845 Facility claim detail FACILITY CLAIM HEADER OMOP:32846 Facility claim header GEOGRAPHIC ISOLATION RECORD OMOP:32847 Geographic isolation record GOVERNMENT REPORT OMOP:32848 Government report HEALTH INFORMATION EXCHANGE RECORD OMOP:32849 Health Information Exchange record HEALTH RISK ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE PROFESSIONAL FILLED SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL COST OMOP:32852 Hospital cost INPATIENT CLAIM OMOP:32853 Inpatient claim INPATIENT CLAIM DETAIL OMOP:32854 Inpatient claim detail INPATIENT CLAIM HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL ORDER RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT CLAIM OMOP:32859 Outpatient claim OUTPATIENT CLAIM DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT CLAIM HEADER OMOP:32861 Outpatient claim header PATIENT FILLED SURVEY OMOP:32862 Patient filled survey PATIENT OR PAYER PAID RECORD OMOP:32863 Patient or payer paid record PATIENT REPORTED COST OMOP:32864 Patient reported cost PATIENT SELF-REPORT OMOP:32865 Patient self-report PATIENT SELF-TESTED OMOP:705183 Patient self-tested PAYER SYSTEM RECORD (PAID PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER SYSTEM RECORD (PRIMARY PAYER) OMOP:32867 Payer system record (primary payer) PAYER SYSTEM RECORD (SECONDARY PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY CLAIM OMOP:32869 Pharmacy claim POINT OF CARE/EXPRESS LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION TIME PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL CLAIM OMOP:32871 Professional claim PROFESSIONAL CLAIM DETAIL OMOP:32872 Professional claim detail PROFESSIONAL CLAIM HEADER OMOP:32873 Professional claim header PROVIDER CHARGE LIST PRICE OMOP:32874 Provider charge list price PROVIDER FINANCIAL SYSTEM OMOP:32875 Provider financial system PROVIDER INCURRED COST RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION RECORD OMOP:32877 Randomization record REFERENCE LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD ALGORITHM OMOP:32880 Standard algorithm STANDARD ALGORITHM FROM CLAIMS OMOP:32881 Standard algorithm from claims STANDARD ALGORITHM FROM EHR OMOP:32882 Standard algorithm from EHR SURVEY OMOP:32883 Survey URGENT LAB OMOP:32884 Urgent lab US SOCIAL SECURITY DEATH MASTER FILE OMOP:32885 US Social Security Death Master File VISION CLAIM OMOP:32886 Vision claim Comments Taken from OMOP Type Concept Domain Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DeviceExposureProvenanceEnum description: Source of device exposure record comments: - Taken from OMOP Type Concept Domain from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE REPORT FORM: text: CASE REPORT FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM AUTHORIZATION: text: CLAIM AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM DISCHARGE RECORD: text: CLAIM DISCHARGE RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM ENROLMENT RECORD: text: CLAIM ENROLMENT RECORD description: Claim enrolment record meaning: OMOP:32813 COST RECORD: text: COST RECORD description: Cost record meaning: OMOP:32814 DEATH CERTIFICATE: text: DEATH CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL CLAIM: text: DENTAL CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR ADMINISTRATION RECORD: text: EHR ADMINISTRATION RECORD description: EHR administration record meaning: OMOP:32818 EHR ADMISSION NOTE: text: EHR ADMISSION NOTE description: EHR admission note meaning: OMOP:32819 EHR ANCILLARY REPORT: text: EHR ANCILLARY REPORT description: EHR ancillary report meaning: OMOP:32820 EHR BILLING RECORD: text: EHR BILLING RECORD description: EHR billing record meaning: OMOP:32821 EHR CHIEF COMPLAINT: text: EHR CHIEF COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR DISCHARGE RECORD: text: EHR DISCHARGE RECORD description: EHR discharge record meaning: OMOP:32823 EHR DISCHARGE SUMMARY: text: EHR DISCHARGE SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR DISPENSING RECORD: text: EHR DISPENSING RECORD description: EHR dispensing record meaning: OMOP:32825 EHR EMERGENCY ROOM NOTE: text: EHR EMERGENCY ROOM NOTE description: EHR emergency room note meaning: OMOP:32826 EHR ENCOUNTER RECORD: text: EHR ENCOUNTER RECORD description: EHR encounter record meaning: OMOP:32827 EHR EPISODE RECORD: text: EHR EPISODE RECORD description: EHR episode record meaning: OMOP:32828 EHR INPATIENT NOTE: text: EHR INPATIENT NOTE description: EHR inpatient note meaning: OMOP:32829 EHR MEDICATION LIST: text: EHR MEDICATION LIST description: EHR medication list meaning: OMOP:32830 EHR NOTE: text: EHR NOTE description: EHR note meaning: OMOP:32831 EHR NURSING REPORT: text: EHR NURSING REPORT description: EHR nursing report meaning: OMOP:32832 EHR ORDER: text: EHR ORDER description: EHR order meaning: OMOP:32833 EHR OUTPATIENT NOTE: text: EHR OUTPATIENT NOTE description: EHR outpatient note meaning: OMOP:32834 EHR PATHOLOGY REPORT: text: EHR PATHOLOGY REPORT description: EHR Pathology report meaning: OMOP:32835 EHR PHYSICAL EXAMINATION: text: EHR PHYSICAL EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR PLANNED DISPENSING RECORD: text: EHR PLANNED DISPENSING RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR PERSCRIPTION: text: EHR PERSCRIPTION description: EHR prescription meaning: OMOP:32838 EHR PERSCRIPTION ISSUE RECORD: text: EHR PERSCRIPTION ISSUE RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR PROBLEM LIST: text: EHR PROBLEM LIST description: EHR problem list meaning: OMOP:32840 EHR RADIOLOGY REPORT: text: EHR RADIOLOGY REPORT description: EHR radiology report meaning: OMOP:32841 EHR REFERRAL RECORD: text: EHR REFERRAL RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL CDM INSTANCE: text: EXTERNAL CDM INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY CLAIM: text: FACILITY CLAIM description: Facility claim meaning: OMOP:32844 FACILITY CLAIM DETAIL: text: FACILITY CLAIM DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY CLAIM HEADER: text: FACILITY CLAIM HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC ISOLATION RECORD: text: GEOGRAPHIC ISOLATION RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT REPORT: text: GOVERNMENT REPORT description: Government report meaning: OMOP:32848 HEALTH INFORMATION EXCHANGE RECORD: text: HEALTH INFORMATION EXCHANGE RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH RISK ASSESSMENT: text: HEALTH RISK ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE PROFESSIONAL FILLED SURVEY: text: HEALTHCARE PROFESSIONAL FILLED SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL COST: text: HOSPITAL COST description: Hospital cost meaning: OMOP:32852 INPATIENT CLAIM: text: INPATIENT CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT CLAIM DETAIL: text: INPATIENT CLAIM DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT CLAIM HEADER: text: INPATIENT CLAIM HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL ORDER RECORD: text: MAIL ORDER RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT CLAIM: text: OUTPATIENT CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT CLAIM DETAIL: text: OUTPATIENT CLAIM DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT CLAIM HEADER: text: OUTPATIENT CLAIM HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT FILLED SURVEY: text: PATIENT FILLED SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT OR PAYER PAID RECORD: text: PATIENT OR PAYER PAID RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT REPORTED COST: text: PATIENT REPORTED COST description: Patient reported cost meaning: OMOP:32864 PATIENT SELF-REPORT: text: PATIENT SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT SELF-TESTED: text: PATIENT SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER SYSTEM RECORD (PAID PREMIUM): text: PAYER SYSTEM RECORD (PAID PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER SYSTEM RECORD (PRIMARY PAYER): text: PAYER SYSTEM RECORD (PRIMARY PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER SYSTEM RECORD (SECONDARY PAYER): text: PAYER SYSTEM RECORD (SECONDARY PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY CLAIM: text: PHARMACY CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT OF CARE/EXPRESS LAB: text: POINT OF CARE/EXPRESS LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION TIME PERIOD: text: PRE-QUALIFICATION TIME PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL CLAIM: text: PROFESSIONAL CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL CLAIM DETAIL: text: PROFESSIONAL CLAIM DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL CLAIM HEADER: text: PROFESSIONAL CLAIM HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER CHARGE LIST PRICE: text: PROVIDER CHARGE LIST PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER FINANCIAL SYSTEM: text: PROVIDER FINANCIAL SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER INCURRED COST RECORD: text: PROVIDER INCURRED COST RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION RECORD: text: RANDOMIZATION RECORD description: Randomization record meaning: OMOP:32877 REFERENCE LAB: text: REFERENCE LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD ALGORITHM: text: STANDARD ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD ALGORITHM FROM CLAIMS: text: STANDARD ALGORITHM FROM CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 STANDARD ALGORITHM FROM EHR: text: STANDARD ALGORITHM FROM EHR description: Standard algorithm from EHR meaning: OMOP:32882 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 URGENT LAB: text: URGENT LAB description: Urgent lab meaning: OMOP:32884 US SOCIAL SECURITY DEATH MASTER FILE: text: US SOCIAL SECURITY DEATH MASTER FILE description: US Social Security Death Master File meaning: OMOP:32885 VISION CLAIM: text: VISION CLAIM description: Vision claim meaning: OMOP:32886","title":"Enum: DeviceExposureProvenanceEnum"},{"location":"DeviceExposureProvenanceEnum/#enum-deviceexposureprovenanceenum","text":"Source of device exposure record URI: DeviceExposureProvenanceEnum","title":"Enum: DeviceExposureProvenanceEnum"},{"location":"DeviceExposureProvenanceEnum/#permissible-values","text":"Value Meaning Description CASE REPORT FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM AUTHORIZATION OMOP:32811 Claim authorization CLAIM DISCHARGE RECORD OMOP:32812 Claim discharge record CLAIM ENROLMENT RECORD OMOP:32813 Claim enrolment record COST RECORD OMOP:32814 Cost record DEATH CERTIFICATE OMOP:32815 Death Certificate DENTAL CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR ADMINISTRATION RECORD OMOP:32818 EHR administration record EHR ADMISSION NOTE OMOP:32819 EHR admission note EHR ANCILLARY REPORT OMOP:32820 EHR ancillary report EHR BILLING RECORD OMOP:32821 EHR billing record EHR CHIEF COMPLAINT OMOP:32822 EHR chief complaint EHR DISCHARGE RECORD OMOP:32823 EHR discharge record EHR DISCHARGE SUMMARY OMOP:32824 EHR discharge summary EHR DISPENSING RECORD OMOP:32825 EHR dispensing record EHR EMERGENCY ROOM NOTE OMOP:32826 EHR emergency room note EHR ENCOUNTER RECORD OMOP:32827 EHR encounter record EHR EPISODE RECORD OMOP:32828 EHR episode record EHR INPATIENT NOTE OMOP:32829 EHR inpatient note EHR MEDICATION LIST OMOP:32830 EHR medication list EHR NOTE OMOP:32831 EHR note EHR NURSING REPORT OMOP:32832 EHR nursing report EHR ORDER OMOP:32833 EHR order EHR OUTPATIENT NOTE OMOP:32834 EHR outpatient note EHR PATHOLOGY REPORT OMOP:32835 EHR Pathology report EHR PHYSICAL EXAMINATION OMOP:32836 EHR physical examination EHR PLANNED DISPENSING RECORD OMOP:32837 EHR planned dispensing record EHR PERSCRIPTION OMOP:32838 EHR prescription EHR PERSCRIPTION ISSUE RECORD OMOP:32839 EHR prescription issue record EHR PROBLEM LIST OMOP:32840 EHR problem list EHR RADIOLOGY REPORT OMOP:32841 EHR radiology report EHR REFERRAL RECORD OMOP:32842 EHR referral record EXTERNAL CDM INSTANCE OMOP:32843 External CDM instance FACILITY CLAIM OMOP:32844 Facility claim FACILITY CLAIM DETAIL OMOP:32845 Facility claim detail FACILITY CLAIM HEADER OMOP:32846 Facility claim header GEOGRAPHIC ISOLATION RECORD OMOP:32847 Geographic isolation record GOVERNMENT REPORT OMOP:32848 Government report HEALTH INFORMATION EXCHANGE RECORD OMOP:32849 Health Information Exchange record HEALTH RISK ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE PROFESSIONAL FILLED SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL COST OMOP:32852 Hospital cost INPATIENT CLAIM OMOP:32853 Inpatient claim INPATIENT CLAIM DETAIL OMOP:32854 Inpatient claim detail INPATIENT CLAIM HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL ORDER RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT CLAIM OMOP:32859 Outpatient claim OUTPATIENT CLAIM DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT CLAIM HEADER OMOP:32861 Outpatient claim header PATIENT FILLED SURVEY OMOP:32862 Patient filled survey PATIENT OR PAYER PAID RECORD OMOP:32863 Patient or payer paid record PATIENT REPORTED COST OMOP:32864 Patient reported cost PATIENT SELF-REPORT OMOP:32865 Patient self-report PATIENT SELF-TESTED OMOP:705183 Patient self-tested PAYER SYSTEM RECORD (PAID PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER SYSTEM RECORD (PRIMARY PAYER) OMOP:32867 Payer system record (primary payer) PAYER SYSTEM RECORD (SECONDARY PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY CLAIM OMOP:32869 Pharmacy claim POINT OF CARE/EXPRESS LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION TIME PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL CLAIM OMOP:32871 Professional claim PROFESSIONAL CLAIM DETAIL OMOP:32872 Professional claim detail PROFESSIONAL CLAIM HEADER OMOP:32873 Professional claim header PROVIDER CHARGE LIST PRICE OMOP:32874 Provider charge list price PROVIDER FINANCIAL SYSTEM OMOP:32875 Provider financial system PROVIDER INCURRED COST RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION RECORD OMOP:32877 Randomization record REFERENCE LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD ALGORITHM OMOP:32880 Standard algorithm STANDARD ALGORITHM FROM CLAIMS OMOP:32881 Standard algorithm from claims STANDARD ALGORITHM FROM EHR OMOP:32882 Standard algorithm from EHR SURVEY OMOP:32883 Survey URGENT LAB OMOP:32884 Urgent lab US SOCIAL SECURITY DEATH MASTER FILE OMOP:32885 US Social Security Death Master File VISION CLAIM OMOP:32886 Vision claim","title":"Permissible Values"},{"location":"DeviceExposureProvenanceEnum/#comments","text":"Taken from OMOP Type Concept Domain","title":"Comments"},{"location":"DeviceExposureProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DeviceExposureProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DeviceExposureProvenanceEnum/#linkml-source","text":"name: DeviceExposureProvenanceEnum description: Source of device exposure record comments: - Taken from OMOP Type Concept Domain from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE REPORT FORM: text: CASE REPORT FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM AUTHORIZATION: text: CLAIM AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM DISCHARGE RECORD: text: CLAIM DISCHARGE RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM ENROLMENT RECORD: text: CLAIM ENROLMENT RECORD description: Claim enrolment record meaning: OMOP:32813 COST RECORD: text: COST RECORD description: Cost record meaning: OMOP:32814 DEATH CERTIFICATE: text: DEATH CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL CLAIM: text: DENTAL CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR ADMINISTRATION RECORD: text: EHR ADMINISTRATION RECORD description: EHR administration record meaning: OMOP:32818 EHR ADMISSION NOTE: text: EHR ADMISSION NOTE description: EHR admission note meaning: OMOP:32819 EHR ANCILLARY REPORT: text: EHR ANCILLARY REPORT description: EHR ancillary report meaning: OMOP:32820 EHR BILLING RECORD: text: EHR BILLING RECORD description: EHR billing record meaning: OMOP:32821 EHR CHIEF COMPLAINT: text: EHR CHIEF COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR DISCHARGE RECORD: text: EHR DISCHARGE RECORD description: EHR discharge record meaning: OMOP:32823 EHR DISCHARGE SUMMARY: text: EHR DISCHARGE SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR DISPENSING RECORD: text: EHR DISPENSING RECORD description: EHR dispensing record meaning: OMOP:32825 EHR EMERGENCY ROOM NOTE: text: EHR EMERGENCY ROOM NOTE description: EHR emergency room note meaning: OMOP:32826 EHR ENCOUNTER RECORD: text: EHR ENCOUNTER RECORD description: EHR encounter record meaning: OMOP:32827 EHR EPISODE RECORD: text: EHR EPISODE RECORD description: EHR episode record meaning: OMOP:32828 EHR INPATIENT NOTE: text: EHR INPATIENT NOTE description: EHR inpatient note meaning: OMOP:32829 EHR MEDICATION LIST: text: EHR MEDICATION LIST description: EHR medication list meaning: OMOP:32830 EHR NOTE: text: EHR NOTE description: EHR note meaning: OMOP:32831 EHR NURSING REPORT: text: EHR NURSING REPORT description: EHR nursing report meaning: OMOP:32832 EHR ORDER: text: EHR ORDER description: EHR order meaning: OMOP:32833 EHR OUTPATIENT NOTE: text: EHR OUTPATIENT NOTE description: EHR outpatient note meaning: OMOP:32834 EHR PATHOLOGY REPORT: text: EHR PATHOLOGY REPORT description: EHR Pathology report meaning: OMOP:32835 EHR PHYSICAL EXAMINATION: text: EHR PHYSICAL EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR PLANNED DISPENSING RECORD: text: EHR PLANNED DISPENSING RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR PERSCRIPTION: text: EHR PERSCRIPTION description: EHR prescription meaning: OMOP:32838 EHR PERSCRIPTION ISSUE RECORD: text: EHR PERSCRIPTION ISSUE RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR PROBLEM LIST: text: EHR PROBLEM LIST description: EHR problem list meaning: OMOP:32840 EHR RADIOLOGY REPORT: text: EHR RADIOLOGY REPORT description: EHR radiology report meaning: OMOP:32841 EHR REFERRAL RECORD: text: EHR REFERRAL RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL CDM INSTANCE: text: EXTERNAL CDM INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY CLAIM: text: FACILITY CLAIM description: Facility claim meaning: OMOP:32844 FACILITY CLAIM DETAIL: text: FACILITY CLAIM DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY CLAIM HEADER: text: FACILITY CLAIM HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC ISOLATION RECORD: text: GEOGRAPHIC ISOLATION RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT REPORT: text: GOVERNMENT REPORT description: Government report meaning: OMOP:32848 HEALTH INFORMATION EXCHANGE RECORD: text: HEALTH INFORMATION EXCHANGE RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH RISK ASSESSMENT: text: HEALTH RISK ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE PROFESSIONAL FILLED SURVEY: text: HEALTHCARE PROFESSIONAL FILLED SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL COST: text: HOSPITAL COST description: Hospital cost meaning: OMOP:32852 INPATIENT CLAIM: text: INPATIENT CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT CLAIM DETAIL: text: INPATIENT CLAIM DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT CLAIM HEADER: text: INPATIENT CLAIM HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL ORDER RECORD: text: MAIL ORDER RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT CLAIM: text: OUTPATIENT CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT CLAIM DETAIL: text: OUTPATIENT CLAIM DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT CLAIM HEADER: text: OUTPATIENT CLAIM HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT FILLED SURVEY: text: PATIENT FILLED SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT OR PAYER PAID RECORD: text: PATIENT OR PAYER PAID RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT REPORTED COST: text: PATIENT REPORTED COST description: Patient reported cost meaning: OMOP:32864 PATIENT SELF-REPORT: text: PATIENT SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT SELF-TESTED: text: PATIENT SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER SYSTEM RECORD (PAID PREMIUM): text: PAYER SYSTEM RECORD (PAID PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER SYSTEM RECORD (PRIMARY PAYER): text: PAYER SYSTEM RECORD (PRIMARY PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER SYSTEM RECORD (SECONDARY PAYER): text: PAYER SYSTEM RECORD (SECONDARY PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY CLAIM: text: PHARMACY CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT OF CARE/EXPRESS LAB: text: POINT OF CARE/EXPRESS LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION TIME PERIOD: text: PRE-QUALIFICATION TIME PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL CLAIM: text: PROFESSIONAL CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL CLAIM DETAIL: text: PROFESSIONAL CLAIM DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL CLAIM HEADER: text: PROFESSIONAL CLAIM HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER CHARGE LIST PRICE: text: PROVIDER CHARGE LIST PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER FINANCIAL SYSTEM: text: PROVIDER FINANCIAL SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER INCURRED COST RECORD: text: PROVIDER INCURRED COST RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION RECORD: text: RANDOMIZATION RECORD description: Randomization record meaning: OMOP:32877 REFERENCE LAB: text: REFERENCE LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD ALGORITHM: text: STANDARD ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD ALGORITHM FROM CLAIMS: text: STANDARD ALGORITHM FROM CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 STANDARD ALGORITHM FROM EHR: text: STANDARD ALGORITHM FROM EHR description: Standard algorithm from EHR meaning: OMOP:32882 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 URGENT LAB: text: URGENT LAB description: Urgent lab meaning: OMOP:32884 US SOCIAL SECURITY DEATH MASTER FILE: text: US SOCIAL SECURITY DEATH MASTER FILE description: US Social Security Death Master File meaning: OMOP:32885 VISION CLAIM: text: VISION CLAIM description: Vision claim meaning: OMOP:32886","title":"LinkML Source"},{"location":"DimensionalObservation/","text":"Class: DimensionalObservation A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. URI: bdchm:DimensionalObservation classDiagram class DimensionalObservation Observation <|-- DimensionalObservation DimensionalObservation : age_at_observation DimensionalObservation : associated_participant DimensionalObservation --> Participant : associated_participant DimensionalObservation : associated_visit DimensionalObservation --> Visit : associated_visit DimensionalObservation : category DimensionalObservation : focus DimensionalObservation --> Entity : focus DimensionalObservation : id DimensionalObservation : method_type DimensionalObservation : observation_type DimensionalObservation : performed_by DimensionalObservation --> Organization : performed_by DimensionalObservation : value DimensionalObservation --> ObservationValueQuantity : value Inheritance Entity Observation DimensionalObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used DimensionalObservationSet observations range DimensionalObservation Comments At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DimensionalObservation native bdchm:DimensionalObservation LinkML Source Direct name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true Induced name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: DimensionalObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: DimensionalObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: DimensionalObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: DimensionalObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: DimensionalObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DimensionalObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: DimensionalObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservation domain_of: - Entity range: uriorcurie required: true","title":"Class: DimensionalObservation"},{"location":"DimensionalObservation/#class-dimensionalobservation","text":"A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. URI: bdchm:DimensionalObservation classDiagram class DimensionalObservation Observation <|-- DimensionalObservation DimensionalObservation : age_at_observation DimensionalObservation : associated_participant DimensionalObservation --> Participant : associated_participant DimensionalObservation : associated_visit DimensionalObservation --> Visit : associated_visit DimensionalObservation : category DimensionalObservation : focus DimensionalObservation --> Entity : focus DimensionalObservation : id DimensionalObservation : method_type DimensionalObservation : observation_type DimensionalObservation : performed_by DimensionalObservation --> Organization : performed_by DimensionalObservation : value DimensionalObservation --> ObservationValueQuantity : value","title":"Class: DimensionalObservation"},{"location":"DimensionalObservation/#inheritance","text":"Entity Observation DimensionalObservation","title":"Inheritance"},{"location":"DimensionalObservation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DimensionalObservation/#usages","text":"used by used in type used DimensionalObservationSet observations range DimensionalObservation","title":"Usages"},{"location":"DimensionalObservation/#comments","text":"At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data.","title":"Comments"},{"location":"DimensionalObservation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DimensionalObservation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DimensionalObservation/#mappings","text":"Mapping Type Mapped Value self bdchm:DimensionalObservation native bdchm:DimensionalObservation","title":"Mappings"},{"location":"DimensionalObservation/#linkml-source","text":"","title":"LinkML Source"},{"location":"DimensionalObservation/#direct","text":"name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true","title":"Direct"},{"location":"DimensionalObservation/#induced","text":"name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: DimensionalObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: DimensionalObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: DimensionalObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: DimensionalObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: DimensionalObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DimensionalObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: DimensionalObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DimensionalObservationSet/","text":"Class: DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). URI: bdchm:DimensionalObservationSet classDiagram class DimensionalObservationSet ObservationSet <|-- DimensionalObservationSet DimensionalObservationSet : associated_participant DimensionalObservationSet --> Participant : associated_participant DimensionalObservationSet : category DimensionalObservationSet : focus DimensionalObservationSet --> Entity : focus DimensionalObservationSet : id DimensionalObservationSet : method_type DimensionalObservationSet : observations DimensionalObservationSet --> DimensionalObservation : observations DimensionalObservationSet : performed_by DimensionalObservationSet --> Organization : performed_by Inheritance Entity ObservationSet DimensionalObservationSet Slots Name Cardinality and Range Description Inheritance observations 0..* DimensionalObservation A set of one or more observations ObservationSet category 0..1 String The general category of observation set described ObservationSet focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... ObservationSet associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) ObservationSet method_type 0..* String The type of method used in generating the ObservationSet ObservationSet performed_by 0..1 Organization The organization or group that performed the observation activity ObservationSet id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen dimensional_measures range DimensionalObservationSet Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DimensionalObservationSet native bdchm:DimensionalObservationSet LinkML Source Direct name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation Induced name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation attributes: observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: DimensionalObservationSet domain_of: - ObservationSet range: DimensionalObservation category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: DimensionalObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: DimensionalObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: DimensionalObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Class: DimensionalObservationSet"},{"location":"DimensionalObservationSet/#class-dimensionalobservationset","text":"A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). URI: bdchm:DimensionalObservationSet classDiagram class DimensionalObservationSet ObservationSet <|-- DimensionalObservationSet DimensionalObservationSet : associated_participant DimensionalObservationSet --> Participant : associated_participant DimensionalObservationSet : category DimensionalObservationSet : focus DimensionalObservationSet --> Entity : focus DimensionalObservationSet : id DimensionalObservationSet : method_type DimensionalObservationSet : observations DimensionalObservationSet --> DimensionalObservation : observations DimensionalObservationSet : performed_by DimensionalObservationSet --> Organization : performed_by","title":"Class: DimensionalObservationSet"},{"location":"DimensionalObservationSet/#inheritance","text":"Entity ObservationSet DimensionalObservationSet","title":"Inheritance"},{"location":"DimensionalObservationSet/#slots","text":"Name Cardinality and Range Description Inheritance observations 0..* DimensionalObservation A set of one or more observations ObservationSet category 0..1 String The general category of observation set described ObservationSet focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... ObservationSet associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) ObservationSet method_type 0..* String The type of method used in generating the ObservationSet ObservationSet performed_by 0..1 Organization The organization or group that performed the observation activity ObservationSet id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DimensionalObservationSet/#usages","text":"used by used in type used Specimen dimensional_measures range DimensionalObservationSet","title":"Usages"},{"location":"DimensionalObservationSet/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DimensionalObservationSet/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DimensionalObservationSet/#mappings","text":"Mapping Type Mapped Value self bdchm:DimensionalObservationSet native bdchm:DimensionalObservationSet","title":"Mappings"},{"location":"DimensionalObservationSet/#linkml-source","text":"","title":"LinkML Source"},{"location":"DimensionalObservationSet/#direct","text":"name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation","title":"Direct"},{"location":"DimensionalObservationSet/#induced","text":"name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation attributes: observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: DimensionalObservationSet domain_of: - ObservationSet range: DimensionalObservation category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: DimensionalObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: DimensionalObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: DimensionalObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Document/","text":"Class: Document A collection of information intented to be understood together as a whole, and codified in human-readable form. URI: bdchm:Document classDiagram class Document Entity <|-- Document Document : description Document : document_type Document : focus Document --> Entity : focus Document : id Document : identity Document : url Inheritance Entity Document Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct document_type 0..1 String The high-level type of the document (e direct description 0..1 String A free text description or summary of the report direct focus 0..1 Entity The entity that the report is primarily about direct url 0..* String A URL/web address where the document can be accessed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen related_document range Document Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Document native bdchm:Document LinkML Source Direct name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true Induced name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Document domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: focus owner: Document domain_of: - Document - ObservationSet - Observation range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: url owner: Document domain_of: - ResearchStudy - Questionnaire - Document range: string required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Document domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Document domain_of: - Entity range: uriorcurie required: true","title":"Class: Document"},{"location":"Document/#class-document","text":"A collection of information intented to be understood together as a whole, and codified in human-readable form. URI: bdchm:Document classDiagram class Document Entity <|-- Document Document : description Document : document_type Document : focus Document --> Entity : focus Document : id Document : identity Document : url","title":"Class: Document"},{"location":"Document/#inheritance","text":"Entity Document","title":"Inheritance"},{"location":"Document/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct document_type 0..1 String The high-level type of the document (e direct description 0..1 String A free text description or summary of the report direct focus 0..1 Entity The entity that the report is primarily about direct url 0..* String A URL/web address where the document can be accessed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Document/#usages","text":"used by used in type used Specimen related_document range Document","title":"Usages"},{"location":"Document/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Document/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Document/#mappings","text":"Mapping Type Mapped Value self bdchm:Document native bdchm:Document","title":"Mappings"},{"location":"Document/#linkml-source","text":"","title":"LinkML Source"},{"location":"Document/#direct","text":"name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"Document/#induced","text":"name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Document domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: focus owner: Document domain_of: - Document - ObservationSet - Observation range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: url owner: Document domain_of: - ResearchStudy - Questionnaire - Document range: string required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Document domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Document domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Double/","text":"Type: Double A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Double"},{"location":"Double/#type-double","text":"A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double","title":"Type: Double"},{"location":"Double/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Double/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposure/","text":"Class: DrugExposure DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. URI: bdchm:DrugExposure classDiagram class DrugExposure Entity <|-- DrugExposure DrugExposure : age_at_exposure_end DrugExposure : age_at_exposure_start DrugExposure : associated_participant DrugExposure --> Participant : associated_participant DrugExposure : associated_visit DrugExposure --> Visit : associated_visit DrugExposure : days_supply DrugExposure : drug_concept DrugExposure --> DrugExposureConceptEnum : drug_concept DrugExposure : exposure_provenance DrugExposure --> DrugExposureProvenanceEnum : exposure_provenance DrugExposure : id DrugExposure : identity DrugExposure : quantity DrugExposure : refills DrugExposure : route_concept DrugExposure --> DrugRouteEnum : route_concept DrugExposure : sig Inheritance Entity DrugExposure Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct drug_concept 0..1 DrugExposureConceptEnum The coded value for a drug direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DrugExposureProvenanceEnum A value representing the provenance of the DrugExposure record direct refills 0..1 Integer Intended refills at time of the prescription direct quantity 0..1 Float To find the dose form of a drug the RELATIONSHIP table can be used where the ... direct days_supply 0..1 Integer The number of days of supply of the medication as recorded in the original pr... direct sig 0..1 String This is the verbatim instruction for the drug as written by the provider direct route_concept 0..1 DrugRouteEnum Route of drug administration direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DrugExposure native bdchm:DrugExposure LinkML Source Direct name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false Induced name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_start owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_end owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: exposure_provenance owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DrugExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sig owner: DrugExposure domain_of: - DrugExposure range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DrugExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DrugExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DrugExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DrugExposure domain_of: - Entity range: uriorcurie required: true","title":"Class: DrugExposure"},{"location":"DrugExposure/#class-drugexposure","text":"DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. URI: bdchm:DrugExposure classDiagram class DrugExposure Entity <|-- DrugExposure DrugExposure : age_at_exposure_end DrugExposure : age_at_exposure_start DrugExposure : associated_participant DrugExposure --> Participant : associated_participant DrugExposure : associated_visit DrugExposure --> Visit : associated_visit DrugExposure : days_supply DrugExposure : drug_concept DrugExposure --> DrugExposureConceptEnum : drug_concept DrugExposure : exposure_provenance DrugExposure --> DrugExposureProvenanceEnum : exposure_provenance DrugExposure : id DrugExposure : identity DrugExposure : quantity DrugExposure : refills DrugExposure : route_concept DrugExposure --> DrugRouteEnum : route_concept DrugExposure : sig","title":"Class: DrugExposure"},{"location":"DrugExposure/#inheritance","text":"Entity DrugExposure","title":"Inheritance"},{"location":"DrugExposure/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct drug_concept 0..1 DrugExposureConceptEnum The coded value for a drug direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DrugExposureProvenanceEnum A value representing the provenance of the DrugExposure record direct refills 0..1 Integer Intended refills at time of the prescription direct quantity 0..1 Float To find the dose form of a drug the RELATIONSHIP table can be used where the ... direct days_supply 0..1 Integer The number of days of supply of the medication as recorded in the original pr... direct sig 0..1 String This is the verbatim instruction for the drug as written by the provider direct route_concept 0..1 DrugRouteEnum Route of drug administration direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DrugExposure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugExposure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposure/#mappings","text":"Mapping Type Mapped Value self bdchm:DrugExposure native bdchm:DrugExposure","title":"Mappings"},{"location":"DrugExposure/#linkml-source","text":"","title":"LinkML Source"},{"location":"DrugExposure/#direct","text":"name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false","title":"Direct"},{"location":"DrugExposure/#induced","text":"name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_start owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_end owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: exposure_provenance owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DrugExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sig owner: DrugExposure domain_of: - DrugExposure range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DrugExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DrugExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DrugExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DrugExposure domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DrugExposureConceptEnum/","text":"Enum: DrugExposureConceptEnum Drug codes from RxNorm. URI: DrugExposureConceptEnum This is a dynamic enum Slots Name Description drug_concept The coded value for a drug See Also https://bioregistry.io/registry/rxnorm https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html http://www.nlm.nih.gov/research/umls/rxnorm urn:oid:2.16.840.1.113883.6.88 Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DrugExposureConceptEnum description: Drug codes from RxNorm. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/rxnorm - https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html - http://www.nlm.nih.gov/research/umls/rxnorm - urn:oid:2.16.840.1.113883.6.88 rank: 1000 reachable_from: source_ontology: bioregistry:rxnorm","title":"Enum: DrugExposureConceptEnum"},{"location":"DrugExposureConceptEnum/#enum-drugexposureconceptenum","text":"Drug codes from RxNorm. URI: DrugExposureConceptEnum This is a dynamic enum","title":"Enum: DrugExposureConceptEnum"},{"location":"DrugExposureConceptEnum/#slots","text":"Name Description drug_concept The coded value for a drug","title":"Slots"},{"location":"DrugExposureConceptEnum/#see-also","text":"https://bioregistry.io/registry/rxnorm https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html http://www.nlm.nih.gov/research/umls/rxnorm urn:oid:2.16.840.1.113883.6.88","title":"See Also"},{"location":"DrugExposureConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugExposureConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposureConceptEnum/#linkml-source","text":"name: DrugExposureConceptEnum description: Drug codes from RxNorm. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/rxnorm - https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html - http://www.nlm.nih.gov/research/umls/rxnorm - urn:oid:2.16.840.1.113883.6.88 rank: 1000 reachable_from: source_ontology: bioregistry:rxnorm","title":"LinkML Source"},{"location":"DrugExposureProvenanceEnum/","text":"Enum: DrugExposureProvenanceEnum Source of drug exposure record URI: DrugExposureProvenanceEnum Permissible Values Value Meaning Description RANDOMIZED DRUG OMOP:44777970 Randomized Drug PATIENT SELF-REPORTED MEDICATION OMOP:44787730 Patient Self-Reported Medication NLP DERIVED OMOP:32426 NLP derived PRESCRIPTION DISPENSED IN PHARMACY OMOP:38000175 Prescription dispensed in pharmacy PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) OMOP:581373 Physician administered drug (identified from EHR order) DISPENSED IN OUTPATIENT OFFICE OMOP:581452 Dispensed in Outpatient office PRESCRIPTION DISPENSED THROUGH MAIL ORDER OMOP:38000176 Prescription dispensed through mail order PRESCRIPTION WRITTEN OMOP:38000177 Prescription written MEDICATION LIST ENTRY OMOP:38000178 Medication list entry PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) OMOP:38000179 Physician administered drug (identified as procedure) INPATIENT ADMINISTRATION OMOP:38000180 Inpatient administration DRUG ERA - 0 DAYS PERSISTENCE WINDOW OMOP:38000181 Drug era - 0 days persistence window DRUG ERA - 30 DAYS PERSISTENCE WINDOW OMOP:38000182 Drug era - 30 days persistence window PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) OMOP:43542356 Physician administered drug (identified from EHR problem list) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) OMOP:43542357 Physician administered drug (identified from referral record) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) OMOP:43542358 Physician administered drug (identified from EHR observation) Slots Name Description exposure_provenance A value representing the provenance of the DrugExposure record Comments Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name? Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DrugExposureProvenanceEnum description: Source of drug exposure record comments: - Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: RANDOMIZED DRUG: text: RANDOMIZED DRUG description: Randomized Drug meaning: OMOP:44777970 PATIENT SELF-REPORTED MEDICATION: text: PATIENT SELF-REPORTED MEDICATION description: Patient Self-Reported Medication meaning: OMOP:44787730 NLP DERIVED: text: NLP DERIVED description: NLP derived meaning: OMOP:32426 PRESCRIPTION DISPENSED IN PHARMACY: text: PRESCRIPTION DISPENSED IN PHARMACY description: Prescription dispensed in pharmacy meaning: OMOP:38000175 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) description: Physician administered drug (identified from EHR order) meaning: OMOP:581373 DISPENSED IN OUTPATIENT OFFICE: text: DISPENSED IN OUTPATIENT OFFICE description: Dispensed in Outpatient office meaning: OMOP:581452 PRESCRIPTION DISPENSED THROUGH MAIL ORDER: text: PRESCRIPTION DISPENSED THROUGH MAIL ORDER description: Prescription dispensed through mail order meaning: OMOP:38000176 PRESCRIPTION WRITTEN: text: PRESCRIPTION WRITTEN description: Prescription written meaning: OMOP:38000177 MEDICATION LIST ENTRY: text: MEDICATION LIST ENTRY description: Medication list entry meaning: OMOP:38000178 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) description: Physician administered drug (identified as procedure) meaning: OMOP:38000179 INPATIENT ADMINISTRATION: text: INPATIENT ADMINISTRATION description: Inpatient administration meaning: OMOP:38000180 DRUG ERA - 0 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 0 DAYS PERSISTENCE WINDOW description: Drug era - 0 days persistence window meaning: OMOP:38000181 DRUG ERA - 30 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 30 DAYS PERSISTENCE WINDOW description: Drug era - 30 days persistence window meaning: OMOP:38000182 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) description: Physician administered drug (identified from EHR problem list) meaning: OMOP:43542356 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) description: Physician administered drug (identified from referral record) meaning: OMOP:43542357 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) description: Physician administered drug (identified from EHR observation) meaning: OMOP:43542358","title":"Enum: DrugExposureProvenanceEnum"},{"location":"DrugExposureProvenanceEnum/#enum-drugexposureprovenanceenum","text":"Source of drug exposure record URI: DrugExposureProvenanceEnum","title":"Enum: DrugExposureProvenanceEnum"},{"location":"DrugExposureProvenanceEnum/#permissible-values","text":"Value Meaning Description RANDOMIZED DRUG OMOP:44777970 Randomized Drug PATIENT SELF-REPORTED MEDICATION OMOP:44787730 Patient Self-Reported Medication NLP DERIVED OMOP:32426 NLP derived PRESCRIPTION DISPENSED IN PHARMACY OMOP:38000175 Prescription dispensed in pharmacy PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) OMOP:581373 Physician administered drug (identified from EHR order) DISPENSED IN OUTPATIENT OFFICE OMOP:581452 Dispensed in Outpatient office PRESCRIPTION DISPENSED THROUGH MAIL ORDER OMOP:38000176 Prescription dispensed through mail order PRESCRIPTION WRITTEN OMOP:38000177 Prescription written MEDICATION LIST ENTRY OMOP:38000178 Medication list entry PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) OMOP:38000179 Physician administered drug (identified as procedure) INPATIENT ADMINISTRATION OMOP:38000180 Inpatient administration DRUG ERA - 0 DAYS PERSISTENCE WINDOW OMOP:38000181 Drug era - 0 days persistence window DRUG ERA - 30 DAYS PERSISTENCE WINDOW OMOP:38000182 Drug era - 30 days persistence window PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) OMOP:43542356 Physician administered drug (identified from EHR problem list) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) OMOP:43542357 Physician administered drug (identified from referral record) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) OMOP:43542358 Physician administered drug (identified from EHR observation)","title":"Permissible Values"},{"location":"DrugExposureProvenanceEnum/#slots","text":"Name Description exposure_provenance A value representing the provenance of the DrugExposure record","title":"Slots"},{"location":"DrugExposureProvenanceEnum/#comments","text":"Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name?","title":"Comments"},{"location":"DrugExposureProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugExposureProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposureProvenanceEnum/#linkml-source","text":"name: DrugExposureProvenanceEnum description: Source of drug exposure record comments: - Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: RANDOMIZED DRUG: text: RANDOMIZED DRUG description: Randomized Drug meaning: OMOP:44777970 PATIENT SELF-REPORTED MEDICATION: text: PATIENT SELF-REPORTED MEDICATION description: Patient Self-Reported Medication meaning: OMOP:44787730 NLP DERIVED: text: NLP DERIVED description: NLP derived meaning: OMOP:32426 PRESCRIPTION DISPENSED IN PHARMACY: text: PRESCRIPTION DISPENSED IN PHARMACY description: Prescription dispensed in pharmacy meaning: OMOP:38000175 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) description: Physician administered drug (identified from EHR order) meaning: OMOP:581373 DISPENSED IN OUTPATIENT OFFICE: text: DISPENSED IN OUTPATIENT OFFICE description: Dispensed in Outpatient office meaning: OMOP:581452 PRESCRIPTION DISPENSED THROUGH MAIL ORDER: text: PRESCRIPTION DISPENSED THROUGH MAIL ORDER description: Prescription dispensed through mail order meaning: OMOP:38000176 PRESCRIPTION WRITTEN: text: PRESCRIPTION WRITTEN description: Prescription written meaning: OMOP:38000177 MEDICATION LIST ENTRY: text: MEDICATION LIST ENTRY description: Medication list entry meaning: OMOP:38000178 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) description: Physician administered drug (identified as procedure) meaning: OMOP:38000179 INPATIENT ADMINISTRATION: text: INPATIENT ADMINISTRATION description: Inpatient administration meaning: OMOP:38000180 DRUG ERA - 0 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 0 DAYS PERSISTENCE WINDOW description: Drug era - 0 days persistence window meaning: OMOP:38000181 DRUG ERA - 30 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 30 DAYS PERSISTENCE WINDOW description: Drug era - 30 days persistence window meaning: OMOP:38000182 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) description: Physician administered drug (identified from EHR problem list) meaning: OMOP:43542356 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) description: Physician administered drug (identified from referral record) meaning: OMOP:43542357 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) description: Physician administered drug (identified from EHR observation) meaning: OMOP:43542358","title":"LinkML Source"},{"location":"DrugRouteEnum/","text":"Enum: DrugRouteEnum Routes of drug administration. URI: DrugRouteEnum Permissible Values Value Meaning Description ARTERIOVENOUS FISTULA OMOP:44783786 Arteriovenous fistula HAEMODIAFILTRATION OMOP:44801748 Haemodiafiltration SUBLESIONAL OMOP:46270168 Sublesional INTRANEURAL OMOP:46272911 Intraneural INTRAMURAL OMOP:46272926 Intramural INTRACATHETER INSTILLATION OMOP:605428 Intracatheter instillation SUBLABIAL OMOP:600817 Sublabial INTRA-ARTICULAR OMOP:4006860 Intra-articular INTRADIALYTIC OMOP:618805 Intradialytic ARTERIOVENOUS GRAFT OMOP:762840 Arteriovenous graft OTIC OMOP:4023156 Otic ORAL OMOP:4132161 Oral VAGINAL OMOP:4057765 Vaginal ROUTE OF ADMINISTRATION VALUE OMOP:4106215 Route of administration value GASTROSTOMY OMOP:4132254 Gastrostomy NASOGASTRIC OMOP:4132711 Nasogastric JEJUNOSTOMY OMOP:4133177 Jejunostomy SUBCUTANEOUS OMOP:4142048 Subcutaneous GINGIVAL OMOP:4156704 Gingival INTRACARDIAC OMOP:4156705 Intracardiac INTRADERMAL OMOP:4156706 Intradermal INTRAPLEURAL OMOP:4156707 Intrapleural PERIARTICULAR OMOP:4156708 Periarticular ENDOSINUSIAL OMOP:4157756 Endosinusial INTRACAVERNOUS OMOP:4157757 Intracavernous INTRALESIONAL OMOP:4157758 Intralesional INTRALYMPHATIC OMOP:4157759 Intralymphatic INTRAOCULAR OMOP:4157760 Intraocular PERINEURAL OMOP:4157761 Perineural INTRACRANIAL OMOP:4171079 Intracranial DENTAL OMOP:4163765 Dental INTRAAMNIOTIC OMOP:4163767 Intraamniotic INTRABURSAL OMOP:4163768 Intrabursal INTRADISCAL OMOP:4163769 Intradiscal SUBCONJUNCTIVAL OMOP:4163770 Subconjunctival MUCOUS FISTULA OMOP:4171243 Mucous fistula INTRAPROSTATIC OMOP:4171725 Intraprostatic INTRAVENOUS PERIPHERAL OMOP:4171884 Intravenous peripheral PERIOSTEAL OMOP:4171893 Periosteal ESOPHAGOSTOMY OMOP:4172191 Esophagostomy NASODUODENAL OMOP:4172316 Nasoduodenal PERCUTANEOUS OMOP:4177987 Percutaneous SUBORBITAL OMOP:4166865 Suborbital INTRATHORACIC OMOP:4167393 Intrathoracic ENTERAL OMOP:4167540 Enteral INTRAMYOMETRIAL OMOP:4168038 Intramyometrial COLOSTOMY OMOP:4168047 Colostomy INTRATYMPANIC OMOP:4168656 Intratympanic GASTRO-INTESTINAL STOMA OMOP:4168665 Gastro-intestinal stoma INTRAPULMONARY OMOP:4169270 Intrapulmonary INTRASINAL OMOP:4169440 Intrasinal TUMOR CAVITY OMOP:4169472 Tumor cavity SUBMUCOSAL OMOP:4169634 Submucosal INTRADUCTAL OMOP:4170083 Intraductal INTRAVENOUS CENTRAL OMOP:4170113 Intravenous central PARAVERTEBRAL OMOP:4170267 Paravertebral UROSTOMY OMOP:4170435 Urostomy LARYNGEAL OMOP:4170440 Laryngeal SURGICAL CAVITY OMOP:4170771 Surgical cavity INTRAVENOUS OMOP:4171047 Intravenous INTRATESTICULAR OMOP:4171067 Intratesticular ENDOCERVICAL OMOP:4186831 Endocervical ENDOTRACHEOPULMONARY OMOP:4186832 Endotracheopulmonary EXTRA-AMNIOTIC OMOP:4186833 Extra-amniotic GASTROENTERAL OMOP:4186834 Gastroenteral INTRACERVICAL OMOP:4186835 Intracervical INTRACORONARY OMOP:4186836 Intracoronary INTRASTERNAL OMOP:4186837 Intrasternal INTRAVESICAL OMOP:4186838 Intravesical OROMUCOSAL OMOP:4186839 Oromucosal CAUDAL OMOP:4220455 Caudal BUCCAL OMOP:4181897 Buccal OPHTHALMIC OMOP:4184451 Ophthalmic BODY CAVITY OMOP:4222254 Body cavity INTRAOSSEOUS OMOP:4213522 Intraosseous INTRAVENTRICULAR ROUTE - CARDIAC OMOP:4222259 Intraventricular route - cardiac INTRABILIARY OMOP:4223965 Intrabiliary INTRACEREBROVENTRICULAR OMOP:4224886 Intracerebroventricular INTRATHECAL OMOP:4217202 Intrathecal EPIDURAL OMOP:4225555 Epidural INTRATRACHEAL OMOP:4229543 Intratracheal URETHRAL OMOP:4233974 Urethral TRANSMUCOSAL OMOP:4232601 Transmucosal TRANSDERMAL OMOP:4262099 Transdermal INTRA-ARTERIAL OMOP:4240824 Intra-arterial INTRAPERITONEAL OMOP:4243022 Intraperitoneal INTRAMEDULLARY OMOP:4246511 Intramedullary INTRAUTERINE OMOP:4269621 Intrauterine NASAL OMOP:4262914 Nasal TOPICAL OMOP:4263689 Topical RECTAL OMOP:4290759 Rectal SUBLINGUAL OMOP:4292110 Sublingual INTRALUMINAL OMOP:4292410 Intraluminal TRANSCERVICAL OMOP:4304730 Transcervical INTRAABDOMINAL OMOP:4304882 Intraabdominal TRANSURETHRAL OMOP:4305382 Transurethral PERITENDINOUS OMOP:4305564 Peritendinous ILEOSTOMY OMOP:4305679 Ileostomy INTRACORNEAL OMOP:4305690 Intracorneal NASOJEJUNAL OMOP:4305834 Nasojejunal INTRACISTERNAL OMOP:4305993 Intracisternal SUBGINGIVAL OMOP:4306649 Subgingival INTRAOVARIAN OMOP:4306657 Intraovarian INTERSTITIAL OMOP:4327128 Interstitial INTRASYNOVIAL OMOP:4302352 Intrasynovial INTRADUODENAL OMOP:4302354 Intraduodenal SUBTENDINOUS OMOP:4302493 Subtendinous INTRAMUSCULAR OMOP:4302612 Intramuscular INTRAVITREAL OMOP:4302785 Intravitreal INTRASPINAL OMOP:4302788 Intraspinal INTRABRONCHIAL OMOP:4303263 Intrabronchial OROPHARYNGEAL OMOP:4303277 Oropharyngeal INTRACAMERAL OMOP:4303409 Intracameral PARACERVICAL OMOP:4303515 Paracervical PERIURETHRAL OMOP:4303646 Periurethral INTRACORONAL OMOP:4303667 Intracoronal RETROBULBAR OMOP:4303673 Retrobulbar INTRACARTILAGINOUS OMOP:4303676 Intracartilaginous OROGASTRIC OMOP:4303795 Orogastric INTRATENDINOUS OMOP:4303939 Intratendinous PERIBULBAR OMOP:4304274 Peribulbar FISTULA OMOP:4304277 Fistula SURGICAL DRAIN OMOP:4304412 Surgical drain URETERAL OMOP:4304571 Ureteral EPILESIONAL OMOP:35608078 Epilesional EXTRACORPOREAL HEMODIALYSIS OMOP:35624178 Extracorporeal hemodialysis SUPRACHOROIDAL OMOP:37174548 Suprachoroidal EXTRACORPOREAL OMOP:37018288 Extracorporeal INTRACORPORUS CAVERNOSUM OMOP:37174549 Intracorporus cavernosum INTRAGLANDULAR OMOP:37207460 Intraglandular INTRACHOLANGIOPANCREATIC OMOP:37207461 Intracholangiopancreatic INTRAPORTAL OMOP:37207462 Intraportal PERITUMORAL OMOP:37207463 Peritumoral POSTERIOR JUXTASCLERAL OMOP:37207464 Posterior juxtascleral SUBRETINAL OMOP:37207465 Subretinal INFILTRATION OMOP:37397638 Infiltration TRANSENDOCARDIAL OMOP:40487850 Transendocardial TRANSPLACENTAL OMOP:40487858 Transplacental INTRAEPIDERMAL OMOP:40487983 Intraepidermal INTRACEREBRAL OMOP:40488317 Intracerebral INTRAJEJUNAL OMOP:40489989 Intrajejunal INTRACOLONIC OMOP:40489990 Intracolonic CUTANEOUS OMOP:40490507 Cutaneous INTRAILEAL OMOP:40490837 Intraileal PERIODONTAL OMOP:40490866 Periodontal PERIDURAL OMOP:40490896 Peridural LOWER RESPIRATORY TRACT OMOP:40490898 Lower respiratory tract INTRAMAMMARY OMOP:40491321 Intramammary INTRATUMOR OMOP:40491322 Intratumor TRANSTYMPANIC OMOP:40491830 Transtympanic TRANSTRACHEAL OMOP:40491832 Transtracheal INTRAESOPHAGEAL OMOP:40492284 Intraesophageal INTRAGINGIVAL OMOP:40492286 Intragingival INTRAVASCULAR OMOP:40492287 Intravascular INTRADURAL OMOP:40492288 Intradural INTRAMENINGEAL OMOP:40492300 Intrameningeal INTRAGASTRIC OMOP:40492301 Intragastric INTRAPERICARDIAL OMOP:40492305 Intrapericardial INTRALINGUAL OMOP:40493227 Intralingual RESPIRATORY TRACT OMOP:40486069 Respiratory tract INTRAHEPATIC OMOP:40493258 Intrahepatic CONJUNCTIVAL OMOP:40486444 Conjunctival INTRAEPICARDIAL OMOP:40487473 Intraepicardial DIGESTIVE TRACT OMOP:40487501 Digestive tract OCULAR OMOP:40549429 Ocular Slots Name Description route_concept Route of drug administration Comments OMOP contains 165 standard values; select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null; from SNOMED. Do we need descriptions beyond the name? Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DrugRouteEnum description: Routes of drug administration. comments: - OMOP contains 165 standard values; `select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null;` from SNOMED. Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ARTERIOVENOUS FISTULA: text: ARTERIOVENOUS FISTULA description: Arteriovenous fistula meaning: OMOP:44783786 HAEMODIAFILTRATION: text: HAEMODIAFILTRATION description: Haemodiafiltration meaning: OMOP:44801748 SUBLESIONAL: text: SUBLESIONAL description: Sublesional meaning: OMOP:46270168 INTRANEURAL: text: INTRANEURAL description: Intraneural meaning: OMOP:46272911 INTRAMURAL: text: INTRAMURAL description: Intramural meaning: OMOP:46272926 INTRACATHETER INSTILLATION: text: INTRACATHETER INSTILLATION description: Intracatheter instillation meaning: OMOP:605428 SUBLABIAL: text: SUBLABIAL description: Sublabial meaning: OMOP:600817 INTRA-ARTICULAR: text: INTRA-ARTICULAR description: Intra-articular meaning: OMOP:4006860 INTRADIALYTIC: text: INTRADIALYTIC description: Intradialytic meaning: OMOP:618805 ARTERIOVENOUS GRAFT: text: ARTERIOVENOUS GRAFT description: Arteriovenous graft meaning: OMOP:762840 OTIC: text: OTIC description: Otic meaning: OMOP:4023156 ORAL: text: ORAL description: Oral meaning: OMOP:4132161 VAGINAL: text: VAGINAL description: Vaginal meaning: OMOP:4057765 ROUTE OF ADMINISTRATION VALUE: text: ROUTE OF ADMINISTRATION VALUE description: Route of administration value meaning: OMOP:4106215 GASTROSTOMY: text: GASTROSTOMY description: Gastrostomy meaning: OMOP:4132254 NASOGASTRIC: text: NASOGASTRIC description: Nasogastric meaning: OMOP:4132711 JEJUNOSTOMY: text: JEJUNOSTOMY description: Jejunostomy meaning: OMOP:4133177 SUBCUTANEOUS: text: SUBCUTANEOUS description: Subcutaneous meaning: OMOP:4142048 GINGIVAL: text: GINGIVAL description: Gingival meaning: OMOP:4156704 INTRACARDIAC: text: INTRACARDIAC description: Intracardiac meaning: OMOP:4156705 INTRADERMAL: text: INTRADERMAL description: Intradermal meaning: OMOP:4156706 INTRAPLEURAL: text: INTRAPLEURAL description: Intrapleural meaning: OMOP:4156707 PERIARTICULAR: text: PERIARTICULAR description: Periarticular meaning: OMOP:4156708 ENDOSINUSIAL: text: ENDOSINUSIAL description: Endosinusial meaning: OMOP:4157756 INTRACAVERNOUS: text: INTRACAVERNOUS description: Intracavernous meaning: OMOP:4157757 INTRALESIONAL: text: INTRALESIONAL description: Intralesional meaning: OMOP:4157758 INTRALYMPHATIC: text: INTRALYMPHATIC description: Intralymphatic meaning: OMOP:4157759 INTRAOCULAR: text: INTRAOCULAR description: Intraocular meaning: OMOP:4157760 PERINEURAL: text: PERINEURAL description: Perineural meaning: OMOP:4157761 INTRACRANIAL: text: INTRACRANIAL description: Intracranial meaning: OMOP:4171079 DENTAL: text: DENTAL description: Dental meaning: OMOP:4163765 INTRAAMNIOTIC: text: INTRAAMNIOTIC description: Intraamniotic meaning: OMOP:4163767 INTRABURSAL: text: INTRABURSAL description: Intrabursal meaning: OMOP:4163768 INTRADISCAL: text: INTRADISCAL description: Intradiscal meaning: OMOP:4163769 SUBCONJUNCTIVAL: text: SUBCONJUNCTIVAL description: Subconjunctival meaning: OMOP:4163770 MUCOUS FISTULA: text: MUCOUS FISTULA description: Mucous fistula meaning: OMOP:4171243 INTRAPROSTATIC: text: INTRAPROSTATIC description: Intraprostatic meaning: OMOP:4171725 INTRAVENOUS PERIPHERAL: text: INTRAVENOUS PERIPHERAL description: Intravenous peripheral meaning: OMOP:4171884 PERIOSTEAL: text: PERIOSTEAL description: Periosteal meaning: OMOP:4171893 ESOPHAGOSTOMY: text: ESOPHAGOSTOMY description: Esophagostomy meaning: OMOP:4172191 NASODUODENAL: text: NASODUODENAL description: Nasoduodenal meaning: OMOP:4172316 PERCUTANEOUS: text: PERCUTANEOUS description: Percutaneous meaning: OMOP:4177987 SUBORBITAL: text: SUBORBITAL description: Suborbital meaning: OMOP:4166865 INTRATHORACIC: text: INTRATHORACIC description: Intrathoracic meaning: OMOP:4167393 ENTERAL: text: ENTERAL description: Enteral meaning: OMOP:4167540 INTRAMYOMETRIAL: text: INTRAMYOMETRIAL description: Intramyometrial meaning: OMOP:4168038 COLOSTOMY: text: COLOSTOMY description: Colostomy meaning: OMOP:4168047 INTRATYMPANIC: text: INTRATYMPANIC description: Intratympanic meaning: OMOP:4168656 GASTRO-INTESTINAL STOMA: text: GASTRO-INTESTINAL STOMA description: Gastro-intestinal stoma meaning: OMOP:4168665 INTRAPULMONARY: text: INTRAPULMONARY description: Intrapulmonary meaning: OMOP:4169270 INTRASINAL: text: INTRASINAL description: Intrasinal meaning: OMOP:4169440 TUMOR CAVITY: text: TUMOR CAVITY description: Tumor cavity meaning: OMOP:4169472 SUBMUCOSAL: text: SUBMUCOSAL description: Submucosal meaning: OMOP:4169634 INTRADUCTAL: text: INTRADUCTAL description: Intraductal meaning: OMOP:4170083 INTRAVENOUS CENTRAL: text: INTRAVENOUS CENTRAL description: Intravenous central meaning: OMOP:4170113 PARAVERTEBRAL: text: PARAVERTEBRAL description: Paravertebral meaning: OMOP:4170267 UROSTOMY: text: UROSTOMY description: Urostomy meaning: OMOP:4170435 LARYNGEAL: text: LARYNGEAL description: Laryngeal meaning: OMOP:4170440 SURGICAL CAVITY: text: SURGICAL CAVITY description: Surgical cavity meaning: OMOP:4170771 INTRAVENOUS: text: INTRAVENOUS description: Intravenous meaning: OMOP:4171047 INTRATESTICULAR: text: INTRATESTICULAR description: Intratesticular meaning: OMOP:4171067 ENDOCERVICAL: text: ENDOCERVICAL description: Endocervical meaning: OMOP:4186831 ENDOTRACHEOPULMONARY: text: ENDOTRACHEOPULMONARY description: Endotracheopulmonary meaning: OMOP:4186832 EXTRA-AMNIOTIC: text: EXTRA-AMNIOTIC description: Extra-amniotic meaning: OMOP:4186833 GASTROENTERAL: text: GASTROENTERAL description: Gastroenteral meaning: OMOP:4186834 INTRACERVICAL: text: INTRACERVICAL description: Intracervical meaning: OMOP:4186835 INTRACORONARY: text: INTRACORONARY description: Intracoronary meaning: OMOP:4186836 INTRASTERNAL: text: INTRASTERNAL description: Intrasternal meaning: OMOP:4186837 INTRAVESICAL: text: INTRAVESICAL description: Intravesical meaning: OMOP:4186838 OROMUCOSAL: text: OROMUCOSAL description: Oromucosal meaning: OMOP:4186839 CAUDAL: text: CAUDAL description: Caudal meaning: OMOP:4220455 BUCCAL: text: BUCCAL description: Buccal meaning: OMOP:4181897 OPHTHALMIC: text: OPHTHALMIC description: Ophthalmic meaning: OMOP:4184451 BODY CAVITY: text: BODY CAVITY description: Body cavity meaning: OMOP:4222254 INTRAOSSEOUS: text: INTRAOSSEOUS description: Intraosseous meaning: OMOP:4213522 INTRAVENTRICULAR ROUTE - CARDIAC: text: INTRAVENTRICULAR ROUTE - CARDIAC description: Intraventricular route - cardiac meaning: OMOP:4222259 INTRABILIARY: text: INTRABILIARY description: Intrabiliary meaning: OMOP:4223965 INTRACEREBROVENTRICULAR: text: INTRACEREBROVENTRICULAR description: Intracerebroventricular meaning: OMOP:4224886 INTRATHECAL: text: INTRATHECAL description: Intrathecal meaning: OMOP:4217202 EPIDURAL: text: EPIDURAL description: Epidural meaning: OMOP:4225555 INTRATRACHEAL: text: INTRATRACHEAL description: Intratracheal meaning: OMOP:4229543 URETHRAL: text: URETHRAL description: Urethral meaning: OMOP:4233974 TRANSMUCOSAL: text: TRANSMUCOSAL description: Transmucosal meaning: OMOP:4232601 TRANSDERMAL: text: TRANSDERMAL description: Transdermal meaning: OMOP:4262099 INTRA-ARTERIAL: text: INTRA-ARTERIAL description: Intra-arterial meaning: OMOP:4240824 INTRAPERITONEAL: text: INTRAPERITONEAL description: Intraperitoneal meaning: OMOP:4243022 INTRAMEDULLARY: text: INTRAMEDULLARY description: Intramedullary meaning: OMOP:4246511 INTRAUTERINE: text: INTRAUTERINE description: Intrauterine meaning: OMOP:4269621 NASAL: text: NASAL description: Nasal meaning: OMOP:4262914 TOPICAL: text: TOPICAL description: Topical meaning: OMOP:4263689 RECTAL: text: RECTAL description: Rectal meaning: OMOP:4290759 SUBLINGUAL: text: SUBLINGUAL description: Sublingual meaning: OMOP:4292110 INTRALUMINAL: text: INTRALUMINAL description: Intraluminal meaning: OMOP:4292410 TRANSCERVICAL: text: TRANSCERVICAL description: Transcervical meaning: OMOP:4304730 INTRAABDOMINAL: text: INTRAABDOMINAL description: Intraabdominal meaning: OMOP:4304882 TRANSURETHRAL: text: TRANSURETHRAL description: Transurethral meaning: OMOP:4305382 PERITENDINOUS: text: PERITENDINOUS description: Peritendinous meaning: OMOP:4305564 ILEOSTOMY: text: ILEOSTOMY description: Ileostomy meaning: OMOP:4305679 INTRACORNEAL: text: INTRACORNEAL description: Intracorneal meaning: OMOP:4305690 NASOJEJUNAL: text: NASOJEJUNAL description: Nasojejunal meaning: OMOP:4305834 INTRACISTERNAL: text: INTRACISTERNAL description: Intracisternal meaning: OMOP:4305993 SUBGINGIVAL: text: SUBGINGIVAL description: Subgingival meaning: OMOP:4306649 INTRAOVARIAN: text: INTRAOVARIAN description: Intraovarian meaning: OMOP:4306657 INTERSTITIAL: text: INTERSTITIAL description: Interstitial meaning: OMOP:4327128 INTRASYNOVIAL: text: INTRASYNOVIAL description: Intrasynovial meaning: OMOP:4302352 INTRADUODENAL: text: INTRADUODENAL description: Intraduodenal meaning: OMOP:4302354 SUBTENDINOUS: text: SUBTENDINOUS description: Subtendinous meaning: OMOP:4302493 INTRAMUSCULAR: text: INTRAMUSCULAR description: Intramuscular meaning: OMOP:4302612 INTRAVITREAL: text: INTRAVITREAL description: Intravitreal meaning: OMOP:4302785 INTRASPINAL: text: INTRASPINAL description: Intraspinal meaning: OMOP:4302788 INTRABRONCHIAL: text: INTRABRONCHIAL description: Intrabronchial meaning: OMOP:4303263 OROPHARYNGEAL: text: OROPHARYNGEAL description: Oropharyngeal meaning: OMOP:4303277 INTRACAMERAL: text: INTRACAMERAL description: Intracameral meaning: OMOP:4303409 PARACERVICAL: text: PARACERVICAL description: Paracervical meaning: OMOP:4303515 PERIURETHRAL: text: PERIURETHRAL description: Periurethral meaning: OMOP:4303646 INTRACORONAL: text: INTRACORONAL description: Intracoronal meaning: OMOP:4303667 RETROBULBAR: text: RETROBULBAR description: Retrobulbar meaning: OMOP:4303673 INTRACARTILAGINOUS: text: INTRACARTILAGINOUS description: Intracartilaginous meaning: OMOP:4303676 OROGASTRIC: text: OROGASTRIC description: Orogastric meaning: OMOP:4303795 INTRATENDINOUS: text: INTRATENDINOUS description: Intratendinous meaning: OMOP:4303939 PERIBULBAR: text: PERIBULBAR description: Peribulbar meaning: OMOP:4304274 FISTULA: text: FISTULA description: Fistula meaning: OMOP:4304277 SURGICAL DRAIN: text: SURGICAL DRAIN description: Surgical drain meaning: OMOP:4304412 URETERAL: text: URETERAL description: Ureteral meaning: OMOP:4304571 EPILESIONAL: text: EPILESIONAL description: Epilesional meaning: OMOP:35608078 EXTRACORPOREAL HEMODIALYSIS: text: EXTRACORPOREAL HEMODIALYSIS description: Extracorporeal hemodialysis meaning: OMOP:35624178 SUPRACHOROIDAL: text: SUPRACHOROIDAL description: Suprachoroidal meaning: OMOP:37174548 EXTRACORPOREAL: text: EXTRACORPOREAL description: Extracorporeal meaning: OMOP:37018288 INTRACORPORUS CAVERNOSUM: text: INTRACORPORUS CAVERNOSUM description: Intracorporus cavernosum meaning: OMOP:37174549 INTRAGLANDULAR: text: INTRAGLANDULAR description: Intraglandular meaning: OMOP:37207460 INTRACHOLANGIOPANCREATIC: text: INTRACHOLANGIOPANCREATIC description: Intracholangiopancreatic meaning: OMOP:37207461 INTRAPORTAL: text: INTRAPORTAL description: Intraportal meaning: OMOP:37207462 PERITUMORAL: text: PERITUMORAL description: Peritumoral meaning: OMOP:37207463 POSTERIOR JUXTASCLERAL: text: POSTERIOR JUXTASCLERAL description: Posterior juxtascleral meaning: OMOP:37207464 SUBRETINAL: text: SUBRETINAL description: Subretinal meaning: OMOP:37207465 INFILTRATION: text: INFILTRATION description: Infiltration meaning: OMOP:37397638 TRANSENDOCARDIAL: text: TRANSENDOCARDIAL description: Transendocardial meaning: OMOP:40487850 TRANSPLACENTAL: text: TRANSPLACENTAL description: Transplacental meaning: OMOP:40487858 INTRAEPIDERMAL: text: INTRAEPIDERMAL description: Intraepidermal meaning: OMOP:40487983 INTRACEREBRAL: text: INTRACEREBRAL description: Intracerebral meaning: OMOP:40488317 INTRAJEJUNAL: text: INTRAJEJUNAL description: Intrajejunal meaning: OMOP:40489989 INTRACOLONIC: text: INTRACOLONIC description: Intracolonic meaning: OMOP:40489990 CUTANEOUS: text: CUTANEOUS description: Cutaneous meaning: OMOP:40490507 INTRAILEAL: text: INTRAILEAL description: Intraileal meaning: OMOP:40490837 PERIODONTAL: text: PERIODONTAL description: Periodontal meaning: OMOP:40490866 PERIDURAL: text: PERIDURAL description: Peridural meaning: OMOP:40490896 LOWER RESPIRATORY TRACT: text: LOWER RESPIRATORY TRACT description: Lower respiratory tract meaning: OMOP:40490898 INTRAMAMMARY: text: INTRAMAMMARY description: Intramammary meaning: OMOP:40491321 INTRATUMOR: text: INTRATUMOR description: Intratumor meaning: OMOP:40491322 TRANSTYMPANIC: text: TRANSTYMPANIC description: Transtympanic meaning: OMOP:40491830 TRANSTRACHEAL: text: TRANSTRACHEAL description: Transtracheal meaning: OMOP:40491832 INTRAESOPHAGEAL: text: INTRAESOPHAGEAL description: Intraesophageal meaning: OMOP:40492284 INTRAGINGIVAL: text: INTRAGINGIVAL description: Intragingival meaning: OMOP:40492286 INTRAVASCULAR: text: INTRAVASCULAR description: Intravascular meaning: OMOP:40492287 INTRADURAL: text: INTRADURAL description: Intradural meaning: OMOP:40492288 INTRAMENINGEAL: text: INTRAMENINGEAL description: Intrameningeal meaning: OMOP:40492300 INTRAGASTRIC: text: INTRAGASTRIC description: Intragastric meaning: OMOP:40492301 INTRAPERICARDIAL: text: INTRAPERICARDIAL description: Intrapericardial meaning: OMOP:40492305 INTRALINGUAL: text: INTRALINGUAL description: Intralingual meaning: OMOP:40493227 RESPIRATORY TRACT: text: RESPIRATORY TRACT description: Respiratory tract meaning: OMOP:40486069 INTRAHEPATIC: text: INTRAHEPATIC description: Intrahepatic meaning: OMOP:40493258 CONJUNCTIVAL: text: CONJUNCTIVAL description: Conjunctival meaning: OMOP:40486444 INTRAEPICARDIAL: text: INTRAEPICARDIAL description: Intraepicardial meaning: OMOP:40487473 DIGESTIVE TRACT: text: DIGESTIVE TRACT description: Digestive tract meaning: OMOP:40487501 OCULAR: text: OCULAR description: Ocular meaning: OMOP:40549429","title":"Enum: DrugRouteEnum"},{"location":"DrugRouteEnum/#enum-drugrouteenum","text":"Routes of drug administration. URI: DrugRouteEnum","title":"Enum: DrugRouteEnum"},{"location":"DrugRouteEnum/#permissible-values","text":"Value Meaning Description ARTERIOVENOUS FISTULA OMOP:44783786 Arteriovenous fistula HAEMODIAFILTRATION OMOP:44801748 Haemodiafiltration SUBLESIONAL OMOP:46270168 Sublesional INTRANEURAL OMOP:46272911 Intraneural INTRAMURAL OMOP:46272926 Intramural INTRACATHETER INSTILLATION OMOP:605428 Intracatheter instillation SUBLABIAL OMOP:600817 Sublabial INTRA-ARTICULAR OMOP:4006860 Intra-articular INTRADIALYTIC OMOP:618805 Intradialytic ARTERIOVENOUS GRAFT OMOP:762840 Arteriovenous graft OTIC OMOP:4023156 Otic ORAL OMOP:4132161 Oral VAGINAL OMOP:4057765 Vaginal ROUTE OF ADMINISTRATION VALUE OMOP:4106215 Route of administration value GASTROSTOMY OMOP:4132254 Gastrostomy NASOGASTRIC OMOP:4132711 Nasogastric JEJUNOSTOMY OMOP:4133177 Jejunostomy SUBCUTANEOUS OMOP:4142048 Subcutaneous GINGIVAL OMOP:4156704 Gingival INTRACARDIAC OMOP:4156705 Intracardiac INTRADERMAL OMOP:4156706 Intradermal INTRAPLEURAL OMOP:4156707 Intrapleural PERIARTICULAR OMOP:4156708 Periarticular ENDOSINUSIAL OMOP:4157756 Endosinusial INTRACAVERNOUS OMOP:4157757 Intracavernous INTRALESIONAL OMOP:4157758 Intralesional INTRALYMPHATIC OMOP:4157759 Intralymphatic INTRAOCULAR OMOP:4157760 Intraocular PERINEURAL OMOP:4157761 Perineural INTRACRANIAL OMOP:4171079 Intracranial DENTAL OMOP:4163765 Dental INTRAAMNIOTIC OMOP:4163767 Intraamniotic INTRABURSAL OMOP:4163768 Intrabursal INTRADISCAL OMOP:4163769 Intradiscal SUBCONJUNCTIVAL OMOP:4163770 Subconjunctival MUCOUS FISTULA OMOP:4171243 Mucous fistula INTRAPROSTATIC OMOP:4171725 Intraprostatic INTRAVENOUS PERIPHERAL OMOP:4171884 Intravenous peripheral PERIOSTEAL OMOP:4171893 Periosteal ESOPHAGOSTOMY OMOP:4172191 Esophagostomy NASODUODENAL OMOP:4172316 Nasoduodenal PERCUTANEOUS OMOP:4177987 Percutaneous SUBORBITAL OMOP:4166865 Suborbital INTRATHORACIC OMOP:4167393 Intrathoracic ENTERAL OMOP:4167540 Enteral INTRAMYOMETRIAL OMOP:4168038 Intramyometrial COLOSTOMY OMOP:4168047 Colostomy INTRATYMPANIC OMOP:4168656 Intratympanic GASTRO-INTESTINAL STOMA OMOP:4168665 Gastro-intestinal stoma INTRAPULMONARY OMOP:4169270 Intrapulmonary INTRASINAL OMOP:4169440 Intrasinal TUMOR CAVITY OMOP:4169472 Tumor cavity SUBMUCOSAL OMOP:4169634 Submucosal INTRADUCTAL OMOP:4170083 Intraductal INTRAVENOUS CENTRAL OMOP:4170113 Intravenous central PARAVERTEBRAL OMOP:4170267 Paravertebral UROSTOMY OMOP:4170435 Urostomy LARYNGEAL OMOP:4170440 Laryngeal SURGICAL CAVITY OMOP:4170771 Surgical cavity INTRAVENOUS OMOP:4171047 Intravenous INTRATESTICULAR OMOP:4171067 Intratesticular ENDOCERVICAL OMOP:4186831 Endocervical ENDOTRACHEOPULMONARY OMOP:4186832 Endotracheopulmonary EXTRA-AMNIOTIC OMOP:4186833 Extra-amniotic GASTROENTERAL OMOP:4186834 Gastroenteral INTRACERVICAL OMOP:4186835 Intracervical INTRACORONARY OMOP:4186836 Intracoronary INTRASTERNAL OMOP:4186837 Intrasternal INTRAVESICAL OMOP:4186838 Intravesical OROMUCOSAL OMOP:4186839 Oromucosal CAUDAL OMOP:4220455 Caudal BUCCAL OMOP:4181897 Buccal OPHTHALMIC OMOP:4184451 Ophthalmic BODY CAVITY OMOP:4222254 Body cavity INTRAOSSEOUS OMOP:4213522 Intraosseous INTRAVENTRICULAR ROUTE - CARDIAC OMOP:4222259 Intraventricular route - cardiac INTRABILIARY OMOP:4223965 Intrabiliary INTRACEREBROVENTRICULAR OMOP:4224886 Intracerebroventricular INTRATHECAL OMOP:4217202 Intrathecal EPIDURAL OMOP:4225555 Epidural INTRATRACHEAL OMOP:4229543 Intratracheal URETHRAL OMOP:4233974 Urethral TRANSMUCOSAL OMOP:4232601 Transmucosal TRANSDERMAL OMOP:4262099 Transdermal INTRA-ARTERIAL OMOP:4240824 Intra-arterial INTRAPERITONEAL OMOP:4243022 Intraperitoneal INTRAMEDULLARY OMOP:4246511 Intramedullary INTRAUTERINE OMOP:4269621 Intrauterine NASAL OMOP:4262914 Nasal TOPICAL OMOP:4263689 Topical RECTAL OMOP:4290759 Rectal SUBLINGUAL OMOP:4292110 Sublingual INTRALUMINAL OMOP:4292410 Intraluminal TRANSCERVICAL OMOP:4304730 Transcervical INTRAABDOMINAL OMOP:4304882 Intraabdominal TRANSURETHRAL OMOP:4305382 Transurethral PERITENDINOUS OMOP:4305564 Peritendinous ILEOSTOMY OMOP:4305679 Ileostomy INTRACORNEAL OMOP:4305690 Intracorneal NASOJEJUNAL OMOP:4305834 Nasojejunal INTRACISTERNAL OMOP:4305993 Intracisternal SUBGINGIVAL OMOP:4306649 Subgingival INTRAOVARIAN OMOP:4306657 Intraovarian INTERSTITIAL OMOP:4327128 Interstitial INTRASYNOVIAL OMOP:4302352 Intrasynovial INTRADUODENAL OMOP:4302354 Intraduodenal SUBTENDINOUS OMOP:4302493 Subtendinous INTRAMUSCULAR OMOP:4302612 Intramuscular INTRAVITREAL OMOP:4302785 Intravitreal INTRASPINAL OMOP:4302788 Intraspinal INTRABRONCHIAL OMOP:4303263 Intrabronchial OROPHARYNGEAL OMOP:4303277 Oropharyngeal INTRACAMERAL OMOP:4303409 Intracameral PARACERVICAL OMOP:4303515 Paracervical PERIURETHRAL OMOP:4303646 Periurethral INTRACORONAL OMOP:4303667 Intracoronal RETROBULBAR OMOP:4303673 Retrobulbar INTRACARTILAGINOUS OMOP:4303676 Intracartilaginous OROGASTRIC OMOP:4303795 Orogastric INTRATENDINOUS OMOP:4303939 Intratendinous PERIBULBAR OMOP:4304274 Peribulbar FISTULA OMOP:4304277 Fistula SURGICAL DRAIN OMOP:4304412 Surgical drain URETERAL OMOP:4304571 Ureteral EPILESIONAL OMOP:35608078 Epilesional EXTRACORPOREAL HEMODIALYSIS OMOP:35624178 Extracorporeal hemodialysis SUPRACHOROIDAL OMOP:37174548 Suprachoroidal EXTRACORPOREAL OMOP:37018288 Extracorporeal INTRACORPORUS CAVERNOSUM OMOP:37174549 Intracorporus cavernosum INTRAGLANDULAR OMOP:37207460 Intraglandular INTRACHOLANGIOPANCREATIC OMOP:37207461 Intracholangiopancreatic INTRAPORTAL OMOP:37207462 Intraportal PERITUMORAL OMOP:37207463 Peritumoral POSTERIOR JUXTASCLERAL OMOP:37207464 Posterior juxtascleral SUBRETINAL OMOP:37207465 Subretinal INFILTRATION OMOP:37397638 Infiltration TRANSENDOCARDIAL OMOP:40487850 Transendocardial TRANSPLACENTAL OMOP:40487858 Transplacental INTRAEPIDERMAL OMOP:40487983 Intraepidermal INTRACEREBRAL OMOP:40488317 Intracerebral INTRAJEJUNAL OMOP:40489989 Intrajejunal INTRACOLONIC OMOP:40489990 Intracolonic CUTANEOUS OMOP:40490507 Cutaneous INTRAILEAL OMOP:40490837 Intraileal PERIODONTAL OMOP:40490866 Periodontal PERIDURAL OMOP:40490896 Peridural LOWER RESPIRATORY TRACT OMOP:40490898 Lower respiratory tract INTRAMAMMARY OMOP:40491321 Intramammary INTRATUMOR OMOP:40491322 Intratumor TRANSTYMPANIC OMOP:40491830 Transtympanic TRANSTRACHEAL OMOP:40491832 Transtracheal INTRAESOPHAGEAL OMOP:40492284 Intraesophageal INTRAGINGIVAL OMOP:40492286 Intragingival INTRAVASCULAR OMOP:40492287 Intravascular INTRADURAL OMOP:40492288 Intradural INTRAMENINGEAL OMOP:40492300 Intrameningeal INTRAGASTRIC OMOP:40492301 Intragastric INTRAPERICARDIAL OMOP:40492305 Intrapericardial INTRALINGUAL OMOP:40493227 Intralingual RESPIRATORY TRACT OMOP:40486069 Respiratory tract INTRAHEPATIC OMOP:40493258 Intrahepatic CONJUNCTIVAL OMOP:40486444 Conjunctival INTRAEPICARDIAL OMOP:40487473 Intraepicardial DIGESTIVE TRACT OMOP:40487501 Digestive tract OCULAR OMOP:40549429 Ocular","title":"Permissible Values"},{"location":"DrugRouteEnum/#slots","text":"Name Description route_concept Route of drug administration","title":"Slots"},{"location":"DrugRouteEnum/#comments","text":"OMOP contains 165 standard values; select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null; from SNOMED. Do we need descriptions beyond the name?","title":"Comments"},{"location":"DrugRouteEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugRouteEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugRouteEnum/#linkml-source","text":"name: DrugRouteEnum description: Routes of drug administration. comments: - OMOP contains 165 standard values; `select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null;` from SNOMED. Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ARTERIOVENOUS FISTULA: text: ARTERIOVENOUS FISTULA description: Arteriovenous fistula meaning: OMOP:44783786 HAEMODIAFILTRATION: text: HAEMODIAFILTRATION description: Haemodiafiltration meaning: OMOP:44801748 SUBLESIONAL: text: SUBLESIONAL description: Sublesional meaning: OMOP:46270168 INTRANEURAL: text: INTRANEURAL description: Intraneural meaning: OMOP:46272911 INTRAMURAL: text: INTRAMURAL description: Intramural meaning: OMOP:46272926 INTRACATHETER INSTILLATION: text: INTRACATHETER INSTILLATION description: Intracatheter instillation meaning: OMOP:605428 SUBLABIAL: text: SUBLABIAL description: Sublabial meaning: OMOP:600817 INTRA-ARTICULAR: text: INTRA-ARTICULAR description: Intra-articular meaning: OMOP:4006860 INTRADIALYTIC: text: INTRADIALYTIC description: Intradialytic meaning: OMOP:618805 ARTERIOVENOUS GRAFT: text: ARTERIOVENOUS GRAFT description: Arteriovenous graft meaning: OMOP:762840 OTIC: text: OTIC description: Otic meaning: OMOP:4023156 ORAL: text: ORAL description: Oral meaning: OMOP:4132161 VAGINAL: text: VAGINAL description: Vaginal meaning: OMOP:4057765 ROUTE OF ADMINISTRATION VALUE: text: ROUTE OF ADMINISTRATION VALUE description: Route of administration value meaning: OMOP:4106215 GASTROSTOMY: text: GASTROSTOMY description: Gastrostomy meaning: OMOP:4132254 NASOGASTRIC: text: NASOGASTRIC description: Nasogastric meaning: OMOP:4132711 JEJUNOSTOMY: text: JEJUNOSTOMY description: Jejunostomy meaning: OMOP:4133177 SUBCUTANEOUS: text: SUBCUTANEOUS description: Subcutaneous meaning: OMOP:4142048 GINGIVAL: text: GINGIVAL description: Gingival meaning: OMOP:4156704 INTRACARDIAC: text: INTRACARDIAC description: Intracardiac meaning: OMOP:4156705 INTRADERMAL: text: INTRADERMAL description: Intradermal meaning: OMOP:4156706 INTRAPLEURAL: text: INTRAPLEURAL description: Intrapleural meaning: OMOP:4156707 PERIARTICULAR: text: PERIARTICULAR description: Periarticular meaning: OMOP:4156708 ENDOSINUSIAL: text: ENDOSINUSIAL description: Endosinusial meaning: OMOP:4157756 INTRACAVERNOUS: text: INTRACAVERNOUS description: Intracavernous meaning: OMOP:4157757 INTRALESIONAL: text: INTRALESIONAL description: Intralesional meaning: OMOP:4157758 INTRALYMPHATIC: text: INTRALYMPHATIC description: Intralymphatic meaning: OMOP:4157759 INTRAOCULAR: text: INTRAOCULAR description: Intraocular meaning: OMOP:4157760 PERINEURAL: text: PERINEURAL description: Perineural meaning: OMOP:4157761 INTRACRANIAL: text: INTRACRANIAL description: Intracranial meaning: OMOP:4171079 DENTAL: text: DENTAL description: Dental meaning: OMOP:4163765 INTRAAMNIOTIC: text: INTRAAMNIOTIC description: Intraamniotic meaning: OMOP:4163767 INTRABURSAL: text: INTRABURSAL description: Intrabursal meaning: OMOP:4163768 INTRADISCAL: text: INTRADISCAL description: Intradiscal meaning: OMOP:4163769 SUBCONJUNCTIVAL: text: SUBCONJUNCTIVAL description: Subconjunctival meaning: OMOP:4163770 MUCOUS FISTULA: text: MUCOUS FISTULA description: Mucous fistula meaning: OMOP:4171243 INTRAPROSTATIC: text: INTRAPROSTATIC description: Intraprostatic meaning: OMOP:4171725 INTRAVENOUS PERIPHERAL: text: INTRAVENOUS PERIPHERAL description: Intravenous peripheral meaning: OMOP:4171884 PERIOSTEAL: text: PERIOSTEAL description: Periosteal meaning: OMOP:4171893 ESOPHAGOSTOMY: text: ESOPHAGOSTOMY description: Esophagostomy meaning: OMOP:4172191 NASODUODENAL: text: NASODUODENAL description: Nasoduodenal meaning: OMOP:4172316 PERCUTANEOUS: text: PERCUTANEOUS description: Percutaneous meaning: OMOP:4177987 SUBORBITAL: text: SUBORBITAL description: Suborbital meaning: OMOP:4166865 INTRATHORACIC: text: INTRATHORACIC description: Intrathoracic meaning: OMOP:4167393 ENTERAL: text: ENTERAL description: Enteral meaning: OMOP:4167540 INTRAMYOMETRIAL: text: INTRAMYOMETRIAL description: Intramyometrial meaning: OMOP:4168038 COLOSTOMY: text: COLOSTOMY description: Colostomy meaning: OMOP:4168047 INTRATYMPANIC: text: INTRATYMPANIC description: Intratympanic meaning: OMOP:4168656 GASTRO-INTESTINAL STOMA: text: GASTRO-INTESTINAL STOMA description: Gastro-intestinal stoma meaning: OMOP:4168665 INTRAPULMONARY: text: INTRAPULMONARY description: Intrapulmonary meaning: OMOP:4169270 INTRASINAL: text: INTRASINAL description: Intrasinal meaning: OMOP:4169440 TUMOR CAVITY: text: TUMOR CAVITY description: Tumor cavity meaning: OMOP:4169472 SUBMUCOSAL: text: SUBMUCOSAL description: Submucosal meaning: OMOP:4169634 INTRADUCTAL: text: INTRADUCTAL description: Intraductal meaning: OMOP:4170083 INTRAVENOUS CENTRAL: text: INTRAVENOUS CENTRAL description: Intravenous central meaning: OMOP:4170113 PARAVERTEBRAL: text: PARAVERTEBRAL description: Paravertebral meaning: OMOP:4170267 UROSTOMY: text: UROSTOMY description: Urostomy meaning: OMOP:4170435 LARYNGEAL: text: LARYNGEAL description: Laryngeal meaning: OMOP:4170440 SURGICAL CAVITY: text: SURGICAL CAVITY description: Surgical cavity meaning: OMOP:4170771 INTRAVENOUS: text: INTRAVENOUS description: Intravenous meaning: OMOP:4171047 INTRATESTICULAR: text: INTRATESTICULAR description: Intratesticular meaning: OMOP:4171067 ENDOCERVICAL: text: ENDOCERVICAL description: Endocervical meaning: OMOP:4186831 ENDOTRACHEOPULMONARY: text: ENDOTRACHEOPULMONARY description: Endotracheopulmonary meaning: OMOP:4186832 EXTRA-AMNIOTIC: text: EXTRA-AMNIOTIC description: Extra-amniotic meaning: OMOP:4186833 GASTROENTERAL: text: GASTROENTERAL description: Gastroenteral meaning: OMOP:4186834 INTRACERVICAL: text: INTRACERVICAL description: Intracervical meaning: OMOP:4186835 INTRACORONARY: text: INTRACORONARY description: Intracoronary meaning: OMOP:4186836 INTRASTERNAL: text: INTRASTERNAL description: Intrasternal meaning: OMOP:4186837 INTRAVESICAL: text: INTRAVESICAL description: Intravesical meaning: OMOP:4186838 OROMUCOSAL: text: OROMUCOSAL description: Oromucosal meaning: OMOP:4186839 CAUDAL: text: CAUDAL description: Caudal meaning: OMOP:4220455 BUCCAL: text: BUCCAL description: Buccal meaning: OMOP:4181897 OPHTHALMIC: text: OPHTHALMIC description: Ophthalmic meaning: OMOP:4184451 BODY CAVITY: text: BODY CAVITY description: Body cavity meaning: OMOP:4222254 INTRAOSSEOUS: text: INTRAOSSEOUS description: Intraosseous meaning: OMOP:4213522 INTRAVENTRICULAR ROUTE - CARDIAC: text: INTRAVENTRICULAR ROUTE - CARDIAC description: Intraventricular route - cardiac meaning: OMOP:4222259 INTRABILIARY: text: INTRABILIARY description: Intrabiliary meaning: OMOP:4223965 INTRACEREBROVENTRICULAR: text: INTRACEREBROVENTRICULAR description: Intracerebroventricular meaning: OMOP:4224886 INTRATHECAL: text: INTRATHECAL description: Intrathecal meaning: OMOP:4217202 EPIDURAL: text: EPIDURAL description: Epidural meaning: OMOP:4225555 INTRATRACHEAL: text: INTRATRACHEAL description: Intratracheal meaning: OMOP:4229543 URETHRAL: text: URETHRAL description: Urethral meaning: OMOP:4233974 TRANSMUCOSAL: text: TRANSMUCOSAL description: Transmucosal meaning: OMOP:4232601 TRANSDERMAL: text: TRANSDERMAL description: Transdermal meaning: OMOP:4262099 INTRA-ARTERIAL: text: INTRA-ARTERIAL description: Intra-arterial meaning: OMOP:4240824 INTRAPERITONEAL: text: INTRAPERITONEAL description: Intraperitoneal meaning: OMOP:4243022 INTRAMEDULLARY: text: INTRAMEDULLARY description: Intramedullary meaning: OMOP:4246511 INTRAUTERINE: text: INTRAUTERINE description: Intrauterine meaning: OMOP:4269621 NASAL: text: NASAL description: Nasal meaning: OMOP:4262914 TOPICAL: text: TOPICAL description: Topical meaning: OMOP:4263689 RECTAL: text: RECTAL description: Rectal meaning: OMOP:4290759 SUBLINGUAL: text: SUBLINGUAL description: Sublingual meaning: OMOP:4292110 INTRALUMINAL: text: INTRALUMINAL description: Intraluminal meaning: OMOP:4292410 TRANSCERVICAL: text: TRANSCERVICAL description: Transcervical meaning: OMOP:4304730 INTRAABDOMINAL: text: INTRAABDOMINAL description: Intraabdominal meaning: OMOP:4304882 TRANSURETHRAL: text: TRANSURETHRAL description: Transurethral meaning: OMOP:4305382 PERITENDINOUS: text: PERITENDINOUS description: Peritendinous meaning: OMOP:4305564 ILEOSTOMY: text: ILEOSTOMY description: Ileostomy meaning: OMOP:4305679 INTRACORNEAL: text: INTRACORNEAL description: Intracorneal meaning: OMOP:4305690 NASOJEJUNAL: text: NASOJEJUNAL description: Nasojejunal meaning: OMOP:4305834 INTRACISTERNAL: text: INTRACISTERNAL description: Intracisternal meaning: OMOP:4305993 SUBGINGIVAL: text: SUBGINGIVAL description: Subgingival meaning: OMOP:4306649 INTRAOVARIAN: text: INTRAOVARIAN description: Intraovarian meaning: OMOP:4306657 INTERSTITIAL: text: INTERSTITIAL description: Interstitial meaning: OMOP:4327128 INTRASYNOVIAL: text: INTRASYNOVIAL description: Intrasynovial meaning: OMOP:4302352 INTRADUODENAL: text: INTRADUODENAL description: Intraduodenal meaning: OMOP:4302354 SUBTENDINOUS: text: SUBTENDINOUS description: Subtendinous meaning: OMOP:4302493 INTRAMUSCULAR: text: INTRAMUSCULAR description: Intramuscular meaning: OMOP:4302612 INTRAVITREAL: text: INTRAVITREAL description: Intravitreal meaning: OMOP:4302785 INTRASPINAL: text: INTRASPINAL description: Intraspinal meaning: OMOP:4302788 INTRABRONCHIAL: text: INTRABRONCHIAL description: Intrabronchial meaning: OMOP:4303263 OROPHARYNGEAL: text: OROPHARYNGEAL description: Oropharyngeal meaning: OMOP:4303277 INTRACAMERAL: text: INTRACAMERAL description: Intracameral meaning: OMOP:4303409 PARACERVICAL: text: PARACERVICAL description: Paracervical meaning: OMOP:4303515 PERIURETHRAL: text: PERIURETHRAL description: Periurethral meaning: OMOP:4303646 INTRACORONAL: text: INTRACORONAL description: Intracoronal meaning: OMOP:4303667 RETROBULBAR: text: RETROBULBAR description: Retrobulbar meaning: OMOP:4303673 INTRACARTILAGINOUS: text: INTRACARTILAGINOUS description: Intracartilaginous meaning: OMOP:4303676 OROGASTRIC: text: OROGASTRIC description: Orogastric meaning: OMOP:4303795 INTRATENDINOUS: text: INTRATENDINOUS description: Intratendinous meaning: OMOP:4303939 PERIBULBAR: text: PERIBULBAR description: Peribulbar meaning: OMOP:4304274 FISTULA: text: FISTULA description: Fistula meaning: OMOP:4304277 SURGICAL DRAIN: text: SURGICAL DRAIN description: Surgical drain meaning: OMOP:4304412 URETERAL: text: URETERAL description: Ureteral meaning: OMOP:4304571 EPILESIONAL: text: EPILESIONAL description: Epilesional meaning: OMOP:35608078 EXTRACORPOREAL HEMODIALYSIS: text: EXTRACORPOREAL HEMODIALYSIS description: Extracorporeal hemodialysis meaning: OMOP:35624178 SUPRACHOROIDAL: text: SUPRACHOROIDAL description: Suprachoroidal meaning: OMOP:37174548 EXTRACORPOREAL: text: EXTRACORPOREAL description: Extracorporeal meaning: OMOP:37018288 INTRACORPORUS CAVERNOSUM: text: INTRACORPORUS CAVERNOSUM description: Intracorporus cavernosum meaning: OMOP:37174549 INTRAGLANDULAR: text: INTRAGLANDULAR description: Intraglandular meaning: OMOP:37207460 INTRACHOLANGIOPANCREATIC: text: INTRACHOLANGIOPANCREATIC description: Intracholangiopancreatic meaning: OMOP:37207461 INTRAPORTAL: text: INTRAPORTAL description: Intraportal meaning: OMOP:37207462 PERITUMORAL: text: PERITUMORAL description: Peritumoral meaning: OMOP:37207463 POSTERIOR JUXTASCLERAL: text: POSTERIOR JUXTASCLERAL description: Posterior juxtascleral meaning: OMOP:37207464 SUBRETINAL: text: SUBRETINAL description: Subretinal meaning: OMOP:37207465 INFILTRATION: text: INFILTRATION description: Infiltration meaning: OMOP:37397638 TRANSENDOCARDIAL: text: TRANSENDOCARDIAL description: Transendocardial meaning: OMOP:40487850 TRANSPLACENTAL: text: TRANSPLACENTAL description: Transplacental meaning: OMOP:40487858 INTRAEPIDERMAL: text: INTRAEPIDERMAL description: Intraepidermal meaning: OMOP:40487983 INTRACEREBRAL: text: INTRACEREBRAL description: Intracerebral meaning: OMOP:40488317 INTRAJEJUNAL: text: INTRAJEJUNAL description: Intrajejunal meaning: OMOP:40489989 INTRACOLONIC: text: INTRACOLONIC description: Intracolonic meaning: OMOP:40489990 CUTANEOUS: text: CUTANEOUS description: Cutaneous meaning: OMOP:40490507 INTRAILEAL: text: INTRAILEAL description: Intraileal meaning: OMOP:40490837 PERIODONTAL: text: PERIODONTAL description: Periodontal meaning: OMOP:40490866 PERIDURAL: text: PERIDURAL description: Peridural meaning: OMOP:40490896 LOWER RESPIRATORY TRACT: text: LOWER RESPIRATORY TRACT description: Lower respiratory tract meaning: OMOP:40490898 INTRAMAMMARY: text: INTRAMAMMARY description: Intramammary meaning: OMOP:40491321 INTRATUMOR: text: INTRATUMOR description: Intratumor meaning: OMOP:40491322 TRANSTYMPANIC: text: TRANSTYMPANIC description: Transtympanic meaning: OMOP:40491830 TRANSTRACHEAL: text: TRANSTRACHEAL description: Transtracheal meaning: OMOP:40491832 INTRAESOPHAGEAL: text: INTRAESOPHAGEAL description: Intraesophageal meaning: OMOP:40492284 INTRAGINGIVAL: text: INTRAGINGIVAL description: Intragingival meaning: OMOP:40492286 INTRAVASCULAR: text: INTRAVASCULAR description: Intravascular meaning: OMOP:40492287 INTRADURAL: text: INTRADURAL description: Intradural meaning: OMOP:40492288 INTRAMENINGEAL: text: INTRAMENINGEAL description: Intrameningeal meaning: OMOP:40492300 INTRAGASTRIC: text: INTRAGASTRIC description: Intragastric meaning: OMOP:40492301 INTRAPERICARDIAL: text: INTRAPERICARDIAL description: Intrapericardial meaning: OMOP:40492305 INTRALINGUAL: text: INTRALINGUAL description: Intralingual meaning: OMOP:40493227 RESPIRATORY TRACT: text: RESPIRATORY TRACT description: Respiratory tract meaning: OMOP:40486069 INTRAHEPATIC: text: INTRAHEPATIC description: Intrahepatic meaning: OMOP:40493258 CONJUNCTIVAL: text: CONJUNCTIVAL description: Conjunctival meaning: OMOP:40486444 INTRAEPICARDIAL: text: INTRAEPICARDIAL description: Intraepicardial meaning: OMOP:40487473 DIGESTIVE TRACT: text: DIGESTIVE TRACT description: Digestive tract meaning: OMOP:40487501 OCULAR: text: OCULAR description: Ocular meaning: OMOP:40549429","title":"LinkML Source"},{"location":"Entity/","text":"Class: Entity Any resource that has its own identifier NOTE : this is an abstract class and should not be instantiated directly URI: schema:Thing classDiagram class Entity Entity <|-- Person Entity <|-- Demography Entity <|-- Participant Entity <|-- ResearchStudy Entity <|-- Consent Entity <|-- Visit Entity <|-- Organization Entity <|-- TimePoint Entity <|-- Questionnaire Entity <|-- QuestionnaireItem Entity <|-- QuestionnaireResponse Entity <|-- Condition Entity <|-- Procedure Entity <|-- DrugExposure Entity <|-- DeviceExposure Entity <|-- File Entity <|-- Document Entity <|-- Specimen Entity <|-- SpecimenContainer Entity <|-- SpecimenCreationActivity Entity <|-- SpecimenProcessingActivity Entity <|-- SpecimenStorageActivity Entity <|-- SpecimenTransportActivity Entity <|-- BiologicProduct Entity <|-- Substance Entity <|-- Quantity Entity <|-- BodySite Entity <|-- ObservationSet Entity <|-- Observation Entity : id 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The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Entity domain_of: - Entity range: uriorcurie class_uri: schema:Thing","title":"Induced"},{"location":"EthnicityEnum/","text":"Enum: EthnicityEnum A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for ethnicity. URI: EthnicityEnum Permissible Values Value Meaning Description HISPANIC_OR_LATINO OMOP:38003563 A person of Cuban, Mexican, Puerto Rican, South or Central American, or other... NOT_HISPANIC_OR_LATINO OMOP:38003564 A person not of Cuban, Mexican, Puerto Rican, South or Central American, or o... Slots Name Description ethnicity An individual's self-described social and cultural grouping, specifically whe... 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(OMB) meaning: OMOP:38003563 NOT_HISPANIC_OR_LATINO: text: NOT_HISPANIC_OR_LATINO description: A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. meaning: OMOP:38003564","title":"Enum: EthnicityEnum"},{"location":"EthnicityEnum/#enum-ethnicityenum","text":"A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for ethnicity. URI: EthnicityEnum","title":"Enum: EthnicityEnum"},{"location":"EthnicityEnum/#permissible-values","text":"Value Meaning Description HISPANIC_OR_LATINO OMOP:38003563 A person of Cuban, Mexican, Puerto Rican, South or Central American, or other... 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The term, \"Spanish origin\" can be used in addition to \"Hispanic or Latino\". (OMB) meaning: OMOP:38003563 NOT_HISPANIC_OR_LATINO: text: NOT_HISPANIC_OR_LATINO description: A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. meaning: OMOP:38003564","title":"LinkML Source"},{"location":"File/","text":"Class: File Abstract class for various kinds of files. Subclasses will be defined for specific file types. URI: bdchm:File classDiagram class File Entity <|-- File File : associated_participant File --> Participant : associated_participant File : data_category File : data_type File : description File : file_name File : file_size File : format File : id File : identity File : uri Inheritance Entity File Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct file_name 0..1 String The name (or part of a name) of a file (of any type) direct file_size 0..1 Integer The size of the data file (object) in bytes direct uri 0..1 Uriorcurie A unique identifier or url for identifying or locating the file direct data_type 0..1 String The nature or genre of the resource direct data_category 0..1 String A broad categorization of the contents of the data file direct format 0..1 String The file format, physical medium, or dimensions of the resource direct description 0..1 String An account of the resource direct associated_participant 0..1 Participant A reference to the Participant to which this file relates direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Comments This is taken largely from the Gen3 Core Metadata Collection definition. Gen3 apparently took most of the attributes listed here from the Dublin Core /elements/1.1/ namespace . Attributes different from those in Dublin Core are noted as such in the comments. The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? Tentatively including three attribute for addressing this -- identifier, file_path, and uri. There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:File native bdchm:File LinkML Source Direct name: File description: Abstract class for various kinds of files. Subclasses will be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer uri: name: uri description: A unique identifier or url for identifying or locating the file. comments: - Not included in the Gen3 Core Metadata or Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: uriorcurie data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant Induced name: File description: Abstract class for various kinds of files. Subclasses will be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer uri: name: uri description: A unique identifier or url for identifying or locating the file. comments: - Not included in the Gen3 Core Metadata or Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: uri owner: File domain_of: - File range: uriorcurie data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: File domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: File domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: File domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: File domain_of: - Entity range: uriorcurie required: true","title":"Class: File"},{"location":"File/#class-file","text":"Abstract class for various kinds of files. Subclasses will be defined for specific file types. URI: bdchm:File classDiagram class File Entity <|-- File File : associated_participant File --> Participant : associated_participant File : data_category File : data_type File : description File : file_name File : file_size File : format File : id File : identity File : uri","title":"Class: File"},{"location":"File/#inheritance","text":"Entity File","title":"Inheritance"},{"location":"File/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct file_name 0..1 String The name (or part of a name) of a file (of any type) direct file_size 0..1 Integer The size of the data file (object) in bytes direct uri 0..1 Uriorcurie A unique identifier or url for identifying or locating the file direct data_type 0..1 String The nature or genre of the resource direct data_category 0..1 String A broad categorization of the contents of the data file direct format 0..1 String The file format, physical medium, or dimensions of the resource direct description 0..1 String An account of the resource direct associated_participant 0..1 Participant A reference to the Participant to which this file relates direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"File/#comments","text":"This is taken largely from the Gen3 Core Metadata Collection definition. Gen3 apparently took most of the attributes listed here from the Dublin Core /elements/1.1/ namespace . Attributes different from those in Dublin Core are noted as such in the comments. The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? Tentatively including three attribute for addressing this -- identifier, file_path, and uri. There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files.","title":"Comments"},{"location":"File/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"File/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"File/#mappings","text":"Mapping Type Mapped Value self bdchm:File native bdchm:File","title":"Mappings"},{"location":"File/#linkml-source","text":"","title":"LinkML Source"},{"location":"File/#direct","text":"name: File description: Abstract class for various kinds of files. Subclasses will be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer uri: name: uri description: A unique identifier or url for identifying or locating the file. comments: - Not included in the Gen3 Core Metadata or Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: uriorcurie data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant","title":"Direct"},{"location":"File/#induced","text":"name: File description: Abstract class for various kinds of files. Subclasses will be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer uri: name: uri description: A unique identifier or url for identifying or locating the file. comments: - Not included in the Gen3 Core Metadata or Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: uri owner: File domain_of: - File range: uriorcurie data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: File domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: File domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: File domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: File domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Float/","text":"Type: Float A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Float"},{"location":"Float/#type-float","text":"A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float","title":"Type: Float"},{"location":"Float/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Float/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"HpoPhenotypicAbnormalityEnum/","text":"Enum: HpoPhenotypicAbnormalityEnum A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. URI: HpoPhenotypicAbnormalityEnum This is a dynamic enum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: HpoPhenotypicAbnormalityEnum description: A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:hp source_nodes: - HP:0000118 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: HpoPhenotypicAbnormalityEnum"},{"location":"HpoPhenotypicAbnormalityEnum/#enum-hpophenotypicabnormalityenum","text":"A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. URI: HpoPhenotypicAbnormalityEnum This is a dynamic enum","title":"Enum: HpoPhenotypicAbnormalityEnum"},{"location":"HpoPhenotypicAbnormalityEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"HpoPhenotypicAbnormalityEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"HpoPhenotypicAbnormalityEnum/#linkml-source","text":"name: HpoPhenotypicAbnormalityEnum description: A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:hp source_nodes: - HP:0000118 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Integer/","text":"Type: Integer An integer URI: xsd:integer base : int uri : xsd:integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Integer"},{"location":"Integer/#type-integer","text":"An integer URI: xsd:integer base : int uri : xsd:integer","title":"Type: Integer"},{"location":"Integer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Integer/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Jsonpath/","text":"Type: Jsonpath A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Jsonpath"},{"location":"Jsonpath/#type-jsonpath","text":"A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Jsonpath"},{"location":"Jsonpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpath/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Jsonpointer/","text":"Type: Jsonpointer A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#type-jsonpointer","text":"A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpointer/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"MondoHumanDiseaseEnum/","text":"Enum: MondoHumanDiseaseEnum A constrained set of enumerative values containing the MONDO values for human diseases. URI: MondoHumanDiseaseEnum This is a dynamic enum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: MondoHumanDiseaseEnum description: A constrained set of enumerative values containing the MONDO values for human diseases. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:mondo source_nodes: - MONDO:0700096 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: MondoHumanDiseaseEnum"},{"location":"MondoHumanDiseaseEnum/#enum-mondohumandiseaseenum","text":"A constrained set of enumerative values containing the MONDO values for human diseases. URI: MondoHumanDiseaseEnum This is a dynamic enum","title":"Enum: MondoHumanDiseaseEnum"},{"location":"MondoHumanDiseaseEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"MondoHumanDiseaseEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"MondoHumanDiseaseEnum/#linkml-source","text":"name: MondoHumanDiseaseEnum description: A constrained set of enumerative values containing the MONDO values for human diseases. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:mondo source_nodes: - MONDO:0700096 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Ncname/","text":"Type: Ncname Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Ncname"},{"location":"Ncname/#type-ncname","text":"Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str","title":"Type: Ncname"},{"location":"Ncname/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ncname/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Nodeidentifier/","text":"Type: Nodeidentifier A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#type-nodeidentifier","text":"A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Nodeidentifier/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Objectidentifier/","text":"Type: Objectidentifier A URI or CURIE that represents an object in the model. URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str Comments Used for inheritance and type checking Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#type-objectidentifier","text":"A URI or CURIE that represents an object in the model. URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#comments","text":"Used for inheritance and type checking","title":"Comments"},{"location":"Objectidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Objectidentifier/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Observation/","text":"Class: Observation A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. URI: bdchm:Observation classDiagram class Observation Entity <|-- Observation Observation <|-- DimensionalObservation Observation <|-- SpecimenQualityObservation Observation <|-- SpecimenQuantityObservation Observation : age_at_observation Observation : associated_participant Observation --> Participant : associated_participant Observation : associated_visit Observation --> Visit : associated_visit Observation : category Observation : focus Observation --> Entity : focus Observation : id Observation : method_type Observation : observation_type Observation : performed_by Observation --> Organization : performed_by Observation : value Observation --> ObservationValue : value Inheritance Entity Observation DimensionalObservation SpecimenQualityObservation SpecimenQuantityObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made direct category 0..1 String The general category of observation described direct observation_type 1..1 String The type of Observation being represented (e direct method_type 0..1 String A type of method used in generating the Observation result direct focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) direct associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded direct performed_by 0..1 Organization The organization or group that performed the observation activity direct value 1..1 ObservationValue The value for an Observation direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used ObservationSet observations range Observation Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Observation native bdchm:Observation LinkML Source Direct name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: ObservationValue required: true Induced name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: Observation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: Observation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: Observation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: Observation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: Observation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: Observation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Observation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: Observation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: Observation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValue required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Observation domain_of: - Entity range: uriorcurie required: true","title":"Class: Observation"},{"location":"Observation/#class-observation","text":"A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. URI: bdchm:Observation classDiagram class Observation Entity <|-- Observation Observation <|-- DimensionalObservation Observation <|-- SpecimenQualityObservation Observation <|-- SpecimenQuantityObservation Observation : age_at_observation Observation : associated_participant Observation --> Participant : associated_participant Observation : associated_visit Observation --> Visit : associated_visit Observation : category Observation : focus Observation --> Entity : focus Observation : id Observation : method_type Observation : observation_type Observation : performed_by Observation --> Organization : performed_by Observation : value Observation --> ObservationValue : value","title":"Class: Observation"},{"location":"Observation/#inheritance","text":"Entity Observation DimensionalObservation SpecimenQualityObservation SpecimenQuantityObservation","title":"Inheritance"},{"location":"Observation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made direct category 0..1 String The general category of observation described direct observation_type 1..1 String The type of Observation being represented (e direct method_type 0..1 String A type of method used in generating the Observation result direct focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) direct associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded direct performed_by 0..1 Organization The organization or group that performed the observation activity direct value 1..1 ObservationValue The value for an Observation direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Observation/#usages","text":"used by used in type used ObservationSet observations range Observation","title":"Usages"},{"location":"Observation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Observation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Observation/#mappings","text":"Mapping Type Mapped Value self bdchm:Observation native bdchm:Observation","title":"Mappings"},{"location":"Observation/#linkml-source","text":"","title":"LinkML Source"},{"location":"Observation/#direct","text":"name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: ObservationValue required: true","title":"Direct"},{"location":"Observation/#induced","text":"name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: Observation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: Observation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: Observation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: Observation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: Observation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: Observation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Observation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: Observation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: Observation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValue required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Observation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ObservationSet/","text":"Class: ObservationSet A structured object to hold related Observations in a set. URI: bdchm:ObservationSet classDiagram class ObservationSet Entity <|-- ObservationSet ObservationSet <|-- DimensionalObservationSet ObservationSet : associated_participant ObservationSet --> Participant : associated_participant ObservationSet : category ObservationSet : focus ObservationSet --> Entity : focus ObservationSet : id ObservationSet : method_type ObservationSet : observations ObservationSet --> Observation : observations ObservationSet : performed_by ObservationSet --> Organization : performed_by Inheritance Entity ObservationSet DimensionalObservationSet Slots Name Cardinality and Range Description Inheritance observations 0..* Observation A set of one or more observations direct category 0..1 String The general category of observation set described direct focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) direct method_type 0..* String The type of method used in generating the ObservationSet direct performed_by 0..1 Organization The organization or group that performed the observation activity direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationSet native bdchm:ObservationSet LinkML Source Direct name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - observations attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false Induced name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: ObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: ObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: ObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: ObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: ObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: ObservationSet domain_of: - ObservationSet range: Observation id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Class: ObservationSet"},{"location":"ObservationSet/#class-observationset","text":"A structured object to hold related Observations in a set. URI: bdchm:ObservationSet classDiagram class ObservationSet Entity <|-- ObservationSet ObservationSet <|-- DimensionalObservationSet ObservationSet : associated_participant ObservationSet --> Participant : associated_participant ObservationSet : category ObservationSet : focus ObservationSet --> Entity : focus ObservationSet : id ObservationSet : method_type ObservationSet : observations ObservationSet --> Observation : observations ObservationSet : performed_by ObservationSet --> Organization : performed_by","title":"Class: ObservationSet"},{"location":"ObservationSet/#inheritance","text":"Entity ObservationSet DimensionalObservationSet","title":"Inheritance"},{"location":"ObservationSet/#slots","text":"Name Cardinality and Range Description Inheritance observations 0..* Observation A set of one or more observations direct category 0..1 String The general category of observation set described direct focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) direct method_type 0..* String The type of method used in generating the ObservationSet direct performed_by 0..1 Organization The organization or group that performed the observation activity direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"ObservationSet/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationSet/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationSet/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationSet native bdchm:ObservationSet","title":"Mappings"},{"location":"ObservationSet/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationSet/#direct","text":"name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - observations attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false","title":"Direct"},{"location":"ObservationSet/#induced","text":"name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: ObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: ObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: ObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: ObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: ObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: ObservationSet domain_of: - ObservationSet range: Observation id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ObservationValue/","text":"Class: ObservationValue Single-valued observation valueholiding slot NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:ObservationValue classDiagram class ObservationValue ObservationValue <|-- ObservationValueDecimal ObservationValue <|-- ObservationValueInteger ObservationValue <|-- ObservationValueBoolean ObservationValue <|-- ObservationValueString ObservationValue <|-- ObservationValueQuantity ObservationValue : name ObservationValue : type ObservationValue : value Inheritance ObservationValue ObservationValueDecimal ObservationValueInteger ObservationValueBoolean ObservationValueString ObservationValueQuantity Slots Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct Usages used by used in type used Observation value range ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValue native bdchm:ObservationValue LinkML Source Direct name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string Induced name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Class: ObservationValue"},{"location":"ObservationValue/#class-observationvalue","text":"Single-valued observation valueholiding slot NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:ObservationValue classDiagram class ObservationValue ObservationValue <|-- ObservationValueDecimal ObservationValue <|-- ObservationValueInteger ObservationValue <|-- ObservationValueBoolean ObservationValue <|-- ObservationValueString ObservationValue <|-- ObservationValueQuantity ObservationValue : name ObservationValue : type ObservationValue : value","title":"Class: ObservationValue"},{"location":"ObservationValue/#inheritance","text":"ObservationValue ObservationValueDecimal ObservationValueInteger ObservationValueBoolean ObservationValueString ObservationValueQuantity","title":"Inheritance"},{"location":"ObservationValue/#slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct","title":"Slots"},{"location":"ObservationValue/#usages","text":"used by used in type used Observation value range ObservationValue","title":"Usages"},{"location":"ObservationValue/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValue/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValue/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValue native bdchm:ObservationValue","title":"Mappings"},{"location":"ObservationValue/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValue/#direct","text":"name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string","title":"Direct"},{"location":"ObservationValue/#induced","text":"name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueBoolean/","text":"Class: ObservationValueBoolean Single-valued boolean observation URI: bdchm:ObservationValueBoolean classDiagram class ObservationValueBoolean ObservationValue <|-- ObservationValueBoolean ObservationValueBoolean : name ObservationValueBoolean : type ObservationValueBoolean : value Inheritance ObservationValue ObservationValueBoolean Slots Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueBoolean native bdchm:ObservationValueBoolean LinkML Source Direct name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true Induced name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueBoolean"},{"location":"ObservationValueBoolean/#class-observationvalueboolean","text":"Single-valued boolean observation URI: bdchm:ObservationValueBoolean classDiagram class ObservationValueBoolean ObservationValue <|-- ObservationValueBoolean ObservationValueBoolean : name ObservationValueBoolean : type ObservationValueBoolean : value","title":"Class: ObservationValueBoolean"},{"location":"ObservationValueBoolean/#inheritance","text":"ObservationValue ObservationValueBoolean","title":"Inheritance"},{"location":"ObservationValueBoolean/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueBoolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueBoolean/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueBoolean/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueBoolean native bdchm:ObservationValueBoolean","title":"Mappings"},{"location":"ObservationValueBoolean/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueBoolean/#direct","text":"name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true","title":"Direct"},{"location":"ObservationValueBoolean/#induced","text":"name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueDecimal/","text":"Class: ObservationValueDecimal Single-valued decimal observation URI: bdchm:ObservationValueDecimal classDiagram class ObservationValueDecimal ObservationValue <|-- ObservationValueDecimal ObservationValueDecimal : name ObservationValueDecimal : type ObservationValueDecimal : value Inheritance ObservationValue ObservationValueDecimal Slots Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueDecimal native bdchm:ObservationValueDecimal LinkML Source Direct name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true Induced name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueDecimal"},{"location":"ObservationValueDecimal/#class-observationvaluedecimal","text":"Single-valued decimal observation URI: bdchm:ObservationValueDecimal classDiagram class ObservationValueDecimal ObservationValue <|-- ObservationValueDecimal ObservationValueDecimal : name ObservationValueDecimal : type ObservationValueDecimal : value","title":"Class: ObservationValueDecimal"},{"location":"ObservationValueDecimal/#inheritance","text":"ObservationValue ObservationValueDecimal","title":"Inheritance"},{"location":"ObservationValueDecimal/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueDecimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueDecimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueDecimal/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueDecimal native bdchm:ObservationValueDecimal","title":"Mappings"},{"location":"ObservationValueDecimal/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueDecimal/#direct","text":"name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true","title":"Direct"},{"location":"ObservationValueDecimal/#induced","text":"name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueInteger/","text":"Class: ObservationValueInteger Single-valued integer observation URI: bdchm:ObservationValueInteger classDiagram class ObservationValueInteger ObservationValue <|-- ObservationValueInteger ObservationValueInteger : name ObservationValueInteger : type ObservationValueInteger : value Inheritance ObservationValue ObservationValueInteger Slots Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueInteger native bdchm:ObservationValueInteger LinkML Source Direct name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true Induced name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueInteger"},{"location":"ObservationValueInteger/#class-observationvalueinteger","text":"Single-valued integer observation URI: bdchm:ObservationValueInteger classDiagram class ObservationValueInteger ObservationValue <|-- ObservationValueInteger ObservationValueInteger : name ObservationValueInteger : type ObservationValueInteger : value","title":"Class: ObservationValueInteger"},{"location":"ObservationValueInteger/#inheritance","text":"ObservationValue ObservationValueInteger","title":"Inheritance"},{"location":"ObservationValueInteger/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueInteger/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueInteger/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueInteger/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueInteger native bdchm:ObservationValueInteger","title":"Mappings"},{"location":"ObservationValueInteger/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueInteger/#direct","text":"name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true","title":"Direct"},{"location":"ObservationValueInteger/#induced","text":"name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueQuantity/","text":"Class: ObservationValueQuantity Single-valued Quantity observation URI: bdchm:ObservationValueQuantity classDiagram class ObservationValueQuantity ObservationValue <|-- ObservationValueQuantity ObservationValueQuantity : name ObservationValueQuantity : type ObservationValueQuantity : value ObservationValueQuantity --> Quantity : value Inheritance ObservationValue ObservationValueQuantity Slots Name Cardinality and Range Description Inheritance value 1..1 Quantity A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Usages used by used in type used DimensionalObservation value range ObservationValueQuantity SpecimenQuantityObservation value range ObservationValueQuantity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueQuantity native bdchm:ObservationValueQuantity LinkML Source Direct name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true Induced name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueQuantity domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueQuantity"},{"location":"ObservationValueQuantity/#class-observationvaluequantity","text":"Single-valued Quantity observation URI: bdchm:ObservationValueQuantity classDiagram class ObservationValueQuantity ObservationValue <|-- ObservationValueQuantity ObservationValueQuantity : name ObservationValueQuantity : type ObservationValueQuantity : value ObservationValueQuantity --> Quantity : value","title":"Class: ObservationValueQuantity"},{"location":"ObservationValueQuantity/#inheritance","text":"ObservationValue ObservationValueQuantity","title":"Inheritance"},{"location":"ObservationValueQuantity/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Quantity A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueQuantity/#usages","text":"used by used in type used DimensionalObservation value range ObservationValueQuantity SpecimenQuantityObservation value range ObservationValueQuantity","title":"Usages"},{"location":"ObservationValueQuantity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueQuantity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueQuantity/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueQuantity native bdchm:ObservationValueQuantity","title":"Mappings"},{"location":"ObservationValueQuantity/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueQuantity/#direct","text":"name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true","title":"Direct"},{"location":"ObservationValueQuantity/#induced","text":"name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueQuantity domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueString/","text":"Class: ObservationValueString Single-valued string observation URI: bdchm:ObservationValueString classDiagram class ObservationValueString ObservationValue <|-- ObservationValueString ObservationValueString : name ObservationValueString : type ObservationValueString : value Inheritance ObservationValue ObservationValueString Slots Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Usages used by used in type used SpecimenQualityObservation value range ObservationValueString Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueString native bdchm:ObservationValueString LinkML Source Direct name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true Induced name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueString"},{"location":"ObservationValueString/#class-observationvaluestring","text":"Single-valued string observation URI: bdchm:ObservationValueString classDiagram class ObservationValueString ObservationValue <|-- ObservationValueString ObservationValueString : name ObservationValueString : type ObservationValueString : value","title":"Class: ObservationValueString"},{"location":"ObservationValueString/#inheritance","text":"ObservationValue ObservationValueString","title":"Inheritance"},{"location":"ObservationValueString/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueString/#usages","text":"used by used in type used SpecimenQualityObservation value range ObservationValueString","title":"Usages"},{"location":"ObservationValueString/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueString/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueString/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueString native bdchm:ObservationValueString","title":"Mappings"},{"location":"ObservationValueString/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueString/#direct","text":"name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true","title":"Direct"},{"location":"ObservationValueString/#induced","text":"name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"Organization/","text":"Class: Organization A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. URI: bdchm:Organization classDiagram class Organization Entity <|-- Organization Organization : alias Organization : id Organization : identity Organization : name Organization : organization_type Inheritance Entity Organization Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String The full legal name by which the organization is known (e direct alias 0..1 String A secondary name for the organization such as a short name or abbreviation (e direct organization_type 0..1 String The type of the organization (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant originating_site range Organization DimensionalObservation performed_by range Organization DimensionalObservationSet performed_by range Organization SpecimenCreationActivity performed_by range Organization SpecimenQualityObservation performed_by range Organization SpecimenQuantityObservation performed_by range Organization SpecimenTransportActivity transport_origin range Organization SpecimenTransportActivity transport_destination range Organization ObservationSet performed_by range Organization Observation performed_by range Organization Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Organization native bdchm:Organization LinkML Source Direct name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string Induced name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Organization domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: alias owner: Organization domain_of: - Organization range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: organization_type owner: Organization domain_of: - Organization range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Organization domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Organization domain_of: - Entity range: uriorcurie required: true","title":"Class: Organization"},{"location":"Organization/#class-organization","text":"A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. URI: bdchm:Organization classDiagram class Organization Entity <|-- Organization Organization : alias Organization : id Organization : identity Organization : name Organization : organization_type","title":"Class: Organization"},{"location":"Organization/#inheritance","text":"Entity Organization","title":"Inheritance"},{"location":"Organization/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String The full legal name by which the organization is known (e direct alias 0..1 String A secondary name for the organization such as a short name or abbreviation (e direct organization_type 0..1 String The type of the organization (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Organization/#usages","text":"used by used in type used Participant originating_site range Organization DimensionalObservation performed_by range Organization DimensionalObservationSet performed_by range Organization SpecimenCreationActivity performed_by range Organization SpecimenQualityObservation performed_by range Organization SpecimenQuantityObservation performed_by range Organization SpecimenTransportActivity transport_origin range Organization SpecimenTransportActivity transport_destination range Organization ObservationSet performed_by range Organization Observation performed_by range Organization","title":"Usages"},{"location":"Organization/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Organization/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Organization/#mappings","text":"Mapping Type Mapped Value self bdchm:Organization native bdchm:Organization","title":"Mappings"},{"location":"Organization/#linkml-source","text":"","title":"LinkML Source"},{"location":"Organization/#direct","text":"name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string","title":"Direct"},{"location":"Organization/#induced","text":"name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Organization domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: alias owner: Organization domain_of: - Organization range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: organization_type owner: Organization domain_of: - Organization range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Organization domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Organization domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Participant/","text":"Class: Participant A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. URI: bdchm:Participant classDiagram class Participant Entity <|-- Participant Participant : age_at_enrollment Participant : associated_person Participant --> Person : associated_person Participant : consents Participant --> Consent : consents Participant : description Participant : id Participant : identity Participant : index_timepoint Participant : member_of_research_study Participant --> ResearchStudy : member_of_research_study Participant : originating_site Participant --> Organization : originating_site Participant : study_arm Inheritance Entity Participant Slots Name Cardinality and Range Description Inheritance associated_person 0..1 Person A reference to the Person that is associated with this record direct identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the research s... direct member_of_research_study 0..1 ResearchStudy A reference to the Study(s) of which this Participant is a member direct age_at_enrollment 0..1 Integer The age in days when the Participant enrolled on the ResearchStudy direct index_timepoint 0..1 String The text term used to describe the reference or anchor date used for date obf... direct originating_site 0..1 Organization The Organization through which a subject was enrolled on a ResearchStudy direct study_arm 0..* String The arm(s) of the study on which the Participant is enrolled direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Demography associated_participant range Participant Visit associated_participant range Participant Condition associated_participant range Participant Procedure associated_participant range Participant DrugExposure associated_participant range Participant DeviceExposure associated_participant range Participant DimensionalObservation associated_participant range Participant DimensionalObservationSet associated_participant range Participant File associated_participant range Participant Specimen source_participant range Participant SpecimenQualityObservation associated_participant range Participant SpecimenQuantityObservation associated_participant range Participant ObservationSet associated_participant range Participant Observation associated_participant range Participant Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Participant native bdchm:Participant LinkML Source Direct name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - associated_person - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Consent Induced name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description owner: Participant domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: member_of_research_study owner: Participant domain_of: - Participant range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_enrollment owner: Participant domain_of: - Participant range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_timepoint owner: Participant domain_of: - Participant range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: originating_site owner: Participant domain_of: - Participant range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: consents owner: Participant domain_of: - Participant - ResearchStudy range: Consent associated_person: name: associated_person description: A reference to the Person that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_person owner: Participant domain_of: - Participant range: Person identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Participant domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Participant domain_of: - Entity range: uriorcurie required: true","title":"Class: Participant"},{"location":"Participant/#class-participant","text":"A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. URI: bdchm:Participant classDiagram class Participant Entity <|-- Participant Participant : age_at_enrollment Participant : associated_person Participant --> Person : associated_person Participant : consents Participant --> Consent : consents Participant : description Participant : id Participant : identity Participant : index_timepoint Participant : member_of_research_study Participant --> ResearchStudy : member_of_research_study Participant : originating_site Participant --> Organization : originating_site Participant : study_arm","title":"Class: Participant"},{"location":"Participant/#inheritance","text":"Entity Participant","title":"Inheritance"},{"location":"Participant/#slots","text":"Name Cardinality and Range Description Inheritance associated_person 0..1 Person A reference to the Person that is associated with this record direct identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the research s... direct member_of_research_study 0..1 ResearchStudy A reference to the Study(s) of which this Participant is a member direct age_at_enrollment 0..1 Integer The age in days when the Participant enrolled on the ResearchStudy direct index_timepoint 0..1 String The text term used to describe the reference or anchor date used for date obf... direct originating_site 0..1 Organization The Organization through which a subject was enrolled on a ResearchStudy direct study_arm 0..* String The arm(s) of the study on which the Participant is enrolled direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Participant/#usages","text":"used by used in type used Demography associated_participant range Participant Visit associated_participant range Participant Condition associated_participant range Participant Procedure associated_participant range Participant DrugExposure associated_participant range Participant DeviceExposure associated_participant range Participant DimensionalObservation associated_participant range Participant DimensionalObservationSet associated_participant range Participant File associated_participant range Participant Specimen source_participant range Participant SpecimenQualityObservation associated_participant range Participant SpecimenQuantityObservation associated_participant range Participant ObservationSet associated_participant range Participant Observation associated_participant range Participant","title":"Usages"},{"location":"Participant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Participant/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Participant/#mappings","text":"Mapping Type Mapped Value self bdchm:Participant native bdchm:Participant","title":"Mappings"},{"location":"Participant/#linkml-source","text":"","title":"LinkML Source"},{"location":"Participant/#direct","text":"name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - associated_person - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Consent","title":"Direct"},{"location":"Participant/#induced","text":"name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description owner: Participant domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: member_of_research_study owner: Participant domain_of: - Participant range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_enrollment owner: Participant domain_of: - Participant range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_timepoint owner: Participant domain_of: - Participant range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: originating_site owner: Participant domain_of: - Participant range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: consents owner: Participant domain_of: - Participant - ResearchStudy range: Consent associated_person: name: associated_person description: A reference to the Person that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_person owner: Participant domain_of: - Participant range: Person identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Participant domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Participant domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Person/","text":"Class: Person Administrative information about an individual or animal receiving care or other health-related services. URI: bdchm:Person classDiagram class Person Entity <|-- Person Person : age_at_death Person : breed Person --> VertebrateBreedEnum : breed Person : cause_of_death Person : id Person : identity Person : species Person --> CellularOrganismSpeciesEnum : species Person : vital_status Person --> VitalStatusEnum : vital_status Person : year_of_birth Person : year_of_death Inheritance Entity Person Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct species 0..1 CellularOrganismSpeciesEnum The scientific binomial name for the species of the Person (e direct breed 0..1 VertebrateBreedEnum A label given to a group of animals homogeneous in appearance and other chara... direct year_of_birth 0..1 Integer Numeric value to represent the calendar year in which an individual was born direct vital_status 0..1 VitalStatusEnum Coded value indicating the state or condition of being living or deceased; al... direct age_at_death 0..1 Integer The age of an individual at the time of death, expressed in days since birth direct year_of_death 0..1 Integer Numeric value to represent the calendar year in which an individual died direct cause_of_death 0..1 String Coded value indicating the circumstance or condition that results in the deat... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant associated_person range Person Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Person native bdchm:Person LinkML Source Direct name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string Induced name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: species owner: Person domain_of: - Person range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_birth owner: Person domain_of: - Person range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_death owner: Person domain_of: - Person range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_death owner: Person domain_of: - Person range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Person domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Person domain_of: - Entity range: uriorcurie required: true","title":"Class: Person"},{"location":"Person/#class-person","text":"Administrative information about an individual or animal receiving care or other health-related services. URI: bdchm:Person classDiagram class Person Entity <|-- Person Person : age_at_death Person : breed Person --> VertebrateBreedEnum : breed Person : cause_of_death Person : id Person : identity Person : species Person --> CellularOrganismSpeciesEnum : species Person : vital_status Person --> VitalStatusEnum : vital_status Person : year_of_birth Person : year_of_death","title":"Class: Person"},{"location":"Person/#inheritance","text":"Entity Person","title":"Inheritance"},{"location":"Person/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct species 0..1 CellularOrganismSpeciesEnum The scientific binomial name for the species of the Person (e direct breed 0..1 VertebrateBreedEnum A label given to a group of animals homogeneous in appearance and other chara... direct year_of_birth 0..1 Integer Numeric value to represent the calendar year in which an individual was born direct vital_status 0..1 VitalStatusEnum Coded value indicating the state or condition of being living or deceased; al... direct age_at_death 0..1 Integer The age of an individual at the time of death, expressed in days since birth direct year_of_death 0..1 Integer Numeric value to represent the calendar year in which an individual died direct cause_of_death 0..1 String Coded value indicating the circumstance or condition that results in the deat... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Person/#usages","text":"used by used in type used Participant associated_person range Person","title":"Usages"},{"location":"Person/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Person/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Person/#mappings","text":"Mapping Type Mapped Value self bdchm:Person native bdchm:Person","title":"Mappings"},{"location":"Person/#linkml-source","text":"","title":"LinkML Source"},{"location":"Person/#direct","text":"name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string","title":"Direct"},{"location":"Person/#induced","text":"name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: species owner: Person domain_of: - Person range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_birth owner: Person domain_of: - Person range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_death owner: Person domain_of: - Person range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_death owner: Person domain_of: - Person range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Person domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Person domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Procedure/","text":"Class: Procedure Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] URI: bdchm:Procedure classDiagram class Procedure Entity <|-- Procedure Procedure : age_at_procedure Procedure : associated_participant Procedure --> Participant : associated_participant Procedure : associated_visit Procedure --> Visit : associated_visit Procedure : id Procedure : identity Procedure : procedure_concept Procedure --> ProcedureConceptEnum : procedure_concept Procedure : procedure_provenance Procedure --> ProvenanceEnum : procedure_provenance Procedure : quantity Procedure --> Quantity : quantity Inheritance Entity Procedure Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct procedure_concept 0..1 ProcedureConceptEnum The coded value that describes the procedure, derived from OMOP codes direct age_at_procedure 0..1 Integer The Participant's age (expressed in days) when the procedure was performed direct procedure_provenance 0..1 ProvenanceEnum A value representing the provenance of the Procedure record direct quantity 0..1 Quantity The quantity of procedures ordered or administered direct associated_participant 0..1 Participant A reference to the Participant on which the Procedure was performed direct associated_visit 0..1 Visit A reference to the Visit during which this Procedure was performed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Procedure native bdchm:Procedure LinkML Source Direct name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit Induced name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_concept owner: Procedure domain_of: - Procedure range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_procedure owner: Procedure domain_of: - Procedure range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_provenance owner: Procedure domain_of: - Procedure range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: quantity owner: Procedure domain_of: - Procedure - DrugExposure - DeviceExposure range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Procedure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Procedure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Procedure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Procedure domain_of: - Entity range: uriorcurie required: true","title":"Class: Procedure"},{"location":"Procedure/#class-procedure","text":"Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] URI: bdchm:Procedure classDiagram class Procedure Entity <|-- Procedure Procedure : age_at_procedure Procedure : associated_participant Procedure --> Participant : associated_participant Procedure : associated_visit Procedure --> Visit : associated_visit Procedure : id Procedure : identity Procedure : procedure_concept Procedure --> ProcedureConceptEnum : procedure_concept Procedure : procedure_provenance Procedure --> ProvenanceEnum : procedure_provenance Procedure : quantity Procedure --> Quantity : quantity","title":"Class: Procedure"},{"location":"Procedure/#inheritance","text":"Entity Procedure","title":"Inheritance"},{"location":"Procedure/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct procedure_concept 0..1 ProcedureConceptEnum The coded value that describes the procedure, derived from OMOP codes direct age_at_procedure 0..1 Integer The Participant's age (expressed in days) when the procedure was performed direct procedure_provenance 0..1 ProvenanceEnum A value representing the provenance of the Procedure record direct quantity 0..1 Quantity The quantity of procedures ordered or administered direct associated_participant 0..1 Participant A reference to the Participant on which the Procedure was performed direct associated_visit 0..1 Visit A reference to the Visit during which this Procedure was performed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Procedure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Procedure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Procedure/#mappings","text":"Mapping Type Mapped Value self bdchm:Procedure native bdchm:Procedure","title":"Mappings"},{"location":"Procedure/#linkml-source","text":"","title":"LinkML Source"},{"location":"Procedure/#direct","text":"name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit","title":"Direct"},{"location":"Procedure/#induced","text":"name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_concept owner: Procedure domain_of: - Procedure range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_procedure owner: Procedure domain_of: - Procedure range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_provenance owner: Procedure domain_of: - Procedure range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: quantity owner: Procedure domain_of: - Procedure - DrugExposure - DeviceExposure range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Procedure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Procedure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Procedure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Procedure domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ProcedureConceptEnum/","text":"Enum: ProcedureConceptEnum Procedure codes from OMOP. URI: ProcedureConceptEnum This is a dynamic enum Slots Name Description procedure_concept The coded value that describes the procedure, derived from OMOP codes Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ProcedureConceptEnum description: Procedure codes from OMOP. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: OMOP","title":"Enum: ProcedureConceptEnum"},{"location":"ProcedureConceptEnum/#enum-procedureconceptenum","text":"Procedure codes from OMOP. URI: ProcedureConceptEnum This is a dynamic enum","title":"Enum: ProcedureConceptEnum"},{"location":"ProcedureConceptEnum/#slots","text":"Name Description procedure_concept The coded value that describes the procedure, derived from OMOP codes","title":"Slots"},{"location":"ProcedureConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ProcedureConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ProcedureConceptEnum/#linkml-source","text":"name: ProcedureConceptEnum description: Procedure codes from OMOP. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: OMOP","title":"LinkML Source"},{"location":"ProvenanceEnum/","text":"Enum: ProvenanceEnum A constrained set of enumerative values containing the OMOP values for provenance. URI: ProvenanceEnum Permissible Values Value Meaning Description EHR_BILLING_DIAGNOSIS OMOP:4822159 EHR_CHIEF_COMPLAINT OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS OMOP:4822160 EHR_EPISODE_ENTRY OMOP:4822135 EHR_PROBLEM_LIST_ENTRY OMOP:4822121 FIRST_POSITION_CONDITION OMOP:4822128 NLP_DERIVED OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION OMOP:4822157 PRIMARY_CONDITION OMOP:4822127 REFERRAL_RECORD OMOP:4822125 SECONDARY_CONDITION OMOP:4822129 TUMOR_REGISTRY OMOP:4822266 Slots Name Description condition_provenance A value representing the provenance of the Condition record procedure_provenance A value representing the provenance of the Procedure record Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: EHR_BILLING_DIAGNOSIS: text: EHR_BILLING_DIAGNOSIS meaning: OMOP:4822159 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT meaning: OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS: text: EHR_ENCOUNTER_DIAGNOSIS meaning: OMOP:4822160 EHR_EPISODE_ENTRY: text: EHR_EPISODE_ENTRY meaning: OMOP:4822135 EHR_PROBLEM_LIST_ENTRY: text: EHR_PROBLEM_LIST_ENTRY meaning: OMOP:4822121 FIRST_POSITION_CONDITION: text: FIRST_POSITION_CONDITION meaning: OMOP:4822128 NLP_DERIVED: text: NLP_DERIVED meaning: OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR: text: OBSERVATION_RECORDED_FROM_EHR meaning: OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION: text: PATIENT_SELF-REPORTED_CONDITION meaning: OMOP:4822157 PRIMARY_CONDITION: text: PRIMARY_CONDITION meaning: OMOP:4822127 REFERRAL_RECORD: text: REFERRAL_RECORD meaning: OMOP:4822125 SECONDARY_CONDITION: text: SECONDARY_CONDITION meaning: OMOP:4822129 TUMOR_REGISTRY: text: TUMOR_REGISTRY meaning: OMOP:4822266","title":"Enum: ProvenanceEnum"},{"location":"ProvenanceEnum/#enum-provenanceenum","text":"A constrained set of enumerative values containing the OMOP values for provenance. URI: ProvenanceEnum","title":"Enum: ProvenanceEnum"},{"location":"ProvenanceEnum/#permissible-values","text":"Value Meaning Description EHR_BILLING_DIAGNOSIS OMOP:4822159 EHR_CHIEF_COMPLAINT OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS OMOP:4822160 EHR_EPISODE_ENTRY OMOP:4822135 EHR_PROBLEM_LIST_ENTRY OMOP:4822121 FIRST_POSITION_CONDITION OMOP:4822128 NLP_DERIVED OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION OMOP:4822157 PRIMARY_CONDITION OMOP:4822127 REFERRAL_RECORD OMOP:4822125 SECONDARY_CONDITION OMOP:4822129 TUMOR_REGISTRY OMOP:4822266","title":"Permissible Values"},{"location":"ProvenanceEnum/#slots","text":"Name Description condition_provenance A value representing the provenance of the Condition record procedure_provenance A value representing the provenance of the Procedure record","title":"Slots"},{"location":"ProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ProvenanceEnum/#linkml-source","text":"name: ProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: EHR_BILLING_DIAGNOSIS: text: EHR_BILLING_DIAGNOSIS meaning: OMOP:4822159 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT meaning: OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS: text: EHR_ENCOUNTER_DIAGNOSIS meaning: OMOP:4822160 EHR_EPISODE_ENTRY: text: EHR_EPISODE_ENTRY meaning: OMOP:4822135 EHR_PROBLEM_LIST_ENTRY: text: EHR_PROBLEM_LIST_ENTRY meaning: OMOP:4822121 FIRST_POSITION_CONDITION: text: FIRST_POSITION_CONDITION meaning: OMOP:4822128 NLP_DERIVED: text: NLP_DERIVED meaning: OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR: text: OBSERVATION_RECORDED_FROM_EHR meaning: OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION: text: PATIENT_SELF-REPORTED_CONDITION meaning: OMOP:4822157 PRIMARY_CONDITION: text: PRIMARY_CONDITION meaning: OMOP:4822127 REFERRAL_RECORD: text: REFERRAL_RECORD meaning: OMOP:4822125 SECONDARY_CONDITION: text: SECONDARY_CONDITION meaning: OMOP:4822129 TUMOR_REGISTRY: text: TUMOR_REGISTRY meaning: OMOP:4822266","title":"LinkML Source"},{"location":"Quantity/","text":"Class: Quantity A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. URI: bdchm:Quantity classDiagram class Quantity Entity <|-- Quantity Quantity : id Quantity : unit Quantity --> UnitOfMeasurementEnum : unit Quantity : value_concept Quantity : value_decimal Inheritance Entity Quantity Slots Name Cardinality and Range Description Inheritance value_decimal 0..1 Decimal An amount, in the given units (if specified) direct value_concept 0..1 String A coded value representing a quantity (e direct unit 0..1 UnitOfMeasurementEnum A coded or free text (in the direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Procedure quantity range Quantity SpecimenCreationActivity quantity_collected range Quantity SpecimenProcessingActivity duration range Quantity SpecimenStorageActivity duration range Quantity Substance substance_quantity range Quantity ObservationValueQuantity value range Quantity Comments QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Quantity native bdchm:Quantity LinkML Source Direct name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: UnitOfMeasurementEnum required: false Induced name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Quantity domain_of: - Entity range: uriorcurie required: true","title":"Class: Quantity"},{"location":"Quantity/#class-quantity","text":"A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. URI: bdchm:Quantity classDiagram class Quantity Entity <|-- Quantity Quantity : id Quantity : unit Quantity --> UnitOfMeasurementEnum : unit Quantity : value_concept Quantity : value_decimal","title":"Class: Quantity"},{"location":"Quantity/#inheritance","text":"Entity Quantity","title":"Inheritance"},{"location":"Quantity/#slots","text":"Name Cardinality and Range Description Inheritance value_decimal 0..1 Decimal An amount, in the given units (if specified) direct value_concept 0..1 String A coded value representing a quantity (e direct unit 0..1 UnitOfMeasurementEnum A coded or free text (in the direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Quantity/#usages","text":"used by used in type used Procedure quantity range Quantity SpecimenCreationActivity quantity_collected range Quantity SpecimenProcessingActivity duration range Quantity SpecimenStorageActivity duration range Quantity Substance substance_quantity range Quantity ObservationValueQuantity value range Quantity","title":"Usages"},{"location":"Quantity/#comments","text":"QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate.","title":"Comments"},{"location":"Quantity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Quantity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Quantity/#mappings","text":"Mapping Type Mapped Value self bdchm:Quantity native bdchm:Quantity","title":"Mappings"},{"location":"Quantity/#linkml-source","text":"","title":"LinkML Source"},{"location":"Quantity/#direct","text":"name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: UnitOfMeasurementEnum required: false","title":"Direct"},{"location":"Quantity/#induced","text":"name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Quantity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Questionnaire/","text":"Class: Questionnaire A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) URI: bdchm:Questionnaire classDiagram class Questionnaire Entity <|-- Questionnaire Questionnaire : copyright Questionnaire : copyright_label Questionnaire : description Questionnaire : id Questionnaire : identity Questionnaire : items Questionnaire --> QuestionnaireItem : items Questionnaire : language Questionnaire : name Questionnaire : publisher Questionnaire : title Questionnaire : url Questionnaire : version Inheritance Entity Questionnaire Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String Name for this Questionnaire (computer friendly) direct title 0..1 String Name for this Questionnaire (human friendly) direct description 0..1 String Natural language description of the Questionnaire direct url 0..1 Uriorcurie Canonical identifier for this Questionnaire, represented as an absolute URI (... direct version 0..1 String The identifier that is used to identify this version of the questionnaire whe... direct publisher 0..1 String Name of the publisher/steward (organization or individual) of this Questionna... direct copyright 0..1 String Textual description of any use and/or publishing restrictions direct copyright_label 0..1 String Copyright holder and year(s) direct language 0..* String The language(s) in which questions are presented direct items 1..* QuestionnaireItem A collection of QuestionnaireItem objects which encapsulate the question bein... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Questionnaire native bdchm:Questionnaire LinkML Source Direct name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: QuestionnaireItem required: true Induced name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Questionnaire domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: Questionnaire domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: url owner: Questionnaire domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: publisher owner: Questionnaire domain_of: - Questionnaire range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: language owner: Questionnaire domain_of: - Questionnaire range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: items owner: Questionnaire domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireItem required: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Questionnaire domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Questionnaire domain_of: - Entity range: uriorcurie required: true","title":"Class: Questionnaire"},{"location":"Questionnaire/#class-questionnaire","text":"A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) URI: bdchm:Questionnaire classDiagram class Questionnaire Entity <|-- Questionnaire Questionnaire : copyright Questionnaire : copyright_label Questionnaire : description Questionnaire : id Questionnaire : identity Questionnaire : items Questionnaire --> QuestionnaireItem : items Questionnaire : language Questionnaire : name Questionnaire : publisher Questionnaire : title Questionnaire : url Questionnaire : version","title":"Class: Questionnaire"},{"location":"Questionnaire/#inheritance","text":"Entity Questionnaire","title":"Inheritance"},{"location":"Questionnaire/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String Name for this Questionnaire (computer friendly) direct title 0..1 String Name for this Questionnaire (human friendly) direct description 0..1 String Natural language description of the Questionnaire direct url 0..1 Uriorcurie Canonical identifier for this Questionnaire, represented as an absolute URI (... direct version 0..1 String The identifier that is used to identify this version of the questionnaire whe... direct publisher 0..1 String Name of the publisher/steward (organization or individual) of this Questionna... direct copyright 0..1 String Textual description of any use and/or publishing restrictions direct copyright_label 0..1 String Copyright holder and year(s) direct language 0..* String The language(s) in which questions are presented direct items 1..* QuestionnaireItem A collection of QuestionnaireItem objects which encapsulate the question bein... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Questionnaire/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Questionnaire/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Questionnaire/#mappings","text":"Mapping Type Mapped Value self bdchm:Questionnaire native bdchm:Questionnaire","title":"Mappings"},{"location":"Questionnaire/#linkml-source","text":"","title":"LinkML Source"},{"location":"Questionnaire/#direct","text":"name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: QuestionnaireItem required: true","title":"Direct"},{"location":"Questionnaire/#induced","text":"name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Questionnaire domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: Questionnaire domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: url owner: Questionnaire domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: publisher owner: Questionnaire domain_of: - Questionnaire range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: language owner: Questionnaire domain_of: - Questionnaire range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: items owner: Questionnaire domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireItem required: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Questionnaire domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Questionnaire domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"QuestionnaireItem/","text":"Class: QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire URI: bdchm:QuestionnaireItem classDiagram class QuestionnaireItem Entity <|-- QuestionnaireItem QuestionnaireItem : code QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : part_of QuestionnaireItem --> QuestionnaireItem : part_of QuestionnaireItem : text Inheritance Entity QuestionnaireItem Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct text 0..1 String Name for group or question text direct code 0..1 String Corresponding concept for this item in a terminology direct part_of 0..1 QuestionnaireItem A reference to a parent QuestionnaireItem direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Questionnaire items range QuestionnaireItem QuestionnaireItem part_of range QuestionnaireItem QuestionnaireResponseItem has_questionnaire_item range QuestionnaireItem Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireItem native bdchm:QuestionnaireItem LinkML Source Direct name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm range: QuestionnaireItem Induced name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: text owner: QuestionnaireItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: part_of owner: QuestionnaireItem domain_of: - ResearchStudy - QuestionnaireItem range: QuestionnaireItem identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: QuestionnaireItem domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireItem domain_of: - Entity range: uriorcurie required: true","title":"Class: QuestionnaireItem"},{"location":"QuestionnaireItem/#class-questionnaireitem","text":"QuestionnaireItem defines a question or section within the Questionnaire URI: bdchm:QuestionnaireItem classDiagram class QuestionnaireItem Entity <|-- QuestionnaireItem QuestionnaireItem : code QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : part_of QuestionnaireItem --> QuestionnaireItem : part_of QuestionnaireItem : text","title":"Class: QuestionnaireItem"},{"location":"QuestionnaireItem/#inheritance","text":"Entity QuestionnaireItem","title":"Inheritance"},{"location":"QuestionnaireItem/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct text 0..1 String Name for group or question text direct code 0..1 String Corresponding concept for this item in a terminology direct part_of 0..1 QuestionnaireItem A reference to a parent QuestionnaireItem direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"QuestionnaireItem/#usages","text":"used by used in type used Questionnaire items range QuestionnaireItem QuestionnaireItem part_of range QuestionnaireItem QuestionnaireResponseItem has_questionnaire_item range QuestionnaireItem","title":"Usages"},{"location":"QuestionnaireItem/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireItem/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireItem/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireItem native bdchm:QuestionnaireItem","title":"Mappings"},{"location":"QuestionnaireItem/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireItem/#direct","text":"name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm range: QuestionnaireItem","title":"Direct"},{"location":"QuestionnaireItem/#induced","text":"name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: text owner: QuestionnaireItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: part_of owner: QuestionnaireItem domain_of: - ResearchStudy - QuestionnaireItem range: QuestionnaireItem identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: QuestionnaireItem domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireItem domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"QuestionnaireResponse/","text":"Class: QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponse classDiagram class QuestionnaireResponse Entity <|-- QuestionnaireResponse QuestionnaireResponse : age_at_response QuestionnaireResponse : associated_visit QuestionnaireResponse --> Visit : associated_visit QuestionnaireResponse : id QuestionnaireResponse : items QuestionnaireResponse --> QuestionnaireResponseItem : items Inheritance Entity QuestionnaireResponse Slots Name Cardinality and Range Description Inheritance age_at_response 0..1 Integer The age (in days) of the Participant when the QuestionnaireResponse was captu... direct items 1..* QuestionnaireResponseItem A collection of QuestionnaireResponseItem objects which encapsulate the quest... direct associated_visit 0..1 Visit A reference to the Visit during which this QuestionnaireResponse was captured direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponse native bdchm:QuestionnaireResponse LinkML Source Direct name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Visit Induced name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_response owner: QuestionnaireResponse domain_of: - QuestionnaireResponse range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: items owner: QuestionnaireResponse domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_visit owner: QuestionnaireResponse domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireResponse domain_of: - Entity range: uriorcurie required: true","title":"Class: QuestionnaireResponse"},{"location":"QuestionnaireResponse/#class-questionnaireresponse","text":"QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponse classDiagram class QuestionnaireResponse Entity <|-- QuestionnaireResponse QuestionnaireResponse : age_at_response QuestionnaireResponse : associated_visit QuestionnaireResponse --> Visit : associated_visit QuestionnaireResponse : id QuestionnaireResponse : items QuestionnaireResponse --> QuestionnaireResponseItem : items","title":"Class: QuestionnaireResponse"},{"location":"QuestionnaireResponse/#inheritance","text":"Entity QuestionnaireResponse","title":"Inheritance"},{"location":"QuestionnaireResponse/#slots","text":"Name Cardinality and Range Description Inheritance age_at_response 0..1 Integer The age (in days) of the Participant when the QuestionnaireResponse was captu... direct items 1..* QuestionnaireResponseItem A collection of QuestionnaireResponseItem objects which encapsulate the quest... direct associated_visit 0..1 Visit A reference to the Visit during which this QuestionnaireResponse was captured direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"QuestionnaireResponse/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponse/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponse/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponse native bdchm:QuestionnaireResponse","title":"Mappings"},{"location":"QuestionnaireResponse/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponse/#direct","text":"name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Visit","title":"Direct"},{"location":"QuestionnaireResponse/#induced","text":"name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_response owner: QuestionnaireResponse domain_of: - QuestionnaireResponse range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: items owner: QuestionnaireResponse domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_visit owner: QuestionnaireResponse domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireResponse domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"QuestionnaireResponseItem/","text":"Class: QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponseItem classDiagram class QuestionnaireResponseItem QuestionnaireResponseItem : has_questionnaire_item QuestionnaireResponseItem --> QuestionnaireItem : has_questionnaire_item QuestionnaireResponseItem : response_value QuestionnaireResponseItem --> QuestionnaireResponseValue : response_value QuestionnaireResponseItem : text Slots Name Cardinality and Range Description Inheritance has_questionnaire_item 0..1 QuestionnaireItem A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... direct text 0..1 String Name for group or question text direct response_value 1..1 QuestionnaireResponseValue direct Usages used by used in type used QuestionnaireResponse items range QuestionnaireResponseItem Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseItem native bdchm:QuestionnaireResponseItem LinkML Source Direct name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireResponseValue required: true Induced name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm alias: text owner: QuestionnaireResponseItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: response_value owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"Class: QuestionnaireResponseItem"},{"location":"QuestionnaireResponseItem/#class-questionnaireresponseitem","text":"QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponseItem classDiagram class QuestionnaireResponseItem QuestionnaireResponseItem : has_questionnaire_item QuestionnaireResponseItem --> QuestionnaireItem : has_questionnaire_item QuestionnaireResponseItem : response_value QuestionnaireResponseItem --> QuestionnaireResponseValue : response_value QuestionnaireResponseItem : text","title":"Class: QuestionnaireResponseItem"},{"location":"QuestionnaireResponseItem/#slots","text":"Name Cardinality and Range Description Inheritance has_questionnaire_item 0..1 QuestionnaireItem A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... direct text 0..1 String Name for group or question text direct response_value 1..1 QuestionnaireResponseValue direct","title":"Slots"},{"location":"QuestionnaireResponseItem/#usages","text":"used by used in type used QuestionnaireResponse items range QuestionnaireResponseItem","title":"Usages"},{"location":"QuestionnaireResponseItem/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseItem/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseItem/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseItem native bdchm:QuestionnaireResponseItem","title":"Mappings"},{"location":"QuestionnaireResponseItem/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseItem/#direct","text":"name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireResponseValue required: true","title":"Direct"},{"location":"QuestionnaireResponseItem/#induced","text":"name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm alias: text owner: QuestionnaireResponseItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: response_value owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"Induced"},{"location":"QuestionnaireResponseValue/","text":"Class: QuestionnaireResponseValue Single-valued answer to the question. (FHIR) NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:QuestionnaireResponseValue classDiagram class QuestionnaireResponseValue QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValue : name QuestionnaireResponseValue : type QuestionnaireResponseValue : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueDecimal QuestionnaireResponseValueBoolean QuestionnaireResponseValueInteger QuestionnaireResponseValueTimePoint QuestionnaireResponseValueString Slots Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct Usages used by used in type used QuestionnaireResponseItem response_value range QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValue native bdchm:QuestionnaireResponseValue LinkML Source Direct name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string Induced name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Class: QuestionnaireResponseValue"},{"location":"QuestionnaireResponseValue/#class-questionnaireresponsevalue","text":"Single-valued answer to the question. (FHIR) NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:QuestionnaireResponseValue classDiagram class QuestionnaireResponseValue QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValue : name QuestionnaireResponseValue : type QuestionnaireResponseValue : value","title":"Class: QuestionnaireResponseValue"},{"location":"QuestionnaireResponseValue/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueDecimal QuestionnaireResponseValueBoolean QuestionnaireResponseValueInteger QuestionnaireResponseValueTimePoint QuestionnaireResponseValueString","title":"Inheritance"},{"location":"QuestionnaireResponseValue/#slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct","title":"Slots"},{"location":"QuestionnaireResponseValue/#usages","text":"used by used in type used QuestionnaireResponseItem response_value range QuestionnaireResponseValue","title":"Usages"},{"location":"QuestionnaireResponseValue/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValue/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValue/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValue native bdchm:QuestionnaireResponseValue","title":"Mappings"},{"location":"QuestionnaireResponseValue/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValue/#direct","text":"name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string","title":"Direct"},{"location":"QuestionnaireResponseValue/#induced","text":"name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueBoolean/","text":"Class: QuestionnaireResponseValueBoolean Single-valued boolean answer to the question URI: bdchm:QuestionnaireResponseValueBoolean classDiagram class QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValueBoolean : name QuestionnaireResponseValueBoolean : type QuestionnaireResponseValueBoolean : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueBoolean Slots Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueBoolean native bdchm:QuestionnaireResponseValueBoolean LinkML Source Direct name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true Induced name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueBoolean"},{"location":"QuestionnaireResponseValueBoolean/#class-questionnaireresponsevalueboolean","text":"Single-valued boolean answer to the question URI: bdchm:QuestionnaireResponseValueBoolean classDiagram class QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValueBoolean : name QuestionnaireResponseValueBoolean : type QuestionnaireResponseValueBoolean : value","title":"Class: QuestionnaireResponseValueBoolean"},{"location":"QuestionnaireResponseValueBoolean/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueBoolean","title":"Inheritance"},{"location":"QuestionnaireResponseValueBoolean/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueBoolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueBoolean/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueBoolean/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueBoolean native bdchm:QuestionnaireResponseValueBoolean","title":"Mappings"},{"location":"QuestionnaireResponseValueBoolean/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueBoolean/#direct","text":"name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true","title":"Direct"},{"location":"QuestionnaireResponseValueBoolean/#induced","text":"name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueDecimal/","text":"Class: QuestionnaireResponseValueDecimal Single-valued decimal answer to the question URI: bdchm:QuestionnaireResponseValueDecimal classDiagram class QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValueDecimal : name QuestionnaireResponseValueDecimal : type QuestionnaireResponseValueDecimal : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueDecimal Slots Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueDecimal native bdchm:QuestionnaireResponseValueDecimal LinkML Source Direct name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true Induced name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueDecimal"},{"location":"QuestionnaireResponseValueDecimal/#class-questionnaireresponsevaluedecimal","text":"Single-valued decimal answer to the question URI: bdchm:QuestionnaireResponseValueDecimal classDiagram class QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValueDecimal : name QuestionnaireResponseValueDecimal : type QuestionnaireResponseValueDecimal : value","title":"Class: QuestionnaireResponseValueDecimal"},{"location":"QuestionnaireResponseValueDecimal/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueDecimal","title":"Inheritance"},{"location":"QuestionnaireResponseValueDecimal/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueDecimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueDecimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueDecimal/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueDecimal native bdchm:QuestionnaireResponseValueDecimal","title":"Mappings"},{"location":"QuestionnaireResponseValueDecimal/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueDecimal/#direct","text":"name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true","title":"Direct"},{"location":"QuestionnaireResponseValueDecimal/#induced","text":"name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueInteger/","text":"Class: QuestionnaireResponseValueInteger Single-valued integer answer to the question URI: bdchm:QuestionnaireResponseValueInteger classDiagram class QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValueInteger : name QuestionnaireResponseValueInteger : type QuestionnaireResponseValueInteger : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueInteger Slots Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueInteger native bdchm:QuestionnaireResponseValueInteger LinkML Source Direct name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true Induced name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueInteger"},{"location":"QuestionnaireResponseValueInteger/#class-questionnaireresponsevalueinteger","text":"Single-valued integer answer to the question URI: bdchm:QuestionnaireResponseValueInteger classDiagram class QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValueInteger : name QuestionnaireResponseValueInteger : type QuestionnaireResponseValueInteger : value","title":"Class: QuestionnaireResponseValueInteger"},{"location":"QuestionnaireResponseValueInteger/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueInteger","title":"Inheritance"},{"location":"QuestionnaireResponseValueInteger/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueInteger/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueInteger/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueInteger/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueInteger native bdchm:QuestionnaireResponseValueInteger","title":"Mappings"},{"location":"QuestionnaireResponseValueInteger/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueInteger/#direct","text":"name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true","title":"Direct"},{"location":"QuestionnaireResponseValueInteger/#induced","text":"name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueString/","text":"Class: QuestionnaireResponseValueString Single-valued string answer to the question URI: bdchm:QuestionnaireResponseValueString classDiagram class QuestionnaireResponseValueString QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValueString : name QuestionnaireResponseValueString : type QuestionnaireResponseValueString : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueString Slots Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueString native bdchm:QuestionnaireResponseValueString LinkML Source Direct name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true Induced name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueString"},{"location":"QuestionnaireResponseValueString/#class-questionnaireresponsevaluestring","text":"Single-valued string answer to the question URI: bdchm:QuestionnaireResponseValueString classDiagram class QuestionnaireResponseValueString QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValueString : name QuestionnaireResponseValueString : type QuestionnaireResponseValueString : value","title":"Class: QuestionnaireResponseValueString"},{"location":"QuestionnaireResponseValueString/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueString","title":"Inheritance"},{"location":"QuestionnaireResponseValueString/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueString/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueString/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueString/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueString native bdchm:QuestionnaireResponseValueString","title":"Mappings"},{"location":"QuestionnaireResponseValueString/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueString/#direct","text":"name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true","title":"Direct"},{"location":"QuestionnaireResponseValueString/#induced","text":"name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueTimePoint/","text":"Class: QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question URI: bdchm:QuestionnaireResponseValueTimePoint classDiagram class QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValueTimePoint : name QuestionnaireResponseValueTimePoint : type QuestionnaireResponseValueTimePoint : value QuestionnaireResponseValueTimePoint --> TimePoint : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueTimePoint Slots Name Cardinality and Range Description Inheritance value 1..1 TimePoint A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueTimePoint native bdchm:QuestionnaireResponseValueTimePoint LinkML Source Direct name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true Induced name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueTimePoint domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueTimePoint"},{"location":"QuestionnaireResponseValueTimePoint/#class-questionnaireresponsevaluetimepoint","text":"Single-valued TimePoint answer to the question URI: bdchm:QuestionnaireResponseValueTimePoint classDiagram class QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValueTimePoint : name QuestionnaireResponseValueTimePoint : type QuestionnaireResponseValueTimePoint : value QuestionnaireResponseValueTimePoint --> TimePoint : value","title":"Class: QuestionnaireResponseValueTimePoint"},{"location":"QuestionnaireResponseValueTimePoint/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueTimePoint","title":"Inheritance"},{"location":"QuestionnaireResponseValueTimePoint/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 TimePoint A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueTimePoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueTimePoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueTimePoint/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueTimePoint native bdchm:QuestionnaireResponseValueTimePoint","title":"Mappings"},{"location":"QuestionnaireResponseValueTimePoint/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueTimePoint/#direct","text":"name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true","title":"Direct"},{"location":"QuestionnaireResponseValueTimePoint/#induced","text":"name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueTimePoint domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"RaceEnum/","text":"Enum: RaceEnum A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. URI: RaceEnum Permissible Values Value Meaning Description AMERICAN_INDIAN_OR_ALASKA_NATIVE OMOP:8657 A person having origins in any of the original peoples of North and South Ame... ASIAN OMOP:8515 A person having origins in any of the original peoples of the Far East, South... BLACK_OR_AFRICAN_AMERICAN OMOP:8516 A person having origins in any of the Black racial groups of Africa NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER OMOP:8557 Denotes a person having origins in any of the original peoples of Hawaii, Gua... UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused WHITE OMOP:8527 Denotes person with European, Middle Eastern, or North African ancestral orig... Slots Name Description race An arbitrary classification of a taxonomic group that is a division of a spec... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: RaceEnum description: A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: text: AMERICAN_INDIAN_OR_ALASKA_NATIVE description: A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB) meaning: OMOP:8657 ASIAN: text: ASIAN description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) meaning: OMOP:8515 BLACK_OR_AFRICAN_AMERICAN: text: BLACK_OR_AFRICAN_AMERICAN description: A person having origins in any of the Black racial groups of Africa. Terms such as \"Haitian\" or \"Negro\" can be used in addition to \"Black or African American\". (OMB) meaning: OMOP:8516 NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: text: NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER description: Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuukese (Trukese), Fijian, Kosraean, Melanesian, Micronesian, Northern Mariana Islander, Palauan, Papua New Guinean, Pohnpeian, Polynesian, Solomon Islander, Tahitian, Tokelauan, Tongan, Yapese, or Pacific Islander, not specified. meaning: OMOP:8557 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552 WHITE: text: WHITE description: Denotes person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. meaning: OMOP:8527","title":"Enum: RaceEnum"},{"location":"RaceEnum/#enum-raceenum","text":"A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. URI: RaceEnum","title":"Enum: RaceEnum"},{"location":"RaceEnum/#permissible-values","text":"Value Meaning Description AMERICAN_INDIAN_OR_ALASKA_NATIVE OMOP:8657 A person having origins in any of the original peoples of North and South Ame... ASIAN OMOP:8515 A person having origins in any of the original peoples of the Far East, South... BLACK_OR_AFRICAN_AMERICAN OMOP:8516 A person having origins in any of the Black racial groups of Africa NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER OMOP:8557 Denotes a person having origins in any of the original peoples of Hawaii, Gua... UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused WHITE OMOP:8527 Denotes person with European, Middle Eastern, or North African ancestral orig...","title":"Permissible Values"},{"location":"RaceEnum/#slots","text":"Name Description race An arbitrary classification of a taxonomic group that is a division of a spec...","title":"Slots"},{"location":"RaceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"RaceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"RaceEnum/#linkml-source","text":"name: RaceEnum description: A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: text: AMERICAN_INDIAN_OR_ALASKA_NATIVE description: A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB) meaning: OMOP:8657 ASIAN: text: ASIAN description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) meaning: OMOP:8515 BLACK_OR_AFRICAN_AMERICAN: text: BLACK_OR_AFRICAN_AMERICAN description: A person having origins in any of the Black racial groups of Africa. Terms such as \"Haitian\" or \"Negro\" can be used in addition to \"Black or African American\". (OMB) meaning: OMOP:8516 NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: text: NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER description: Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuukese (Trukese), Fijian, Kosraean, Melanesian, Micronesian, Northern Mariana Islander, Palauan, Papua New Guinean, Pohnpeian, Polynesian, Solomon Islander, Tahitian, Tokelauan, Tongan, Yapese, or Pacific Islander, not specified. meaning: OMOP:8557 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552 WHITE: text: WHITE description: Denotes person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. meaning: OMOP:8527","title":"LinkML Source"},{"location":"ResearchStudy/","text":"Class: ResearchStudy A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. URI: bdchm:ResearchStudy classDiagram class ResearchStudy Entity <|-- ResearchStudy ResearchStudy : associated_timepoint ResearchStudy --> TimePoint : associated_timepoint ResearchStudy : consents ResearchStudy --> Consent : consents ResearchStudy : date_ended ResearchStudy --> TimePoint : date_ended ResearchStudy : date_started ResearchStudy --> TimePoint : date_started ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : part_of ResearchStudy --> ResearchStudy : part_of ResearchStudy : principal_investigator ResearchStudy : research_project_type ResearchStudy : sponsor ResearchStudy : url Inheritance Entity ResearchStudy Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String An unabridged name of a research program, project, or study direct name_shortened 0..1 String An abbreviated name of a research program, project, or study direct description 0..1 String An unabridged description of a research program, project, or study direct description_shortened 0..1 String An abbreviated description of a research program, project, or study direct sponsor 0..1 String An entity that is responsible for the initiation, management, and/or financin... direct date_started 0..1 TimePoint The date when the research project began direct date_ended 0..1 TimePoint The date when the research project ended direct url 0..1 Uriorcurie A URL address for a resource that provides information about a research progr... direct part_of 0..1 ResearchStudy A reference to a parent ResearchStudy (e direct research_project_type 0..1 String The 'type' of ResearchStudy represented (e direct associated_timepoint 0..* TimePoint A collection of timepoint observations that are relevant to research projects... direct principal_investigator 0..* String The investigator or investigators leading a project direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant member_of_research_study range ResearchStudy ResearchStudy part_of range ResearchStudy ResearchStudyCollection entries range ResearchStudy Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ResearchStudy native bdchm:ResearchStudy LinkML Source Direct name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Consent Induced name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name owner: ResearchStudy domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: ResearchStudy domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_started owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_ended owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: url owner: ResearchStudy domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: part_of owner: ResearchStudy domain_of: - ResearchStudy - QuestionnaireItem range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: principal_investigator owner: ResearchStudy domain_of: - ResearchStudy range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: consents owner: ResearchStudy domain_of: - Participant - ResearchStudy range: Consent identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: ResearchStudy domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ResearchStudy domain_of: - Entity range: uriorcurie required: true","title":"Class: ResearchStudy"},{"location":"ResearchStudy/#class-researchstudy","text":"A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. URI: bdchm:ResearchStudy classDiagram class ResearchStudy Entity <|-- ResearchStudy ResearchStudy : associated_timepoint ResearchStudy --> TimePoint : associated_timepoint ResearchStudy : consents ResearchStudy --> Consent : consents ResearchStudy : date_ended ResearchStudy --> TimePoint : date_ended ResearchStudy : date_started ResearchStudy --> TimePoint : date_started ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : part_of ResearchStudy --> ResearchStudy : part_of ResearchStudy : principal_investigator ResearchStudy : research_project_type ResearchStudy : sponsor ResearchStudy : url","title":"Class: ResearchStudy"},{"location":"ResearchStudy/#inheritance","text":"Entity ResearchStudy","title":"Inheritance"},{"location":"ResearchStudy/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String An unabridged name of a research program, project, or study direct name_shortened 0..1 String An abbreviated name of a research program, project, or study direct description 0..1 String An unabridged description of a research program, project, or study direct description_shortened 0..1 String An abbreviated description of a research program, project, or study direct sponsor 0..1 String An entity that is responsible for the initiation, management, and/or financin... direct date_started 0..1 TimePoint The date when the research project began direct date_ended 0..1 TimePoint The date when the research project ended direct url 0..1 Uriorcurie A URL address for a resource that provides information about a research progr... direct part_of 0..1 ResearchStudy A reference to a parent ResearchStudy (e direct research_project_type 0..1 String The 'type' of ResearchStudy represented (e direct associated_timepoint 0..* TimePoint A collection of timepoint observations that are relevant to research projects... direct principal_investigator 0..* String The investigator or investigators leading a project direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"ResearchStudy/#usages","text":"used by used in type used Participant member_of_research_study range ResearchStudy ResearchStudy part_of range ResearchStudy ResearchStudyCollection entries range ResearchStudy","title":"Usages"},{"location":"ResearchStudy/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ResearchStudy/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ResearchStudy/#mappings","text":"Mapping Type Mapped Value self bdchm:ResearchStudy native bdchm:ResearchStudy","title":"Mappings"},{"location":"ResearchStudy/#linkml-source","text":"","title":"LinkML Source"},{"location":"ResearchStudy/#direct","text":"name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Consent","title":"Direct"},{"location":"ResearchStudy/#induced","text":"name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name owner: ResearchStudy domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: ResearchStudy domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_started owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_ended owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: url owner: ResearchStudy domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: part_of owner: ResearchStudy domain_of: - ResearchStudy - QuestionnaireItem range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: principal_investigator owner: ResearchStudy domain_of: - ResearchStudy range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: consents owner: ResearchStudy domain_of: - Participant - ResearchStudy range: Consent identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: ResearchStudy domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ResearchStudy domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ResearchStudyCollection/","text":"Class: ResearchStudyCollection A holder for ResearchStudy objects URI: bdchm:ResearchStudyCollection classDiagram class ResearchStudyCollection ResearchStudyCollection : entries ResearchStudyCollection --> ResearchStudy : entries Slots Name Cardinality and Range Description Inheritance entries 0..* ResearchStudy direct Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ResearchStudyCollection native bdchm:ResearchStudyCollection LinkML Source Direct name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: ResearchStudy inlined: true tree_root: true Induced name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true tree_root: true","title":"Class: ResearchStudyCollection"},{"location":"ResearchStudyCollection/#class-researchstudycollection","text":"A holder for ResearchStudy objects URI: bdchm:ResearchStudyCollection classDiagram class ResearchStudyCollection ResearchStudyCollection : entries ResearchStudyCollection --> ResearchStudy : entries","title":"Class: ResearchStudyCollection"},{"location":"ResearchStudyCollection/#slots","text":"Name Cardinality and Range Description Inheritance entries 0..* ResearchStudy direct","title":"Slots"},{"location":"ResearchStudyCollection/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ResearchStudyCollection/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ResearchStudyCollection/#mappings","text":"Mapping Type Mapped Value self bdchm:ResearchStudyCollection native bdchm:ResearchStudyCollection","title":"Mappings"},{"location":"ResearchStudyCollection/#linkml-source","text":"","title":"LinkML Source"},{"location":"ResearchStudyCollection/#direct","text":"name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: ResearchStudy inlined: true tree_root: true","title":"Direct"},{"location":"ResearchStudyCollection/#induced","text":"name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true tree_root: true","title":"Induced"},{"location":"SectionLocationEnum/","text":"Enum: SectionLocationEnum The location in a parent specimen from which a section/portion was excised. URI: SectionLocationEnum Permissible Values Value Meaning Description BOTTOM None The part of a specimen designated as its 'bottom' based on specified orientat... TOP None The part of a specimen designated as its 'top' based on specified orientation... UNKNOWN None An unknown location on a specimen Slots Name Description section_location The location in a parent specimen from which a section/portion was excised (e Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SectionLocationEnum description: The location in a parent specimen from which a section/portion was excised. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: BOTTOM: text: BOTTOM description: The part of a specimen designated as its 'bottom' based on specified orientation criteria. TOP: text: TOP description: The part of a specimen designated as its 'top' based on specified orientation criteria. UNKNOWN: text: UNKNOWN description: An unknown location on a specimen.","title":"Enum: SectionLocationEnum"},{"location":"SectionLocationEnum/#enum-sectionlocationenum","text":"The location in a parent specimen from which a section/portion was excised. URI: SectionLocationEnum","title":"Enum: SectionLocationEnum"},{"location":"SectionLocationEnum/#permissible-values","text":"Value Meaning Description BOTTOM None The part of a specimen designated as its 'bottom' based on specified orientat... TOP None The part of a specimen designated as its 'top' based on specified orientation... UNKNOWN None An unknown location on a specimen","title":"Permissible Values"},{"location":"SectionLocationEnum/#slots","text":"Name Description section_location The location in a parent specimen from which a section/portion was excised (e","title":"Slots"},{"location":"SectionLocationEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SectionLocationEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SectionLocationEnum/#linkml-source","text":"name: SectionLocationEnum description: The location in a parent specimen from which a section/portion was excised. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: BOTTOM: text: BOTTOM description: The part of a specimen designated as its 'bottom' based on specified orientation criteria. TOP: text: TOP description: The part of a specimen designated as its 'top' based on specified orientation criteria. UNKNOWN: text: UNKNOWN description: An unknown location on a specimen.","title":"LinkML Source"},{"location":"SexEnum/","text":"Enum: SexEnum A constrained set of enumerative values containing the OMOP values for sex. URI: SexEnum Permissible Values Value Meaning Description MALE OMOP:8507 A person who belongs to the sex that normally produces sperm FEMALE OMOP:8532 A person who belongs to the sex that normally produces ova UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused Slots Name Description sex The biologic character or quality that distinguishes male and female from one... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SexEnum description: A constrained set of enumerative values containing the OMOP values for sex. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: MALE: text: MALE description: A person who belongs to the sex that normally produces sperm. meaning: OMOP:8507 FEMALE: text: FEMALE description: A person who belongs to the sex that normally produces ova. meaning: OMOP:8532 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552","title":"Enum: SexEnum"},{"location":"SexEnum/#enum-sexenum","text":"A constrained set of enumerative values containing the OMOP values for sex. URI: SexEnum","title":"Enum: SexEnum"},{"location":"SexEnum/#permissible-values","text":"Value Meaning Description MALE OMOP:8507 A person who belongs to the sex that normally produces sperm FEMALE OMOP:8532 A person who belongs to the sex that normally produces ova UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused","title":"Permissible Values"},{"location":"SexEnum/#slots","text":"Name Description sex The biologic character or quality that distinguishes male and female from one...","title":"Slots"},{"location":"SexEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SexEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SexEnum/#linkml-source","text":"name: SexEnum description: A constrained set of enumerative values containing the OMOP values for sex. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: MALE: text: MALE description: A person who belongs to the sex that normally produces sperm. meaning: OMOP:8507 FEMALE: text: FEMALE description: A person who belongs to the sex that normally produces ova. meaning: OMOP:8532 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552","title":"LinkML Source"},{"location":"SourceMaterialTypeEnum/","text":"Enum: SourceMaterialTypeEnum URI: SourceMaterialTypeEnum Permissible Values Value Meaning Description ADDITIONAL_METASTATIC None ADDITIONAL_NEW_PRIMARY None BENIGN_NEOPLASMS None BLOOD_DERIVED_CANCER_BONE_MARROW None BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT None BLOOD_DERIVED_LIQUID_BIOPSY None BLOOD_DERIVED_NORMAL None BONE_MARROW_NORMAL None BUCCAL_CELL_NORMAL None CELL_LINE_DERIVED_XENOGRAFT_TISSUE None CELL_LINES None CONTROL_ANALYTE None DNA None EBV_IMMORTALIZED_NORMAL None EXPANDED_NEXT_GENERATION_CANCER_MODEL None FFPE_RECURRENT None FFPE_SCROLLS None FIBROBLASTS_FROM_BONE_MARROW_NORMAL None GRANULOCYTES None HUMAN_TUMOR_ORIGINAL_CELLS None IN_SITU_NEOPLASMS None LYMPHOID_NORMAL None METASTATIC None MIXED_ADHERENT_SUSPENSION None MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL None NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR None NEXT_GENERATION_CANCER_MODEL None NORMAL_ADJACENT_TISSUE None PLEURAL_EFFUSION None POST_NEOADJUVANT_THERAPY None PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW None PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None PRIMARY_TUMOR None PRIMARY_XENOGRAFT_TISSUE None RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW None RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None RECURRENT_TUMOR None RNA None SALIVA None SLIDES None SOLID_TISSUE_NORMAL None TOTAL_RNA None TUMOR None TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY None XENOGRAFT_TISSUE None NOT_ALLOWED_TO_COLLECT None NOT_REPORTED None UNKNOWN None Slots Name Description source_material_type The general kind of material from which the specimen was derived Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SourceMaterialTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ADDITIONAL_METASTATIC: text: ADDITIONAL_METASTATIC ADDITIONAL_NEW_PRIMARY: text: ADDITIONAL_NEW_PRIMARY BENIGN_NEOPLASMS: text: BENIGN_NEOPLASMS BLOOD_DERIVED_CANCER_BONE_MARROW: text: BLOOD_DERIVED_CANCER_BONE_MARROW BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT BLOOD_DERIVED_LIQUID_BIOPSY: text: BLOOD_DERIVED_LIQUID_BIOPSY BLOOD_DERIVED_NORMAL: text: BLOOD_DERIVED_NORMAL BONE_MARROW_NORMAL: text: BONE_MARROW_NORMAL BUCCAL_CELL_NORMAL: text: BUCCAL_CELL_NORMAL CELL_LINE_DERIVED_XENOGRAFT_TISSUE: text: CELL_LINE_DERIVED_XENOGRAFT_TISSUE CELL_LINES: text: CELL_LINES CONTROL_ANALYTE: text: CONTROL_ANALYTE DNA: text: DNA EBV_IMMORTALIZED_NORMAL: text: EBV_IMMORTALIZED_NORMAL EXPANDED_NEXT_GENERATION_CANCER_MODEL: text: EXPANDED_NEXT_GENERATION_CANCER_MODEL FFPE_RECURRENT: text: FFPE_RECURRENT FFPE_SCROLLS: text: FFPE_SCROLLS FIBROBLASTS_FROM_BONE_MARROW_NORMAL: text: FIBROBLASTS_FROM_BONE_MARROW_NORMAL GRANULOCYTES: text: GRANULOCYTES HUMAN_TUMOR_ORIGINAL_CELLS: text: HUMAN_TUMOR_ORIGINAL_CELLS IN_SITU_NEOPLASMS: text: IN_SITU_NEOPLASMS LYMPHOID_NORMAL: text: LYMPHOID_NORMAL METASTATIC: text: METASTATIC MIXED_ADHERENT_SUSPENSION: text: MIXED_ADHERENT_SUSPENSION MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL: text: MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR: text: NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR NEXT_GENERATION_CANCER_MODEL: text: NEXT_GENERATION_CANCER_MODEL NORMAL_ADJACENT_TISSUE: text: NORMAL_ADJACENT_TISSUE PLEURAL_EFFUSION: text: PLEURAL_EFFUSION POST_NEOADJUVANT_THERAPY: text: POST_NEOADJUVANT_THERAPY PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW: text: PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD PRIMARY_TUMOR: text: PRIMARY_TUMOR PRIMARY_XENOGRAFT_TISSUE: text: PRIMARY_XENOGRAFT_TISSUE RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW: text: RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD RECURRENT_TUMOR: text: RECURRENT_TUMOR RNA: text: RNA SALIVA: text: SALIVA SLIDES: text: SLIDES SOLID_TISSUE_NORMAL: text: SOLID_TISSUE_NORMAL TOTAL_RNA: text: TOTAL_RNA TUMOR: text: TUMOR TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY: text: TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY XENOGRAFT_TISSUE: text: XENOGRAFT_TISSUE NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT NOT_REPORTED: text: NOT_REPORTED UNKNOWN: text: UNKNOWN","title":"Enum: SourceMaterialTypeEnum"},{"location":"SourceMaterialTypeEnum/#enum-sourcematerialtypeenum","text":"URI: SourceMaterialTypeEnum","title":"Enum: SourceMaterialTypeEnum"},{"location":"SourceMaterialTypeEnum/#permissible-values","text":"Value Meaning Description ADDITIONAL_METASTATIC None ADDITIONAL_NEW_PRIMARY None BENIGN_NEOPLASMS None BLOOD_DERIVED_CANCER_BONE_MARROW None BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT None BLOOD_DERIVED_LIQUID_BIOPSY None BLOOD_DERIVED_NORMAL None BONE_MARROW_NORMAL None BUCCAL_CELL_NORMAL None CELL_LINE_DERIVED_XENOGRAFT_TISSUE None CELL_LINES None CONTROL_ANALYTE None DNA None EBV_IMMORTALIZED_NORMAL None EXPANDED_NEXT_GENERATION_CANCER_MODEL None FFPE_RECURRENT None FFPE_SCROLLS None FIBROBLASTS_FROM_BONE_MARROW_NORMAL None GRANULOCYTES None HUMAN_TUMOR_ORIGINAL_CELLS None IN_SITU_NEOPLASMS None LYMPHOID_NORMAL None METASTATIC None MIXED_ADHERENT_SUSPENSION None MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL None NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR None NEXT_GENERATION_CANCER_MODEL None NORMAL_ADJACENT_TISSUE None PLEURAL_EFFUSION None POST_NEOADJUVANT_THERAPY None PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW None PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None PRIMARY_TUMOR None PRIMARY_XENOGRAFT_TISSUE None RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW None RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None RECURRENT_TUMOR None RNA None SALIVA None SLIDES None SOLID_TISSUE_NORMAL None TOTAL_RNA None TUMOR None TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY None XENOGRAFT_TISSUE None NOT_ALLOWED_TO_COLLECT None NOT_REPORTED None UNKNOWN None","title":"Permissible Values"},{"location":"SourceMaterialTypeEnum/#slots","text":"Name Description source_material_type The general kind of material from which the specimen was derived","title":"Slots"},{"location":"SourceMaterialTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SourceMaterialTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SourceMaterialTypeEnum/#linkml-source","text":"name: SourceMaterialTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ADDITIONAL_METASTATIC: text: ADDITIONAL_METASTATIC ADDITIONAL_NEW_PRIMARY: text: ADDITIONAL_NEW_PRIMARY BENIGN_NEOPLASMS: text: BENIGN_NEOPLASMS BLOOD_DERIVED_CANCER_BONE_MARROW: text: BLOOD_DERIVED_CANCER_BONE_MARROW BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT BLOOD_DERIVED_LIQUID_BIOPSY: text: BLOOD_DERIVED_LIQUID_BIOPSY BLOOD_DERIVED_NORMAL: text: BLOOD_DERIVED_NORMAL BONE_MARROW_NORMAL: text: BONE_MARROW_NORMAL BUCCAL_CELL_NORMAL: text: BUCCAL_CELL_NORMAL CELL_LINE_DERIVED_XENOGRAFT_TISSUE: text: CELL_LINE_DERIVED_XENOGRAFT_TISSUE CELL_LINES: text: CELL_LINES CONTROL_ANALYTE: text: CONTROL_ANALYTE DNA: text: DNA EBV_IMMORTALIZED_NORMAL: text: EBV_IMMORTALIZED_NORMAL EXPANDED_NEXT_GENERATION_CANCER_MODEL: text: EXPANDED_NEXT_GENERATION_CANCER_MODEL FFPE_RECURRENT: text: FFPE_RECURRENT FFPE_SCROLLS: text: FFPE_SCROLLS FIBROBLASTS_FROM_BONE_MARROW_NORMAL: text: FIBROBLASTS_FROM_BONE_MARROW_NORMAL GRANULOCYTES: text: GRANULOCYTES HUMAN_TUMOR_ORIGINAL_CELLS: text: HUMAN_TUMOR_ORIGINAL_CELLS IN_SITU_NEOPLASMS: text: IN_SITU_NEOPLASMS LYMPHOID_NORMAL: text: LYMPHOID_NORMAL METASTATIC: text: METASTATIC MIXED_ADHERENT_SUSPENSION: text: MIXED_ADHERENT_SUSPENSION MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL: text: MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR: text: NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR NEXT_GENERATION_CANCER_MODEL: text: NEXT_GENERATION_CANCER_MODEL NORMAL_ADJACENT_TISSUE: text: NORMAL_ADJACENT_TISSUE PLEURAL_EFFUSION: text: PLEURAL_EFFUSION POST_NEOADJUVANT_THERAPY: text: POST_NEOADJUVANT_THERAPY PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW: text: PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD PRIMARY_TUMOR: text: PRIMARY_TUMOR PRIMARY_XENOGRAFT_TISSUE: text: PRIMARY_XENOGRAFT_TISSUE RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW: text: RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD RECURRENT_TUMOR: text: RECURRENT_TUMOR RNA: text: RNA SALIVA: text: SALIVA SLIDES: text: SLIDES SOLID_TISSUE_NORMAL: text: SOLID_TISSUE_NORMAL TOTAL_RNA: text: TOTAL_RNA TUMOR: text: TUMOR TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY: text: TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY XENOGRAFT_TISSUE: text: XENOGRAFT_TISSUE NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT NOT_REPORTED: text: NOT_REPORTED UNKNOWN: text: UNKNOWN","title":"LinkML Source"},{"location":"Sparqlpath/","text":"Type: Sparqlpath A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#type-sparqlpath","text":"A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Sparqlpath/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Specimen/","text":"Class: Specimen Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. URI: bdchm:Specimen classDiagram class Specimen Entity <|-- Specimen Specimen : analyte_type Specimen --> AnalyteTypeEnum : analyte_type Specimen : cellular_composition_type Specimen : contained_in Specimen --> SpecimenContainer : contained_in Specimen : creation_activity Specimen --> SpecimenCreationActivity : creation_activity Specimen : derived_product Specimen --> BiologicProduct : derived_product Specimen : description Specimen : dimensional_measures Specimen --> DimensionalObservationSet : dimensional_measures Specimen : id Specimen : identity Specimen : parent_specimen Specimen --> Specimen : parent_specimen Specimen : processing_activity Specimen --> SpecimenProcessingActivity : processing_activity Specimen : quality_measure Specimen --> SpecimenQualityObservation : quality_measure Specimen : quantity_measure Specimen --> SpecimenQuantityObservation : quantity_measure Specimen : related_document Specimen --> Document : related_document Specimen : section_location Specimen --> SectionLocationEnum : section_location Specimen : source_material_type Specimen --> SourceMaterialTypeEnum : source_material_type Specimen : source_participant Specimen --> Participant : source_participant Specimen : specimen_type Specimen --> SpecimenTypeEnum : specimen_type Specimen : storage_activity Specimen --> SpecimenStorageActivity : storage_activity Specimen : transport_activity Specimen --> SpecimenTransportActivity : transport_activity Inheritance Entity Specimen Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional information or explanation about the ... direct specimen_type 0..1 SpecimenTypeEnum The high-level type of the specimen, based on its derivation provenance (i direct analyte_type 0..1 AnalyteTypeEnum For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... direct source_material_type 0..1 SourceMaterialTypeEnum The general kind of material from which the specimen was derived direct parent_specimen 0..* Specimen An existing specimen from which the specimen of interest was directly derived... direct source_participant 0..1 Participant A specific Subject from which the specimen was directly or indirectly derived direct creation_activity 0..1 SpecimenCreationActivity The activity through which a specimen was created, by removing material from ... direct processing_activity 0..* SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... direct storage_activity 0..* SpecimenStorageActivity An activity that results in the storage or maintenance of a specimen in a par... direct transport_activity 0..* SpecimenTransportActivity An activity through which the specimen is transported between locations direct contained_in 0..1 SpecimenContainer A physical container in which a specimen is presently held or attached - as ... direct dimensional_measures 0..1 DimensionalObservationSet Observations about the current physical dimensions of an object (e direct quantity_measure 0..* SpecimenQuantityObservation An observation related to the present quantity of a specimen - e direct quality_measure 0..* SpecimenQualityObservation An observation about characteristics of a specimen that are indicative of its... direct cellular_composition_type 0..1 String A term describing the type of cell or cellular material comprising a specimen direct related_document 0..* Document A reference to an external document that is about or related to the specimen ... direct section_location 0..1 SectionLocationEnum The location in a parent specimen from which a section/portion was excised (e direct derived_product 0..* BiologicProduct A 'living' biologically active product that was derived from the specimen (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen parent_specimen range Specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Specimen native bdchm:Specimen LinkML Source Direct name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: BiologicProduct required: false inlined: true inlined_as_list: true Induced name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Specimen domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false alias: analyte_type owner: Specimen domain_of: - Specimen range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_material_type owner: Specimen domain_of: - Specimen range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: parent_specimen owner: Specimen domain_of: - Specimen range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: processing_activity owner: Specimen domain_of: - Specimen range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quantity_measure owner: Specimen domain_of: - Specimen range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quality_measure owner: Specimen domain_of: - Specimen range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false alias: section_location owner: Specimen domain_of: - Specimen range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Specimen domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Specimen domain_of: - Entity range: uriorcurie required: true","title":"Class: Specimen"},{"location":"Specimen/#class-specimen","text":"Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. URI: bdchm:Specimen classDiagram class Specimen Entity <|-- Specimen Specimen : analyte_type Specimen --> AnalyteTypeEnum : analyte_type Specimen : cellular_composition_type Specimen : contained_in Specimen --> SpecimenContainer : contained_in Specimen : creation_activity Specimen --> SpecimenCreationActivity : creation_activity Specimen : derived_product Specimen --> BiologicProduct : derived_product Specimen : description Specimen : dimensional_measures Specimen --> DimensionalObservationSet : dimensional_measures Specimen : id Specimen : identity Specimen : parent_specimen Specimen --> Specimen : parent_specimen Specimen : processing_activity Specimen --> SpecimenProcessingActivity : processing_activity Specimen : quality_measure Specimen --> SpecimenQualityObservation : quality_measure Specimen : quantity_measure Specimen --> SpecimenQuantityObservation : quantity_measure Specimen : related_document Specimen --> Document : related_document Specimen : section_location Specimen --> SectionLocationEnum : section_location Specimen : source_material_type Specimen --> SourceMaterialTypeEnum : source_material_type Specimen : source_participant Specimen --> Participant : source_participant Specimen : specimen_type Specimen --> SpecimenTypeEnum : specimen_type Specimen : storage_activity Specimen --> SpecimenStorageActivity : storage_activity Specimen : transport_activity Specimen --> SpecimenTransportActivity : transport_activity","title":"Class: Specimen"},{"location":"Specimen/#inheritance","text":"Entity Specimen","title":"Inheritance"},{"location":"Specimen/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional information or explanation about the ... direct specimen_type 0..1 SpecimenTypeEnum The high-level type of the specimen, based on its derivation provenance (i direct analyte_type 0..1 AnalyteTypeEnum For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... direct source_material_type 0..1 SourceMaterialTypeEnum The general kind of material from which the specimen was derived direct parent_specimen 0..* Specimen An existing specimen from which the specimen of interest was directly derived... direct source_participant 0..1 Participant A specific Subject from which the specimen was directly or indirectly derived direct creation_activity 0..1 SpecimenCreationActivity The activity through which a specimen was created, by removing material from ... direct processing_activity 0..* SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... direct storage_activity 0..* SpecimenStorageActivity An activity that results in the storage or maintenance of a specimen in a par... direct transport_activity 0..* SpecimenTransportActivity An activity through which the specimen is transported between locations direct contained_in 0..1 SpecimenContainer A physical container in which a specimen is presently held or attached - as ... direct dimensional_measures 0..1 DimensionalObservationSet Observations about the current physical dimensions of an object (e direct quantity_measure 0..* SpecimenQuantityObservation An observation related to the present quantity of a specimen - e direct quality_measure 0..* SpecimenQualityObservation An observation about characteristics of a specimen that are indicative of its... direct cellular_composition_type 0..1 String A term describing the type of cell or cellular material comprising a specimen direct related_document 0..* Document A reference to an external document that is about or related to the specimen ... direct section_location 0..1 SectionLocationEnum The location in a parent specimen from which a section/portion was excised (e direct derived_product 0..* BiologicProduct A 'living' biologically active product that was derived from the specimen (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Specimen/#usages","text":"used by used in type used Specimen parent_specimen range Specimen","title":"Usages"},{"location":"Specimen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Specimen/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Specimen/#mappings","text":"Mapping Type Mapped Value self bdchm:Specimen native bdchm:Specimen","title":"Mappings"},{"location":"Specimen/#linkml-source","text":"","title":"LinkML Source"},{"location":"Specimen/#direct","text":"name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: BiologicProduct required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"Specimen/#induced","text":"name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Specimen domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false alias: analyte_type owner: Specimen domain_of: - Specimen range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_material_type owner: Specimen domain_of: - Specimen range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: parent_specimen owner: Specimen domain_of: - Specimen range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: processing_activity owner: Specimen domain_of: - Specimen range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quantity_measure owner: Specimen domain_of: - Specimen range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quality_measure owner: Specimen domain_of: - Specimen range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false alias: section_location owner: Specimen domain_of: - Specimen range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Specimen domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Specimen domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenCollectionMethodType/","text":"Enum: SpecimenCollectionMethodType URI: SpecimenCollectionMethodType Permissible Values Value Meaning Description ORCHIECTOMY None METASTASECTOMY None AUTOPSY None UNKNOWN None ASPIRATE None RIGHT_HEMICOLECTOMY None INCISIONAL_BIOPSY None BLOOD_DRAW None PERITONEAL_LAVAGE None OPEN_RADICAL_PROSTATECTOMY None ABDOMINO_PERINEAL_RESECTION_OF_RECTUM None SALPINGECTOMY None ENDO_RECTAL_TUMOR_RESECTION None BIOPSY None SALPINGO_OOPHORECTOMY None NOT_ALLOWED_TO_COLLECT None WHIPPLE_PROCEDURE None ENUCLEATION None MODIFIED_RADICAL_MASTECTOMY None PARACENTESIS None OPEN_CRANIOTOMY None WEDGE_RESECTION None LAPAROSCOPIC_RADICAL_NEPHRECTOMY None OPEN_PARTIAL_NEPHRECTOMY None TRANSURETHRAL_RESECTION None SIGMOID_COLECTOMY None OOPHORECTOMY None TOTAL_HEPATECTOMY None INDETERMINANT None SUBTOTAL_RESECTION None LEFT_HEMICOLECTOMY None NEEDLE_BIOPSY None OTHER None PANCREATECTOMY None THORACOSCOPIC_BIOPSY None TOTAL_MASTECTOMY None EXCISIONAL_BIOPSY None BONE_MARROW_ASPIRATE None LOCAL_RESECTION None LOBECTOMY None FINE_NEEDLE_ASPIRATION None OMENTECTOMY None TUMOR_RESECTION None CYSTECTOMY None GROSS_TOTAL_RESECTION None THORACENTESIS None ANTERIOR_RESECTION_OF_RECTUM None TRANSPLANT None LAPAROSCOPIC_PARTIAL_NEPHRECTOMY None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS None PNEUMONECTOMY None PAN_PROCTO_COLECTOMY None HYSTERECTOMY_NOS None CORE_BIOPSY None SIMPLE_MASTECTOMY None LUMPECTOMY None ENDOSCOPIC_BIOPSY None SIMPLE_HYSTERECTOMY None LYMPHADENECTOMY None LAPAROSCOPIC_BIOPSY None TUMOR_DEBULKING None ASCITES_DRAINAGE None ENDOSCOPIC_MUCOSAL_RESECTION None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS None TOTAL_COLECTOMY None LIQUID_BIOPSY None RADICAL_HYSTERECTOMY None SURGICAL_RESECTION None OPEN_RADICAL_NEPHRECTOMY None TRANSVERSE_COLECTOMY None HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY None PUNCH_BIOPSY None PARTIAL_HEPATECTOMY None SUPRACERVICAL_HYSTERECTOMY None OTHER_SURGICAL_RESECTION None NOT_REPORTED None FULL_HYSTERECTOMY None TONSILLECTOMY None SUPRAGLOTTIC_LARYNGECTOMY None SUPERFICIAL_PAROTIDECTOMY None LARYNGOPHARYNGECTOMY None MAXILLECTOMY None PARTIAL_NEPHRECTOMY None MANDIBULECTOMY None BUCCAL_MUCOSAL_RESECTION None VERTICAL_HEMILARYNGECTOMY None TOTAL_NEPHRECTOMY None TOTAL_LARYNGECTOMY None TRANSORAL_LASER_EXCISION None PAROTIDECTOMY_NOS None RADICAL_MAXILLECTOMY None ENDOLARYNGEAL_EXCISION None PALATECTOMY None GLOSSECTOMY None PARTIAL_LARYNGECTOMY None LYMPH_NODE_DISSECTION None RADICAL_PROSTATECTOMY None DEEP_PAROTIDECTOMY None SUBTOTAL_PROSTATECTOMY None RADICAL_NEPHRECTOMY None SUPRACRICOID_LARYNGECTOMY None PARTIAL_MAXILLECTOMY None Slots Name Description collection_method_type The type of method applied in collecting a sample from its original source Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenCollectionMethodType from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ORCHIECTOMY: text: ORCHIECTOMY METASTASECTOMY: text: METASTASECTOMY AUTOPSY: text: AUTOPSY UNKNOWN: text: UNKNOWN ASPIRATE: text: ASPIRATE RIGHT_HEMICOLECTOMY: text: RIGHT_HEMICOLECTOMY INCISIONAL_BIOPSY: text: INCISIONAL_BIOPSY BLOOD_DRAW: text: BLOOD_DRAW PERITONEAL_LAVAGE: text: PERITONEAL_LAVAGE OPEN_RADICAL_PROSTATECTOMY: text: OPEN_RADICAL_PROSTATECTOMY ABDOMINO_PERINEAL_RESECTION_OF_RECTUM: text: ABDOMINO_PERINEAL_RESECTION_OF_RECTUM SALPINGECTOMY: text: SALPINGECTOMY ENDO_RECTAL_TUMOR_RESECTION: text: ENDO_RECTAL_TUMOR_RESECTION BIOPSY: text: BIOPSY SALPINGO_OOPHORECTOMY: text: SALPINGO_OOPHORECTOMY NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT WHIPPLE_PROCEDURE: text: WHIPPLE_PROCEDURE ENUCLEATION: text: ENUCLEATION MODIFIED_RADICAL_MASTECTOMY: text: MODIFIED_RADICAL_MASTECTOMY PARACENTESIS: text: PARACENTESIS OPEN_CRANIOTOMY: text: OPEN_CRANIOTOMY WEDGE_RESECTION: text: WEDGE_RESECTION LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: LAPAROSCOPIC_RADICAL_NEPHRECTOMY OPEN_PARTIAL_NEPHRECTOMY: text: OPEN_PARTIAL_NEPHRECTOMY TRANSURETHRAL_RESECTION: text: TRANSURETHRAL_RESECTION SIGMOID_COLECTOMY: text: SIGMOID_COLECTOMY OOPHORECTOMY: text: OOPHORECTOMY TOTAL_HEPATECTOMY: text: TOTAL_HEPATECTOMY INDETERMINANT: text: INDETERMINANT SUBTOTAL_RESECTION: text: SUBTOTAL_RESECTION LEFT_HEMICOLECTOMY: text: LEFT_HEMICOLECTOMY NEEDLE_BIOPSY: text: NEEDLE_BIOPSY OTHER: text: OTHER PANCREATECTOMY: text: PANCREATECTOMY THORACOSCOPIC_BIOPSY: text: THORACOSCOPIC_BIOPSY TOTAL_MASTECTOMY: text: TOTAL_MASTECTOMY EXCISIONAL_BIOPSY: text: EXCISIONAL_BIOPSY BONE_MARROW_ASPIRATE: text: BONE_MARROW_ASPIRATE LOCAL_RESECTION: text: LOCAL_RESECTION LOBECTOMY: text: LOBECTOMY FINE_NEEDLE_ASPIRATION: text: FINE_NEEDLE_ASPIRATION OMENTECTOMY: text: OMENTECTOMY TUMOR_RESECTION: text: TUMOR_RESECTION CYSTECTOMY: text: CYSTECTOMY GROSS_TOTAL_RESECTION: text: GROSS_TOTAL_RESECTION THORACENTESIS: text: THORACENTESIS ANTERIOR_RESECTION_OF_RECTUM: text: ANTERIOR_RESECTION_OF_RECTUM TRANSPLANT: text: TRANSPLANT LAPAROSCOPIC_PARTIAL_NEPHRECTOMY: text: LAPAROSCOPIC_PARTIAL_NEPHRECTOMY LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS PNEUMONECTOMY: text: PNEUMONECTOMY PAN_PROCTO_COLECTOMY: text: PAN_PROCTO_COLECTOMY HYSTERECTOMY_NOS: text: HYSTERECTOMY_NOS CORE_BIOPSY: text: CORE_BIOPSY SIMPLE_MASTECTOMY: text: SIMPLE_MASTECTOMY LUMPECTOMY: text: LUMPECTOMY ENDOSCOPIC_BIOPSY: text: ENDOSCOPIC_BIOPSY SIMPLE_HYSTERECTOMY: text: SIMPLE_HYSTERECTOMY LYMPHADENECTOMY: text: LYMPHADENECTOMY LAPAROSCOPIC_BIOPSY: text: LAPAROSCOPIC_BIOPSY TUMOR_DEBULKING: text: TUMOR_DEBULKING ASCITES_DRAINAGE: text: ASCITES_DRAINAGE ENDOSCOPIC_MUCOSAL_RESECTION: text: ENDOSCOPIC_MUCOSAL_RESECTION LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS TOTAL_COLECTOMY: text: TOTAL_COLECTOMY LIQUID_BIOPSY: text: LIQUID_BIOPSY RADICAL_HYSTERECTOMY: text: RADICAL_HYSTERECTOMY SURGICAL_RESECTION: text: SURGICAL_RESECTION OPEN_RADICAL_NEPHRECTOMY: text: OPEN_RADICAL_NEPHRECTOMY TRANSVERSE_COLECTOMY: text: TRANSVERSE_COLECTOMY HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY PUNCH_BIOPSY: text: PUNCH_BIOPSY PARTIAL_HEPATECTOMY: text: PARTIAL_HEPATECTOMY SUPRACERVICAL_HYSTERECTOMY: text: SUPRACERVICAL_HYSTERECTOMY OTHER_SURGICAL_RESECTION: text: OTHER_SURGICAL_RESECTION NOT_REPORTED: text: NOT_REPORTED FULL_HYSTERECTOMY: text: FULL_HYSTERECTOMY TONSILLECTOMY: text: TONSILLECTOMY SUPRAGLOTTIC_LARYNGECTOMY: text: SUPRAGLOTTIC_LARYNGECTOMY SUPERFICIAL_PAROTIDECTOMY: text: SUPERFICIAL_PAROTIDECTOMY LARYNGOPHARYNGECTOMY: text: LARYNGOPHARYNGECTOMY MAXILLECTOMY: text: MAXILLECTOMY PARTIAL_NEPHRECTOMY: text: PARTIAL_NEPHRECTOMY MANDIBULECTOMY: text: MANDIBULECTOMY BUCCAL_MUCOSAL_RESECTION: text: BUCCAL_MUCOSAL_RESECTION VERTICAL_HEMILARYNGECTOMY: text: VERTICAL_HEMILARYNGECTOMY TOTAL_NEPHRECTOMY: text: TOTAL_NEPHRECTOMY TOTAL_LARYNGECTOMY: text: TOTAL_LARYNGECTOMY TRANSORAL_LASER_EXCISION: text: TRANSORAL_LASER_EXCISION PAROTIDECTOMY_NOS: text: PAROTIDECTOMY_NOS RADICAL_MAXILLECTOMY: text: RADICAL_MAXILLECTOMY ENDOLARYNGEAL_EXCISION: text: ENDOLARYNGEAL_EXCISION PALATECTOMY: text: PALATECTOMY GLOSSECTOMY: text: GLOSSECTOMY PARTIAL_LARYNGECTOMY: text: PARTIAL_LARYNGECTOMY LYMPH_NODE_DISSECTION: text: LYMPH_NODE_DISSECTION RADICAL_PROSTATECTOMY: text: RADICAL_PROSTATECTOMY DEEP_PAROTIDECTOMY: text: DEEP_PAROTIDECTOMY SUBTOTAL_PROSTATECTOMY: text: SUBTOTAL_PROSTATECTOMY RADICAL_NEPHRECTOMY: text: RADICAL_NEPHRECTOMY SUPRACRICOID_LARYNGECTOMY: text: SUPRACRICOID_LARYNGECTOMY PARTIAL_MAXILLECTOMY: text: PARTIAL_MAXILLECTOMY","title":"Enum: SpecimenCollectionMethodType"},{"location":"SpecimenCollectionMethodType/#enum-specimencollectionmethodtype","text":"URI: SpecimenCollectionMethodType","title":"Enum: SpecimenCollectionMethodType"},{"location":"SpecimenCollectionMethodType/#permissible-values","text":"Value Meaning Description ORCHIECTOMY None METASTASECTOMY None AUTOPSY None UNKNOWN None ASPIRATE None RIGHT_HEMICOLECTOMY None INCISIONAL_BIOPSY None BLOOD_DRAW None PERITONEAL_LAVAGE None OPEN_RADICAL_PROSTATECTOMY None ABDOMINO_PERINEAL_RESECTION_OF_RECTUM None SALPINGECTOMY None ENDO_RECTAL_TUMOR_RESECTION None BIOPSY None SALPINGO_OOPHORECTOMY None NOT_ALLOWED_TO_COLLECT None WHIPPLE_PROCEDURE None ENUCLEATION None MODIFIED_RADICAL_MASTECTOMY None PARACENTESIS None OPEN_CRANIOTOMY None WEDGE_RESECTION None LAPAROSCOPIC_RADICAL_NEPHRECTOMY None OPEN_PARTIAL_NEPHRECTOMY None TRANSURETHRAL_RESECTION None SIGMOID_COLECTOMY None OOPHORECTOMY None TOTAL_HEPATECTOMY None INDETERMINANT None SUBTOTAL_RESECTION None LEFT_HEMICOLECTOMY None NEEDLE_BIOPSY None OTHER None PANCREATECTOMY None THORACOSCOPIC_BIOPSY None TOTAL_MASTECTOMY None EXCISIONAL_BIOPSY None BONE_MARROW_ASPIRATE None LOCAL_RESECTION None LOBECTOMY None FINE_NEEDLE_ASPIRATION None OMENTECTOMY None TUMOR_RESECTION None CYSTECTOMY None GROSS_TOTAL_RESECTION None THORACENTESIS None ANTERIOR_RESECTION_OF_RECTUM None TRANSPLANT None LAPAROSCOPIC_PARTIAL_NEPHRECTOMY None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS None PNEUMONECTOMY None PAN_PROCTO_COLECTOMY None HYSTERECTOMY_NOS None CORE_BIOPSY None SIMPLE_MASTECTOMY None LUMPECTOMY None ENDOSCOPIC_BIOPSY None SIMPLE_HYSTERECTOMY None LYMPHADENECTOMY None LAPAROSCOPIC_BIOPSY None TUMOR_DEBULKING None ASCITES_DRAINAGE None ENDOSCOPIC_MUCOSAL_RESECTION None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS None TOTAL_COLECTOMY None LIQUID_BIOPSY None RADICAL_HYSTERECTOMY None SURGICAL_RESECTION None OPEN_RADICAL_NEPHRECTOMY None TRANSVERSE_COLECTOMY None HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY None PUNCH_BIOPSY None PARTIAL_HEPATECTOMY None SUPRACERVICAL_HYSTERECTOMY None OTHER_SURGICAL_RESECTION None NOT_REPORTED None FULL_HYSTERECTOMY None TONSILLECTOMY None SUPRAGLOTTIC_LARYNGECTOMY None SUPERFICIAL_PAROTIDECTOMY None LARYNGOPHARYNGECTOMY None MAXILLECTOMY None PARTIAL_NEPHRECTOMY None MANDIBULECTOMY None BUCCAL_MUCOSAL_RESECTION None VERTICAL_HEMILARYNGECTOMY None TOTAL_NEPHRECTOMY None TOTAL_LARYNGECTOMY None TRANSORAL_LASER_EXCISION None PAROTIDECTOMY_NOS None RADICAL_MAXILLECTOMY None ENDOLARYNGEAL_EXCISION None PALATECTOMY None GLOSSECTOMY None PARTIAL_LARYNGECTOMY None LYMPH_NODE_DISSECTION None RADICAL_PROSTATECTOMY None DEEP_PAROTIDECTOMY None SUBTOTAL_PROSTATECTOMY None RADICAL_NEPHRECTOMY None SUPRACRICOID_LARYNGECTOMY None PARTIAL_MAXILLECTOMY None","title":"Permissible Values"},{"location":"SpecimenCollectionMethodType/#slots","text":"Name Description collection_method_type The type of method applied in collecting a sample from its original source","title":"Slots"},{"location":"SpecimenCollectionMethodType/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenCollectionMethodType/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenCollectionMethodType/#linkml-source","text":"name: SpecimenCollectionMethodType from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ORCHIECTOMY: text: ORCHIECTOMY METASTASECTOMY: text: METASTASECTOMY AUTOPSY: text: AUTOPSY UNKNOWN: text: UNKNOWN ASPIRATE: text: ASPIRATE RIGHT_HEMICOLECTOMY: text: RIGHT_HEMICOLECTOMY INCISIONAL_BIOPSY: text: INCISIONAL_BIOPSY BLOOD_DRAW: text: BLOOD_DRAW PERITONEAL_LAVAGE: text: PERITONEAL_LAVAGE OPEN_RADICAL_PROSTATECTOMY: text: OPEN_RADICAL_PROSTATECTOMY ABDOMINO_PERINEAL_RESECTION_OF_RECTUM: text: ABDOMINO_PERINEAL_RESECTION_OF_RECTUM SALPINGECTOMY: text: SALPINGECTOMY ENDO_RECTAL_TUMOR_RESECTION: text: ENDO_RECTAL_TUMOR_RESECTION BIOPSY: text: BIOPSY SALPINGO_OOPHORECTOMY: text: SALPINGO_OOPHORECTOMY NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT WHIPPLE_PROCEDURE: text: WHIPPLE_PROCEDURE ENUCLEATION: text: ENUCLEATION MODIFIED_RADICAL_MASTECTOMY: text: MODIFIED_RADICAL_MASTECTOMY PARACENTESIS: text: PARACENTESIS OPEN_CRANIOTOMY: text: OPEN_CRANIOTOMY WEDGE_RESECTION: text: WEDGE_RESECTION LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: LAPAROSCOPIC_RADICAL_NEPHRECTOMY OPEN_PARTIAL_NEPHRECTOMY: text: OPEN_PARTIAL_NEPHRECTOMY TRANSURETHRAL_RESECTION: text: TRANSURETHRAL_RESECTION SIGMOID_COLECTOMY: text: SIGMOID_COLECTOMY OOPHORECTOMY: text: OOPHORECTOMY TOTAL_HEPATECTOMY: text: TOTAL_HEPATECTOMY INDETERMINANT: text: INDETERMINANT SUBTOTAL_RESECTION: text: SUBTOTAL_RESECTION LEFT_HEMICOLECTOMY: text: LEFT_HEMICOLECTOMY NEEDLE_BIOPSY: text: NEEDLE_BIOPSY OTHER: text: OTHER PANCREATECTOMY: text: PANCREATECTOMY THORACOSCOPIC_BIOPSY: text: THORACOSCOPIC_BIOPSY TOTAL_MASTECTOMY: text: TOTAL_MASTECTOMY EXCISIONAL_BIOPSY: text: EXCISIONAL_BIOPSY BONE_MARROW_ASPIRATE: text: BONE_MARROW_ASPIRATE LOCAL_RESECTION: text: LOCAL_RESECTION LOBECTOMY: text: LOBECTOMY FINE_NEEDLE_ASPIRATION: text: FINE_NEEDLE_ASPIRATION OMENTECTOMY: text: OMENTECTOMY TUMOR_RESECTION: text: TUMOR_RESECTION CYSTECTOMY: text: CYSTECTOMY GROSS_TOTAL_RESECTION: text: GROSS_TOTAL_RESECTION THORACENTESIS: text: THORACENTESIS ANTERIOR_RESECTION_OF_RECTUM: text: ANTERIOR_RESECTION_OF_RECTUM TRANSPLANT: text: TRANSPLANT LAPAROSCOPIC_PARTIAL_NEPHRECTOMY: text: LAPAROSCOPIC_PARTIAL_NEPHRECTOMY LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS PNEUMONECTOMY: text: PNEUMONECTOMY PAN_PROCTO_COLECTOMY: text: PAN_PROCTO_COLECTOMY HYSTERECTOMY_NOS: text: HYSTERECTOMY_NOS CORE_BIOPSY: text: CORE_BIOPSY SIMPLE_MASTECTOMY: text: SIMPLE_MASTECTOMY LUMPECTOMY: text: LUMPECTOMY ENDOSCOPIC_BIOPSY: text: ENDOSCOPIC_BIOPSY SIMPLE_HYSTERECTOMY: text: SIMPLE_HYSTERECTOMY LYMPHADENECTOMY: text: LYMPHADENECTOMY LAPAROSCOPIC_BIOPSY: text: LAPAROSCOPIC_BIOPSY TUMOR_DEBULKING: text: TUMOR_DEBULKING ASCITES_DRAINAGE: text: ASCITES_DRAINAGE ENDOSCOPIC_MUCOSAL_RESECTION: text: ENDOSCOPIC_MUCOSAL_RESECTION LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS TOTAL_COLECTOMY: text: TOTAL_COLECTOMY LIQUID_BIOPSY: text: LIQUID_BIOPSY RADICAL_HYSTERECTOMY: text: RADICAL_HYSTERECTOMY SURGICAL_RESECTION: text: SURGICAL_RESECTION OPEN_RADICAL_NEPHRECTOMY: text: OPEN_RADICAL_NEPHRECTOMY TRANSVERSE_COLECTOMY: text: TRANSVERSE_COLECTOMY HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY PUNCH_BIOPSY: text: PUNCH_BIOPSY PARTIAL_HEPATECTOMY: text: PARTIAL_HEPATECTOMY SUPRACERVICAL_HYSTERECTOMY: text: SUPRACERVICAL_HYSTERECTOMY OTHER_SURGICAL_RESECTION: text: OTHER_SURGICAL_RESECTION NOT_REPORTED: text: NOT_REPORTED FULL_HYSTERECTOMY: text: FULL_HYSTERECTOMY TONSILLECTOMY: text: TONSILLECTOMY SUPRAGLOTTIC_LARYNGECTOMY: text: SUPRAGLOTTIC_LARYNGECTOMY SUPERFICIAL_PAROTIDECTOMY: text: SUPERFICIAL_PAROTIDECTOMY LARYNGOPHARYNGECTOMY: text: LARYNGOPHARYNGECTOMY MAXILLECTOMY: text: MAXILLECTOMY PARTIAL_NEPHRECTOMY: text: PARTIAL_NEPHRECTOMY MANDIBULECTOMY: text: MANDIBULECTOMY BUCCAL_MUCOSAL_RESECTION: text: BUCCAL_MUCOSAL_RESECTION VERTICAL_HEMILARYNGECTOMY: text: VERTICAL_HEMILARYNGECTOMY TOTAL_NEPHRECTOMY: text: TOTAL_NEPHRECTOMY TOTAL_LARYNGECTOMY: text: TOTAL_LARYNGECTOMY TRANSORAL_LASER_EXCISION: text: TRANSORAL_LASER_EXCISION PAROTIDECTOMY_NOS: text: PAROTIDECTOMY_NOS RADICAL_MAXILLECTOMY: text: RADICAL_MAXILLECTOMY ENDOLARYNGEAL_EXCISION: text: ENDOLARYNGEAL_EXCISION PALATECTOMY: text: PALATECTOMY GLOSSECTOMY: text: GLOSSECTOMY PARTIAL_LARYNGECTOMY: text: PARTIAL_LARYNGECTOMY LYMPH_NODE_DISSECTION: text: LYMPH_NODE_DISSECTION RADICAL_PROSTATECTOMY: text: RADICAL_PROSTATECTOMY DEEP_PAROTIDECTOMY: text: DEEP_PAROTIDECTOMY SUBTOTAL_PROSTATECTOMY: text: SUBTOTAL_PROSTATECTOMY RADICAL_NEPHRECTOMY: text: RADICAL_NEPHRECTOMY SUPRACRICOID_LARYNGECTOMY: text: SUPRACRICOID_LARYNGECTOMY PARTIAL_MAXILLECTOMY: text: PARTIAL_MAXILLECTOMY","title":"LinkML Source"},{"location":"SpecimenContainer/","text":"Class: SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:SpecimenContainer classDiagram class SpecimenContainer Entity <|-- SpecimenContainer SpecimenContainer : additive SpecimenContainer --> Substance : additive SpecimenContainer : container_number SpecimenContainer : container_type SpecimenContainer : id SpecimenContainer : parent_container SpecimenContainer --> SpecimenContainer : parent_container Inheritance Entity SpecimenContainer Slots Name Cardinality and Range Description Inheritance container_type 0..1 String The kind of the container direct container_number 0..1 String Informal number by which the container is referenced or identified (e direct additive 0..* Substance A material substance added to the container (typically to support the primary... direct parent_container 0..1 SpecimenContainer A larger container of which this container is a part (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen contained_in range SpecimenContainer SpecimenContainer parent_container range SpecimenContainer SpecimenStorageActivity container range SpecimenContainer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenContainer native bdchm:SpecimenContainer LinkML Source Direct name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false Induced name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: additive owner: SpecimenContainer domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: parent_container owner: SpecimenContainer domain_of: - SpecimenContainer range: SpecimenContainer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenContainer domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenContainer"},{"location":"SpecimenContainer/#class-specimencontainer","text":"A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:SpecimenContainer classDiagram class SpecimenContainer Entity <|-- SpecimenContainer SpecimenContainer : additive SpecimenContainer --> Substance : additive SpecimenContainer : container_number SpecimenContainer : container_type SpecimenContainer : id SpecimenContainer : parent_container SpecimenContainer --> SpecimenContainer : parent_container","title":"Class: SpecimenContainer"},{"location":"SpecimenContainer/#inheritance","text":"Entity SpecimenContainer","title":"Inheritance"},{"location":"SpecimenContainer/#slots","text":"Name Cardinality and Range Description Inheritance container_type 0..1 String The kind of the container direct container_number 0..1 String Informal number by which the container is referenced or identified (e direct additive 0..* Substance A material substance added to the container (typically to support the primary... direct parent_container 0..1 SpecimenContainer A larger container of which this container is a part (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenContainer/#usages","text":"used by used in type used Specimen contained_in range SpecimenContainer SpecimenContainer parent_container range SpecimenContainer SpecimenStorageActivity container range SpecimenContainer","title":"Usages"},{"location":"SpecimenContainer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenContainer/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenContainer/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenContainer native bdchm:SpecimenContainer","title":"Mappings"},{"location":"SpecimenContainer/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenContainer/#direct","text":"name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false","title":"Direct"},{"location":"SpecimenContainer/#induced","text":"name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: additive owner: SpecimenContainer domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: parent_container owner: SpecimenContainer domain_of: - SpecimenContainer range: SpecimenContainer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenContainer domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenCreationActivity/","text":"Class: SpecimenCreationActivity The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). URI: bdchm:SpecimenCreationActivity classDiagram class SpecimenCreationActivity Entity <|-- SpecimenCreationActivity SpecimenCreationActivity : activity_type SpecimenCreationActivity --> SpecimenCreationActivityTypeEnum : activity_type SpecimenCreationActivity : additive SpecimenCreationActivity --> Substance : additive SpecimenCreationActivity : collection_method_type SpecimenCreationActivity --> SpecimenCollectionMethodType : collection_method_type SpecimenCreationActivity : collection_site SpecimenCreationActivity --> BodySite : collection_site SpecimenCreationActivity : date_ended SpecimenCreationActivity --> TimePoint : date_ended SpecimenCreationActivity : date_started SpecimenCreationActivity --> TimePoint : date_started SpecimenCreationActivity : derivation_method_type SpecimenCreationActivity : id SpecimenCreationActivity : performed_by SpecimenCreationActivity --> Organization : performed_by SpecimenCreationActivity : quantity_collected SpecimenCreationActivity --> Quantity : quantity_collected SpecimenCreationActivity : specimen_order Inheritance Entity SpecimenCreationActivity Slots Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenCreationActivityTypeEnum The high-level type of creation activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen creation event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a specimen creation event) direct performed_by 0..1 Organization The organization or group that performed the activity direct collection_method_type 0..1 SpecimenCollectionMethodType The type of method applied in collecting a sample from its original source direct derivation_method_type 0..1 String The type of method applied to derive a new specimen from an existing one direct additive 0..* Substance A type of material or reagent used applied as input when creating a specimen direct collection_site 0..1 BodySite The anatomic site from which a specimen was collected direct quantity_collected 0..1 Quantity The quantity of material in the specimen as originally collected from its ori... direct specimen_order 0..1 Integer A numeric value that represents the sequential order of this creation activit... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen creation_activity range SpecimenCreationActivity Comments A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenCreationActivity native bdchm:SpecimenCreationActivity LinkML Source Direct name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: integer required: false Induced name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: activity_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: performed_by owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenCreationActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: quantity_collected owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenCreationActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenCreationActivity"},{"location":"SpecimenCreationActivity/#class-specimencreationactivity","text":"The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). URI: bdchm:SpecimenCreationActivity classDiagram class SpecimenCreationActivity Entity <|-- SpecimenCreationActivity SpecimenCreationActivity : activity_type SpecimenCreationActivity --> SpecimenCreationActivityTypeEnum : activity_type SpecimenCreationActivity : additive SpecimenCreationActivity --> Substance : additive SpecimenCreationActivity : collection_method_type SpecimenCreationActivity --> SpecimenCollectionMethodType : collection_method_type SpecimenCreationActivity : collection_site SpecimenCreationActivity --> BodySite : collection_site SpecimenCreationActivity : date_ended SpecimenCreationActivity --> TimePoint : date_ended SpecimenCreationActivity : date_started SpecimenCreationActivity --> TimePoint : date_started SpecimenCreationActivity : derivation_method_type SpecimenCreationActivity : id SpecimenCreationActivity : performed_by SpecimenCreationActivity --> Organization : performed_by SpecimenCreationActivity : quantity_collected SpecimenCreationActivity --> Quantity : quantity_collected SpecimenCreationActivity : specimen_order","title":"Class: SpecimenCreationActivity"},{"location":"SpecimenCreationActivity/#inheritance","text":"Entity SpecimenCreationActivity","title":"Inheritance"},{"location":"SpecimenCreationActivity/#slots","text":"Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenCreationActivityTypeEnum The high-level type of creation activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen creation event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a specimen creation event) direct performed_by 0..1 Organization The organization or group that performed the activity direct collection_method_type 0..1 SpecimenCollectionMethodType The type of method applied in collecting a sample from its original source direct derivation_method_type 0..1 String The type of method applied to derive a new specimen from an existing one direct additive 0..* Substance A type of material or reagent used applied as input when creating a specimen direct collection_site 0..1 BodySite The anatomic site from which a specimen was collected direct quantity_collected 0..1 Quantity The quantity of material in the specimen as originally collected from its ori... direct specimen_order 0..1 Integer A numeric value that represents the sequential order of this creation activit... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenCreationActivity/#usages","text":"used by used in type used Specimen creation_activity range SpecimenCreationActivity","title":"Usages"},{"location":"SpecimenCreationActivity/#comments","text":"A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported.","title":"Comments"},{"location":"SpecimenCreationActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenCreationActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenCreationActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenCreationActivity native bdchm:SpecimenCreationActivity","title":"Mappings"},{"location":"SpecimenCreationActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenCreationActivity/#direct","text":"name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: integer required: false","title":"Direct"},{"location":"SpecimenCreationActivity/#induced","text":"name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: activity_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: performed_by owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenCreationActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: quantity_collected owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenCreationActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenCreationActivityTypeEnum/","text":"Enum: SpecimenCreationActivityTypeEnum The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) URI: SpecimenCreationActivityTypeEnum Permissible Values Value Meaning Description COLLECTION_FROM_SOURCE None An activity that collects an initial sample directly from a subject / source DERIVATION_FROM_SPECIMEN None An activity that derives a new specimen from an existing one Slots Name Description activity_type The high-level type of creation activity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenCreationActivityTypeEnum description: The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: COLLECTION_FROM_SOURCE: text: COLLECTION_FROM_SOURCE description: An activity that collects an initial sample directly from a subject / source. DERIVATION_FROM_SPECIMEN: text: DERIVATION_FROM_SPECIMEN description: An activity that derives a new specimen from an existing one.","title":"Enum: SpecimenCreationActivityTypeEnum"},{"location":"SpecimenCreationActivityTypeEnum/#enum-specimencreationactivitytypeenum","text":"The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) URI: SpecimenCreationActivityTypeEnum","title":"Enum: SpecimenCreationActivityTypeEnum"},{"location":"SpecimenCreationActivityTypeEnum/#permissible-values","text":"Value Meaning Description COLLECTION_FROM_SOURCE None An activity that collects an initial sample directly from a subject / source DERIVATION_FROM_SPECIMEN None An activity that derives a new specimen from an existing one","title":"Permissible Values"},{"location":"SpecimenCreationActivityTypeEnum/#slots","text":"Name Description activity_type The high-level type of creation activity","title":"Slots"},{"location":"SpecimenCreationActivityTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenCreationActivityTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenCreationActivityTypeEnum/#linkml-source","text":"name: SpecimenCreationActivityTypeEnum description: The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: COLLECTION_FROM_SOURCE: text: COLLECTION_FROM_SOURCE description: An activity that collects an initial sample directly from a subject / source. DERIVATION_FROM_SPECIMEN: text: DERIVATION_FROM_SPECIMEN description: An activity that derives a new specimen from an existing one.","title":"LinkML Source"},{"location":"SpecimenProcessingActivity/","text":"Class: SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. URI: bdchm:SpecimenProcessingActivity classDiagram class SpecimenProcessingActivity Entity <|-- SpecimenProcessingActivity SpecimenProcessingActivity : activity_type SpecimenProcessingActivity --> SpecimenProcessingActivityTypeEnum : activity_type SpecimenProcessingActivity : additive SpecimenProcessingActivity --> Substance : additive SpecimenProcessingActivity : date_ended SpecimenProcessingActivity --> TimePoint : date_ended SpecimenProcessingActivity : date_started SpecimenProcessingActivity --> TimePoint : date_started SpecimenProcessingActivity : duration SpecimenProcessingActivity --> Quantity : duration SpecimenProcessingActivity : id SpecimenProcessingActivity : method_type Inheritance Entity SpecimenProcessingActivity Slots Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenProcessingActivityTypeEnum The high-level type of processing activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct date_ended 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct duration 0..* Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to process the specimen direct additive 0..* Substance A type of material or reagent used as input when processing the specimen direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen processing_activity range SpecimenProcessingActivity Comments \"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied). Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenProcessingActivity native bdchm:SpecimenProcessingActivity LinkML Source Direct name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false inlined: true inlined_as_list: true Induced name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: activity_type owner: SpecimenProcessingActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: duration owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false alias: method_type owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenProcessingActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenProcessingActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenProcessingActivity"},{"location":"SpecimenProcessingActivity/#class-specimenprocessingactivity","text":"An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. URI: bdchm:SpecimenProcessingActivity classDiagram class SpecimenProcessingActivity Entity <|-- SpecimenProcessingActivity SpecimenProcessingActivity : activity_type SpecimenProcessingActivity --> SpecimenProcessingActivityTypeEnum : activity_type SpecimenProcessingActivity : additive SpecimenProcessingActivity --> Substance : additive SpecimenProcessingActivity : date_ended SpecimenProcessingActivity --> TimePoint : date_ended SpecimenProcessingActivity : date_started SpecimenProcessingActivity --> TimePoint : date_started SpecimenProcessingActivity : duration SpecimenProcessingActivity --> Quantity : duration SpecimenProcessingActivity : id SpecimenProcessingActivity : method_type","title":"Class: SpecimenProcessingActivity"},{"location":"SpecimenProcessingActivity/#inheritance","text":"Entity SpecimenProcessingActivity","title":"Inheritance"},{"location":"SpecimenProcessingActivity/#slots","text":"Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenProcessingActivityTypeEnum The high-level type of processing activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct date_ended 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct duration 0..* Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to process the specimen direct additive 0..* Substance A type of material or reagent used as input when processing the specimen direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenProcessingActivity/#usages","text":"used by used in type used Specimen processing_activity range SpecimenProcessingActivity","title":"Usages"},{"location":"SpecimenProcessingActivity/#comments","text":"\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).","title":"Comments"},{"location":"SpecimenProcessingActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenProcessingActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenProcessingActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenProcessingActivity native bdchm:SpecimenProcessingActivity","title":"Mappings"},{"location":"SpecimenProcessingActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenProcessingActivity/#direct","text":"name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"SpecimenProcessingActivity/#induced","text":"name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: activity_type owner: SpecimenProcessingActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: duration owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false alias: method_type owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenProcessingActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenProcessingActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenProcessingActivityTypeEnum/","text":"Enum: SpecimenProcessingActivityTypeEnum The high-level type of processing activity performed. URI: SpecimenProcessingActivityTypeEnum Permissible Values Value Meaning Description FIXATION None A processing activity that applies chemicals to preserve biological tissues f... FREEZING None A processing activity that aims to freeze a specimen MOUNTING None A processing activity that aims to secure a specimen or slide in place in pre... PRESERVATION None A processing activity that aims to preserve a specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenProcessingActivityTypeEnum description: The high-level type of processing activity performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FIXATION: text: FIXATION description: A processing activity that applies chemicals to preserve biological tissues from decay due to autolysis or putrefaction FREEZING: text: FREEZING description: A processing activity that aims to freeze a specimen. MOUNTING: text: MOUNTING description: A processing activity that aims to secure a specimen or slide in place in preparation for further examination (usually via microscopy) PRESERVATION: text: PRESERVATION description: A processing activity that aims to preserve a specimen.","title":"Enum: SpecimenProcessingActivityTypeEnum"},{"location":"SpecimenProcessingActivityTypeEnum/#enum-specimenprocessingactivitytypeenum","text":"The high-level type of processing activity performed. URI: SpecimenProcessingActivityTypeEnum","title":"Enum: SpecimenProcessingActivityTypeEnum"},{"location":"SpecimenProcessingActivityTypeEnum/#permissible-values","text":"Value Meaning Description FIXATION None A processing activity that applies chemicals to preserve biological tissues f... FREEZING None A processing activity that aims to freeze a specimen MOUNTING None A processing activity that aims to secure a specimen or slide in place in pre... PRESERVATION None A processing activity that aims to preserve a specimen","title":"Permissible Values"},{"location":"SpecimenProcessingActivityTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenProcessingActivityTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenProcessingActivityTypeEnum/#linkml-source","text":"name: SpecimenProcessingActivityTypeEnum description: The high-level type of processing activity performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FIXATION: text: FIXATION description: A processing activity that applies chemicals to preserve biological tissues from decay due to autolysis or putrefaction FREEZING: text: FREEZING description: A processing activity that aims to freeze a specimen. MOUNTING: text: MOUNTING description: A processing activity that aims to secure a specimen or slide in place in preparation for further examination (usually via microscopy) PRESERVATION: text: PRESERVATION description: A processing activity that aims to preserve a specimen.","title":"LinkML Source"},{"location":"SpecimenQualityObservation/","text":"Class: SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQualityObservation classDiagram class SpecimenQualityObservation Observation <|-- SpecimenQualityObservation SpecimenQualityObservation : age_at_observation SpecimenQualityObservation : associated_participant SpecimenQualityObservation --> Participant : associated_participant SpecimenQualityObservation : associated_visit SpecimenQualityObservation --> Visit : associated_visit SpecimenQualityObservation : category SpecimenQualityObservation : focus SpecimenQualityObservation --> Entity : focus SpecimenQualityObservation : id SpecimenQualityObservation : method_type SpecimenQualityObservation : observation_type SpecimenQualityObservation : performed_by SpecimenQualityObservation --> Organization : performed_by SpecimenQualityObservation : value SpecimenQualityObservation --> ObservationValueString : value Inheritance Entity Observation SpecimenQualityObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueString The result of the observation, encoded as a free-text Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen quality_measure range SpecimenQualityObservation Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenQualityObservation native bdchm:SpecimenQualityObservation LinkML Source Direct name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true Induced name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQualityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQualityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQualityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQualityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQualityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQualityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQualityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQualityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQualityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQualityObservation domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenQualityObservation"},{"location":"SpecimenQualityObservation/#class-specimenqualityobservation","text":"A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQualityObservation classDiagram class SpecimenQualityObservation Observation <|-- SpecimenQualityObservation SpecimenQualityObservation : age_at_observation SpecimenQualityObservation : associated_participant SpecimenQualityObservation --> Participant : associated_participant SpecimenQualityObservation : associated_visit SpecimenQualityObservation --> Visit : associated_visit SpecimenQualityObservation : category SpecimenQualityObservation : focus SpecimenQualityObservation --> Entity : focus SpecimenQualityObservation : id SpecimenQualityObservation : method_type SpecimenQualityObservation : observation_type SpecimenQualityObservation : performed_by SpecimenQualityObservation --> Organization : performed_by SpecimenQualityObservation : value SpecimenQualityObservation --> ObservationValueString : value","title":"Class: SpecimenQualityObservation"},{"location":"SpecimenQualityObservation/#inheritance","text":"Entity Observation SpecimenQualityObservation","title":"Inheritance"},{"location":"SpecimenQualityObservation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueString The result of the observation, encoded as a free-text Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenQualityObservation/#usages","text":"used by used in type used Specimen quality_measure range SpecimenQualityObservation","title":"Usages"},{"location":"SpecimenQualityObservation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQualityObservation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQualityObservation/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenQualityObservation native bdchm:SpecimenQualityObservation","title":"Mappings"},{"location":"SpecimenQualityObservation/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenQualityObservation/#direct","text":"name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true","title":"Direct"},{"location":"SpecimenQualityObservation/#induced","text":"name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQualityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQualityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQualityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQualityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQualityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQualityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQualityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQualityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQualityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQualityObservation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenQualityObservationMethodEnum/","text":"Enum: SpecimenQualityObservationMethodEnum A type of method used in determining the quantity of a specimen. URI: SpecimenQualityObservationMethodEnum Permissible Values Value Meaning Description UV_SPEC None A technique used to measure light absorbance across the ultraviolet and visib... PICO_GREEN None A technique applying the Pico488 fluorescent sensor dye that is used for quan... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenQualityObservationMethodEnum description: A type of method used in determining the quantity of a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: UV_SPEC: text: UV_SPEC description: A technique used to measure light absorbance across the ultraviolet and visible ranges of the electromagnetic spectrum. PICO_GREEN: text: PICO_GREEN description: A technique applying the Pico488 fluorescent sensor dye that is used for quantifying the amount of double-stranded DNA (dsDNA) present in a given sample.","title":"Enum: SpecimenQualityObservationMethodEnum"},{"location":"SpecimenQualityObservationMethodEnum/#enum-specimenqualityobservationmethodenum","text":"A type of method used in determining the quantity of a specimen. URI: SpecimenQualityObservationMethodEnum","title":"Enum: SpecimenQualityObservationMethodEnum"},{"location":"SpecimenQualityObservationMethodEnum/#permissible-values","text":"Value Meaning Description UV_SPEC None A technique used to measure light absorbance across the ultraviolet and visib... PICO_GREEN None A technique applying the Pico488 fluorescent sensor dye that is used for quan...","title":"Permissible Values"},{"location":"SpecimenQualityObservationMethodEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQualityObservationMethodEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQualityObservationMethodEnum/#linkml-source","text":"name: SpecimenQualityObservationMethodEnum description: A type of method used in determining the quantity of a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: UV_SPEC: text: UV_SPEC description: A technique used to measure light absorbance across the ultraviolet and visible ranges of the electromagnetic spectrum. PICO_GREEN: text: PICO_GREEN description: A technique applying the Pico488 fluorescent sensor dye that is used for quantifying the amount of double-stranded DNA (dsDNA) present in a given sample.","title":"LinkML Source"},{"location":"SpecimenQualityObservationTypeEnum/","text":"Enum: SpecimenQualityObservationTypeEnum Types of measurements that reflect the quality of a specimen or its suitability for use. URI: SpecimenQualityObservationTypeEnum Permissible Values Value Meaning Description A260_A280_RATIO None Ratio of absorbance measured at a wavelength of 260 over that at a wavelength... RIBOSOMAL_RNA_28S_16S_RATIO None Ratio of quantity of 28s RNA over that of 16s RNA Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenQualityObservationTypeEnum description: Types of measurements that reflect the quality of a specimen or its suitability for use. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: A260_A280_RATIO: text: A260_A280_RATIO description: Ratio of absorbance measured at a wavelength of 260 over that at a wavelength of 280. RIBOSOMAL_RNA_28S_16S_RATIO: text: RIBOSOMAL_RNA_28S_16S_RATIO description: Ratio of quantity of 28s RNA over that of 16s RNA.","title":"Enum: SpecimenQualityObservationTypeEnum"},{"location":"SpecimenQualityObservationTypeEnum/#enum-specimenqualityobservationtypeenum","text":"Types of measurements that reflect the quality of a specimen or its suitability for use. URI: SpecimenQualityObservationTypeEnum","title":"Enum: SpecimenQualityObservationTypeEnum"},{"location":"SpecimenQualityObservationTypeEnum/#permissible-values","text":"Value Meaning Description A260_A280_RATIO None Ratio of absorbance measured at a wavelength of 260 over that at a wavelength... RIBOSOMAL_RNA_28S_16S_RATIO None Ratio of quantity of 28s RNA over that of 16s RNA","title":"Permissible Values"},{"location":"SpecimenQualityObservationTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQualityObservationTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQualityObservationTypeEnum/#linkml-source","text":"name: SpecimenQualityObservationTypeEnum description: Types of measurements that reflect the quality of a specimen or its suitability for use. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: A260_A280_RATIO: text: A260_A280_RATIO description: Ratio of absorbance measured at a wavelength of 260 over that at a wavelength of 280. RIBOSOMAL_RNA_28S_16S_RATIO: text: RIBOSOMAL_RNA_28S_16S_RATIO description: Ratio of quantity of 28s RNA over that of 16s RNA.","title":"LinkML Source"},{"location":"SpecimenQuantityObservation/","text":"Class: SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQuantityObservation classDiagram class SpecimenQuantityObservation Observation <|-- SpecimenQuantityObservation SpecimenQuantityObservation : age_at_observation SpecimenQuantityObservation : associated_participant SpecimenQuantityObservation --> Participant : associated_participant SpecimenQuantityObservation : associated_visit SpecimenQuantityObservation --> Visit : associated_visit SpecimenQuantityObservation : category SpecimenQuantityObservation : focus SpecimenQuantityObservation --> Entity : focus SpecimenQuantityObservation : id SpecimenQuantityObservation : method_type SpecimenQuantityObservation : observation_type SpecimenQuantityObservation : performed_by SpecimenQuantityObservation --> Organization : performed_by SpecimenQuantityObservation : value SpecimenQuantityObservation --> ObservationValueQuantity : value Inheritance Entity Observation SpecimenQuantityObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen quantity_measure range SpecimenQuantityObservation Comments At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenQuantityObservation native bdchm:SpecimenQuantityObservation LinkML Source Direct name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true Induced name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQuantityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQuantityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQuantityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQuantityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQuantityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQuantityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQuantityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQuantityObservation domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenQuantityObservation"},{"location":"SpecimenQuantityObservation/#class-specimenquantityobservation","text":"A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQuantityObservation classDiagram class SpecimenQuantityObservation Observation <|-- SpecimenQuantityObservation SpecimenQuantityObservation : age_at_observation SpecimenQuantityObservation : associated_participant SpecimenQuantityObservation --> Participant : associated_participant SpecimenQuantityObservation : associated_visit SpecimenQuantityObservation --> Visit : associated_visit SpecimenQuantityObservation : category SpecimenQuantityObservation : focus SpecimenQuantityObservation --> Entity : focus SpecimenQuantityObservation : id SpecimenQuantityObservation : method_type SpecimenQuantityObservation : observation_type SpecimenQuantityObservation : performed_by SpecimenQuantityObservation --> Organization : performed_by SpecimenQuantityObservation : value SpecimenQuantityObservation --> ObservationValueQuantity : value","title":"Class: SpecimenQuantityObservation"},{"location":"SpecimenQuantityObservation/#inheritance","text":"Entity Observation SpecimenQuantityObservation","title":"Inheritance"},{"location":"SpecimenQuantityObservation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenQuantityObservation/#usages","text":"used by used in type used Specimen quantity_measure range SpecimenQuantityObservation","title":"Usages"},{"location":"SpecimenQuantityObservation/#comments","text":"At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data.","title":"Comments"},{"location":"SpecimenQuantityObservation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQuantityObservation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQuantityObservation/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenQuantityObservation native bdchm:SpecimenQuantityObservation","title":"Mappings"},{"location":"SpecimenQuantityObservation/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenQuantityObservation/#direct","text":"name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true","title":"Direct"},{"location":"SpecimenQuantityObservation/#induced","text":"name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQuantityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQuantityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQuantityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQuantityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQuantityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQuantityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQuantityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQuantityObservation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenQuantityObservationTypeEnum/","text":"Enum: SpecimenQuantityObservationTypeEnum Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. URI: SpecimenQuantityObservationTypeEnum Permissible Values Value Meaning Description WEIGHT None The current weight of the specimen, at the time of recording (as opposed to a... VOLUME None The current total volume of the specimen, at the time of recording CONCENTRATION None The concentration of an extracted analyte that is present in a specimen (spec... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenQuantityObservationTypeEnum description: Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: WEIGHT: text: WEIGHT description: The current weight of the specimen, at the time of recording (as opposed to an initial weight before its processing or portioning). VOLUME: text: VOLUME description: The current total volume of the specimen, at the time of recording. CONCENTRATION: text: CONCENTRATION description: The concentration of an extracted analyte that is present in a specimen (specifically, in a specimen of type 'analyte', or an 'aliquot' derived from an analyte). For example, the concentration of DNA in a specimen created through extracting DNA from a blood sample.","title":"Enum: SpecimenQuantityObservationTypeEnum"},{"location":"SpecimenQuantityObservationTypeEnum/#enum-specimenquantityobservationtypeenum","text":"Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. URI: SpecimenQuantityObservationTypeEnum","title":"Enum: SpecimenQuantityObservationTypeEnum"},{"location":"SpecimenQuantityObservationTypeEnum/#permissible-values","text":"Value Meaning Description WEIGHT None The current weight of the specimen, at the time of recording (as opposed to a... VOLUME None The current total volume of the specimen, at the time of recording CONCENTRATION None The concentration of an extracted analyte that is present in a specimen (spec...","title":"Permissible Values"},{"location":"SpecimenQuantityObservationTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQuantityObservationTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQuantityObservationTypeEnum/#linkml-source","text":"name: SpecimenQuantityObservationTypeEnum description: Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: WEIGHT: text: WEIGHT description: The current weight of the specimen, at the time of recording (as opposed to an initial weight before its processing or portioning). VOLUME: text: VOLUME description: The current total volume of the specimen, at the time of recording. CONCENTRATION: text: CONCENTRATION description: The concentration of an extracted analyte that is present in a specimen (specifically, in a specimen of type 'analyte', or an 'aliquot' derived from an analyte). For example, the concentration of DNA in a specimen created through extracting DNA from a blood sample.","title":"LinkML Source"},{"location":"SpecimenStorageActivity/","text":"Class: SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. URI: bdchm:SpecimenStorageActivity classDiagram class SpecimenStorageActivity Entity <|-- SpecimenStorageActivity SpecimenStorageActivity : container SpecimenStorageActivity --> SpecimenContainer : container SpecimenStorageActivity : date_ended SpecimenStorageActivity --> TimePoint : date_ended SpecimenStorageActivity : date_started SpecimenStorageActivity --> TimePoint : date_started SpecimenStorageActivity : duration SpecimenStorageActivity --> Quantity : duration SpecimenStorageActivity : id SpecimenStorageActivity : method_type Inheritance Entity SpecimenStorageActivity Slots Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a storage event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a storage event) direct duration 0..1 Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to store the specimen direct container 0..* SpecimenContainer A container in which the specimen is held or affixed during its storage direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen storage_activity range SpecimenStorageActivity Comments Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenStorageActivity native bdchm:SpecimenStorageActivity LinkML Source Direct name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenContainer required: false inlined: true inlined_as_list: true Induced name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: duration owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false alias: method_type owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenStorageActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenStorageActivity"},{"location":"SpecimenStorageActivity/#class-specimenstorageactivity","text":"An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. URI: bdchm:SpecimenStorageActivity classDiagram class SpecimenStorageActivity Entity <|-- SpecimenStorageActivity SpecimenStorageActivity : container SpecimenStorageActivity --> SpecimenContainer : container SpecimenStorageActivity : date_ended SpecimenStorageActivity --> TimePoint : date_ended SpecimenStorageActivity : date_started SpecimenStorageActivity --> TimePoint : date_started SpecimenStorageActivity : duration SpecimenStorageActivity --> Quantity : duration SpecimenStorageActivity : id SpecimenStorageActivity : method_type","title":"Class: SpecimenStorageActivity"},{"location":"SpecimenStorageActivity/#inheritance","text":"Entity SpecimenStorageActivity","title":"Inheritance"},{"location":"SpecimenStorageActivity/#slots","text":"Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a storage event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a storage event) direct duration 0..1 Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to store the specimen direct container 0..* SpecimenContainer A container in which the specimen is held or affixed during its storage direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenStorageActivity/#usages","text":"used by used in type used Specimen storage_activity range SpecimenStorageActivity","title":"Usages"},{"location":"SpecimenStorageActivity/#comments","text":"Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each.","title":"Comments"},{"location":"SpecimenStorageActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenStorageActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenStorageActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenStorageActivity native bdchm:SpecimenStorageActivity","title":"Mappings"},{"location":"SpecimenStorageActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenStorageActivity/#direct","text":"name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenContainer required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"SpecimenStorageActivity/#induced","text":"name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: duration owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false alias: method_type owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenStorageActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenTransportActivity/","text":"Class: SpecimenTransportActivity An activity through which a specimen is transported between locations or organizations. URI: bdchm:SpecimenTransportActivity classDiagram class SpecimenTransportActivity Entity <|-- SpecimenTransportActivity SpecimenTransportActivity : date_ended SpecimenTransportActivity --> TimePoint : date_ended SpecimenTransportActivity : date_started SpecimenTransportActivity --> TimePoint : date_started SpecimenTransportActivity : duration SpecimenTransportActivity : id SpecimenTransportActivity : transport_destination SpecimenTransportActivity --> Organization : transport_destination SpecimenTransportActivity : transport_origin SpecimenTransportActivity --> Organization : transport_origin Inheritance Entity SpecimenTransportActivity Slots Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a transport event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a transport event) direct duration 0..* String The length of time over which the activity was performed direct transport_origin 0..1 Organization An organization (facility, site, lab, etc) from which the specimen was transp... direct transport_destination 0..1 Organization An organization (facility, site, lab, etc) to which the specimen is delivered... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen transport_activity range SpecimenTransportActivity Comments Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenTransportActivity native bdchm:SpecimenTransportActivity LinkML Source Direct name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false Induced name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: duration owner: SpecimenTransportActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_origin owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenTransportActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenTransportActivity"},{"location":"SpecimenTransportActivity/#class-specimentransportactivity","text":"An activity through which a specimen is transported between locations or organizations. URI: bdchm:SpecimenTransportActivity classDiagram class SpecimenTransportActivity Entity <|-- SpecimenTransportActivity SpecimenTransportActivity : date_ended SpecimenTransportActivity --> TimePoint : date_ended SpecimenTransportActivity : date_started SpecimenTransportActivity --> TimePoint : date_started SpecimenTransportActivity : duration SpecimenTransportActivity : id SpecimenTransportActivity : transport_destination SpecimenTransportActivity --> Organization : transport_destination SpecimenTransportActivity : transport_origin SpecimenTransportActivity --> Organization : transport_origin","title":"Class: SpecimenTransportActivity"},{"location":"SpecimenTransportActivity/#inheritance","text":"Entity SpecimenTransportActivity","title":"Inheritance"},{"location":"SpecimenTransportActivity/#slots","text":"Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a transport event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a transport event) direct duration 0..* String The length of time over which the activity was performed direct transport_origin 0..1 Organization An organization (facility, site, lab, etc) from which the specimen was transp... direct transport_destination 0..1 Organization An organization (facility, site, lab, etc) to which the specimen is delivered... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenTransportActivity/#usages","text":"used by used in type used Specimen transport_activity range SpecimenTransportActivity","title":"Usages"},{"location":"SpecimenTransportActivity/#comments","text":"Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each.","title":"Comments"},{"location":"SpecimenTransportActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenTransportActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenTransportActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenTransportActivity native bdchm:SpecimenTransportActivity","title":"Mappings"},{"location":"SpecimenTransportActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenTransportActivity/#direct","text":"name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false","title":"Direct"},{"location":"SpecimenTransportActivity/#induced","text":"name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: duration owner: SpecimenTransportActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_origin owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenTransportActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenTypeEnum/","text":"Enum: SpecimenTypeEnum A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: SpecimenTypeEnum Permissible Values Value Meaning Description ALIQUOT None A specimen that results from the division of some parent specimen into equal ... ANALYTE None A specimen generated through the extraction of a specified class of substance... FRESH_SPECIMEN None A specimen representing the material that was directly collected from a subje... PORTION None A physical sub-part taken from an existing specimen SLIDE None A specimen that is mounted on a slide or coverslip for microscopic analysis Slots Name Description specimen_type The high-level type of the specimen, based on its derivation provenance (i Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenTypeEnum description: A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIQUOT: text: ALIQUOT description: A specimen that results from the division of some parent specimen into equal amounts for downstream analysis. ANALYTE: text: ANALYTE description: A specimen generated through the extraction of a specified class of substance/chemical (e.g. DNA, RNA, protein) from a parent specimen, which is stored in solution as an analyte. FRESH_SPECIMEN: text: FRESH_SPECIMEN description: A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen). PORTION: text: PORTION description: A physical sub-part taken from an existing specimen. SLIDE: text: SLIDE description: A specimen that is mounted on a slide or coverslip for microscopic analysis.","title":"Enum: SpecimenTypeEnum"},{"location":"SpecimenTypeEnum/#enum-specimentypeenum","text":"A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: SpecimenTypeEnum","title":"Enum: SpecimenTypeEnum"},{"location":"SpecimenTypeEnum/#permissible-values","text":"Value Meaning Description ALIQUOT None A specimen that results from the division of some parent specimen into equal ... ANALYTE None A specimen generated through the extraction of a specified class of substance... FRESH_SPECIMEN None A specimen representing the material that was directly collected from a subje... PORTION None A physical sub-part taken from an existing specimen SLIDE None A specimen that is mounted on a slide or coverslip for microscopic analysis","title":"Permissible Values"},{"location":"SpecimenTypeEnum/#slots","text":"Name Description specimen_type The high-level type of the specimen, based on its derivation provenance (i","title":"Slots"},{"location":"SpecimenTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenTypeEnum/#linkml-source","text":"name: SpecimenTypeEnum description: A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIQUOT: text: ALIQUOT description: A specimen that results from the division of some parent specimen into equal amounts for downstream analysis. ANALYTE: text: ANALYTE description: A specimen generated through the extraction of a specified class of substance/chemical (e.g. DNA, RNA, protein) from a parent specimen, which is stored in solution as an analyte. FRESH_SPECIMEN: text: FRESH_SPECIMEN description: A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen). PORTION: text: PORTION description: A physical sub-part taken from an existing specimen. SLIDE: text: SLIDE description: A specimen that is mounted on a slide or coverslip for microscopic analysis.","title":"LinkML Source"},{"location":"String/","text":"Type: String A character string URI: xsd:string base : str uri : xsd:string Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: String"},{"location":"String/#type-string","text":"A character string URI: xsd:string base : str uri : xsd:string","title":"Type: String"},{"location":"String/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"String/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Substance/","text":"Class: Substance A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. URI: bdchm:Substance classDiagram class Substance Entity <|-- Substance Substance : id Substance : role Substance : substance_quantity Substance --> Quantity : substance_quantity Substance : substance_type Inheritance Entity Substance Slots Name Cardinality and Range Description Inheritance substance_type 0..1 String The specific type of the substance - at as granular a level as possible direct role 0..* String A role played by the substance in a particular application (e direct substance_quantity 0..1 Quantity The quantity of substance this instance stands for direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used SpecimenContainer additive range Substance SpecimenCreationActivity additive range Substance SpecimenProcessingActivity additive range Substance Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Substance native bdchm:Substance LinkML Source Direct name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false Induced name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: substance_quantity owner: Substance domain_of: - Substance range: Quantity required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Substance domain_of: - Entity range: uriorcurie required: true","title":"Class: Substance"},{"location":"Substance/#class-substance","text":"A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. URI: bdchm:Substance classDiagram class Substance Entity <|-- Substance Substance : id Substance : role Substance : substance_quantity Substance --> Quantity : substance_quantity Substance : substance_type","title":"Class: Substance"},{"location":"Substance/#inheritance","text":"Entity Substance","title":"Inheritance"},{"location":"Substance/#slots","text":"Name Cardinality and Range Description Inheritance substance_type 0..1 String The specific type of the substance - at as granular a level as possible direct role 0..* String A role played by the substance in a particular application (e direct substance_quantity 0..1 Quantity The quantity of substance this instance stands for direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Substance/#usages","text":"used by used in type used SpecimenContainer additive range Substance SpecimenCreationActivity additive range Substance SpecimenProcessingActivity additive range Substance","title":"Usages"},{"location":"Substance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Substance/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Substance/#mappings","text":"Mapping Type Mapped Value self bdchm:Substance native bdchm:Substance","title":"Mappings"},{"location":"Substance/#linkml-source","text":"","title":"LinkML Source"},{"location":"Substance/#direct","text":"name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false","title":"Direct"},{"location":"Substance/#induced","text":"name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: substance_quantity owner: Substance domain_of: - Substance range: Quantity required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Substance domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Time/","text":"Type: Time A time object represents a (local) time of day, independent of any particular day URI: xsd:time base : XSDTime uri : xsd:time repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Time"},{"location":"Time/#type-time","text":"A time object represents a (local) time of day, independent of any particular day URI: xsd:time base : XSDTime uri : xsd:time repr : str","title":"Type: Time"},{"location":"Time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Time/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"TimePeriod/","text":"Class: TimePeriod A period of time between a start and end time point. URI: bdchm:TimePeriod classDiagram class TimePeriod TimePeriod : period_end TimePeriod --> TimePoint : period_end TimePeriod : period_start TimePeriod --> TimePoint : period_start Slots Name Cardinality and Range Description Inheritance period_start 0..1 TimePoint When a period of time started direct period_end 0..1 TimePoint When a period of time ended direct Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:TimePeriod native bdchm:TimePeriod LinkML Source Direct name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint Induced name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_start owner: TimePeriod domain_of: - TimePeriod range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_end owner: TimePeriod domain_of: - TimePeriod range: TimePoint","title":"Class: TimePeriod"},{"location":"TimePeriod/#class-timeperiod","text":"A period of time between a start and end time point. URI: bdchm:TimePeriod classDiagram class TimePeriod TimePeriod : period_end TimePeriod --> TimePoint : period_end TimePeriod : period_start TimePeriod --> TimePoint : period_start","title":"Class: TimePeriod"},{"location":"TimePeriod/#slots","text":"Name Cardinality and Range Description Inheritance period_start 0..1 TimePoint When a period of time started direct period_end 0..1 TimePoint When a period of time ended direct","title":"Slots"},{"location":"TimePeriod/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"TimePeriod/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"TimePeriod/#mappings","text":"Mapping Type Mapped Value self bdchm:TimePeriod native bdchm:TimePeriod","title":"Mappings"},{"location":"TimePeriod/#linkml-source","text":"","title":"LinkML Source"},{"location":"TimePeriod/#direct","text":"name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint","title":"Direct"},{"location":"TimePeriod/#induced","text":"name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_start owner: TimePeriod domain_of: - TimePeriod range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_end owner: TimePeriod domain_of: - TimePeriod range: TimePoint","title":"Induced"},{"location":"TimePoint/","text":"Class: TimePoint A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. URI: bdchm:TimePoint classDiagram class TimePoint Entity <|-- TimePoint TimePoint : date_time TimePoint : event_type TimePoint : id TimePoint : index_time_point TimePoint --> TimePoint : index_time_point TimePoint : offset_from_index Inheritance Entity TimePoint Slots Name Cardinality and Range Description Inheritance date_time 0..1 Datetime An explicitly specified timepoint described in terms of a date and optionally... direct index_time_point 0..1 TimePoint Another TimePoint from which this point is offset direct offset_from_index 0..1 Integer A quantity of time that, together with the index date or event, can be used t... direct event_type 0..1 String An event that occurred at the point in time specified by this TimePoint direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used ResearchStudy date_started range TimePoint ResearchStudy date_ended range TimePoint ResearchStudy associated_timepoint range TimePoint Consent valid_from range TimePoint Consent valid_to range TimePoint TimePoint index_time_point range TimePoint TimePeriod period_start range TimePoint TimePeriod period_end range TimePoint QuestionnaireResponseValueTimePoint value range TimePoint SpecimenCreationActivity date_started range TimePoint SpecimenCreationActivity date_ended range TimePoint SpecimenProcessingActivity date_started range TimePoint SpecimenProcessingActivity date_ended range TimePoint SpecimenStorageActivity date_started range TimePoint SpecimenStorageActivity date_ended range TimePoint SpecimenTransportActivity date_started range TimePoint SpecimenTransportActivity date_ended range TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:TimePoint native bdchm:TimePoint LinkML Source Direct name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string Induced name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_time_point owner: TimePoint domain_of: - TimePoint range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: offset_from_index owner: TimePoint domain_of: - TimePoint range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: TimePoint domain_of: - Entity range: uriorcurie required: true","title":"Class: TimePoint"},{"location":"TimePoint/#class-timepoint","text":"A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. URI: bdchm:TimePoint classDiagram class TimePoint Entity <|-- TimePoint TimePoint : date_time TimePoint : event_type TimePoint : id TimePoint : index_time_point TimePoint --> TimePoint : index_time_point TimePoint : offset_from_index","title":"Class: TimePoint"},{"location":"TimePoint/#inheritance","text":"Entity TimePoint","title":"Inheritance"},{"location":"TimePoint/#slots","text":"Name Cardinality and Range Description Inheritance date_time 0..1 Datetime An explicitly specified timepoint described in terms of a date and optionally... direct index_time_point 0..1 TimePoint Another TimePoint from which this point is offset direct offset_from_index 0..1 Integer A quantity of time that, together with the index date or event, can be used t... direct event_type 0..1 String An event that occurred at the point in time specified by this TimePoint direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"TimePoint/#usages","text":"used by used in type used ResearchStudy date_started range TimePoint ResearchStudy date_ended range TimePoint ResearchStudy associated_timepoint range TimePoint Consent valid_from range TimePoint Consent valid_to range TimePoint TimePoint index_time_point range TimePoint TimePeriod period_start range TimePoint TimePeriod period_end range TimePoint QuestionnaireResponseValueTimePoint value range TimePoint SpecimenCreationActivity date_started range TimePoint SpecimenCreationActivity date_ended range TimePoint SpecimenProcessingActivity date_started range TimePoint SpecimenProcessingActivity date_ended range TimePoint SpecimenStorageActivity date_started range TimePoint SpecimenStorageActivity date_ended range TimePoint SpecimenTransportActivity date_started range TimePoint SpecimenTransportActivity date_ended range TimePoint","title":"Usages"},{"location":"TimePoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"TimePoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"TimePoint/#mappings","text":"Mapping Type Mapped Value self bdchm:TimePoint native bdchm:TimePoint","title":"Mappings"},{"location":"TimePoint/#linkml-source","text":"","title":"LinkML Source"},{"location":"TimePoint/#direct","text":"name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string","title":"Direct"},{"location":"TimePoint/#induced","text":"name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_time_point owner: TimePoint domain_of: - TimePoint range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: offset_from_index owner: TimePoint domain_of: - TimePoint range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: TimePoint domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"UnitOfMeasurementEnum/","text":"Enum: UnitOfMeasurementEnum Standard units of measurement from the Units of Measurement (UOM) ontology . Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. URI: UnitOfMeasurementEnum This is a dynamic enum Slots Name Description unit A coded or free text (in the Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: UnitOfMeasurementEnum description: Standard units of measurement from the [Units of Measurement (UOM) ontology](https://units-of-measurement.org/). Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: UOM","title":"Enum: UnitOfMeasurementEnum"},{"location":"UnitOfMeasurementEnum/#enum-unitofmeasurementenum","text":"Standard units of measurement from the Units of Measurement (UOM) ontology . Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. URI: UnitOfMeasurementEnum This is a dynamic enum","title":"Enum: UnitOfMeasurementEnum"},{"location":"UnitOfMeasurementEnum/#slots","text":"Name Description unit A coded or free text (in the","title":"Slots"},{"location":"UnitOfMeasurementEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"UnitOfMeasurementEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"UnitOfMeasurementEnum/#linkml-source","text":"name: UnitOfMeasurementEnum description: Standard units of measurement from the [Units of Measurement (UOM) ontology](https://units-of-measurement.org/). Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: UOM","title":"LinkML Source"},{"location":"Uri/","text":"Type: Uri a complete URI URI: xsd:anyURI base : URI uri : xsd:anyURI repr : str Comments in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Uri"},{"location":"Uri/#type-uri","text":"a complete URI URI: xsd:anyURI base : URI uri : xsd:anyURI repr : str","title":"Type: Uri"},{"location":"Uri/#comments","text":"in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node","title":"Comments"},{"location":"Uri/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uri/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Uriorcurie/","text":"Type: Uriorcurie a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#type-uriorcurie","text":"a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uriorcurie/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VertebrateBreedEnum/","text":"Enum: VertebrateBreedEnum A constrained set of enumerative values containing the VBO values for vertebrate breeds. URI: VertebrateBreedEnum This is a dynamic enum Slots Name Description breed A label given to a group of animals homogeneous in appearance and other chara... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VertebrateBreedEnum description: A constrained set of enumerative values containing the VBO values for vertebrate breeds. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:vbo source_nodes: - VBO:0400000 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: VertebrateBreedEnum"},{"location":"VertebrateBreedEnum/#enum-vertebratebreedenum","text":"A constrained set of enumerative values containing the VBO values for vertebrate breeds. URI: VertebrateBreedEnum This is a dynamic enum","title":"Enum: VertebrateBreedEnum"},{"location":"VertebrateBreedEnum/#slots","text":"Name Description breed A label given to a group of animals homogeneous in appearance and other chara...","title":"Slots"},{"location":"VertebrateBreedEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VertebrateBreedEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VertebrateBreedEnum/#linkml-source","text":"name: VertebrateBreedEnum description: A constrained set of enumerative values containing the VBO values for vertebrate breeds. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:vbo source_nodes: - VBO:0400000 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Visit/","text":"Class: Visit Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) URI: bdchm:Visit classDiagram class Visit Entity <|-- Visit Visit : age_at_visit_end Visit : age_at_visit_start Visit : associated_participant Visit --> Participant : associated_participant Visit : id Visit : visit_category Visit --> VisitCategoryEnum : visit_category Visit : visit_provenance Visit --> VisitProvenanceEnum : visit_provenance Inheritance Entity Visit Slots Name Cardinality and Range Description Inheritance visit_category 0..1 VisitCategoryEnum A value representing the kind (or category) of visit, like inpatient or outpa... direct age_at_visit_start 0..1 Integer The age of the Participant (in days) at the start of the Visit direct age_at_visit_end 0..1 Integer The age of the Participant (in days) at the end of the Visit direct visit_provenance 0..1 VisitProvenanceEnum A value representing the provenance of the visit record, or where the record ... direct associated_participant 0..1 Participant A reference to the Participant for whom this Visit occurred direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used QuestionnaireResponse associated_visit range Visit Condition associated_visit range Visit Procedure associated_visit range Visit DrugExposure associated_visit range Visit DeviceExposure associated_visit range Visit DimensionalObservation associated_visit range Visit SpecimenQualityObservation associated_visit range Visit SpecimenQuantityObservation associated_visit range Visit Observation associated_visit range Visit Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Visit native bdchm:Visit LinkML Source Direct name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant Induced name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_start owner: Visit domain_of: - Visit range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_end owner: Visit domain_of: - Visit range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Visit domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Visit domain_of: - Entity range: uriorcurie required: true","title":"Class: Visit"},{"location":"Visit/#class-visit","text":"Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) URI: bdchm:Visit classDiagram class Visit Entity <|-- Visit Visit : age_at_visit_end Visit : age_at_visit_start Visit : associated_participant Visit --> Participant : associated_participant Visit : id Visit : visit_category Visit --> VisitCategoryEnum : visit_category Visit : visit_provenance Visit --> VisitProvenanceEnum : visit_provenance","title":"Class: Visit"},{"location":"Visit/#inheritance","text":"Entity Visit","title":"Inheritance"},{"location":"Visit/#slots","text":"Name Cardinality and Range Description Inheritance visit_category 0..1 VisitCategoryEnum A value representing the kind (or category) of visit, like inpatient or outpa... direct age_at_visit_start 0..1 Integer The age of the Participant (in days) at the start of the Visit direct age_at_visit_end 0..1 Integer The age of the Participant (in days) at the end of the Visit direct visit_provenance 0..1 VisitProvenanceEnum A value representing the provenance of the visit record, or where the record ... direct associated_participant 0..1 Participant A reference to the Participant for whom this Visit occurred direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Visit/#usages","text":"used by used in type used QuestionnaireResponse associated_visit range Visit Condition associated_visit range Visit Procedure associated_visit range Visit DrugExposure associated_visit range Visit DeviceExposure associated_visit range Visit DimensionalObservation associated_visit range Visit SpecimenQualityObservation associated_visit range Visit SpecimenQuantityObservation associated_visit range Visit Observation associated_visit range Visit","title":"Usages"},{"location":"Visit/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Visit/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Visit/#mappings","text":"Mapping Type Mapped Value self bdchm:Visit native bdchm:Visit","title":"Mappings"},{"location":"Visit/#linkml-source","text":"","title":"LinkML Source"},{"location":"Visit/#direct","text":"name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant","title":"Direct"},{"location":"Visit/#induced","text":"name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_start owner: Visit domain_of: - Visit range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_end owner: Visit domain_of: - Visit range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Visit domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Visit domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"VisitCategoryEnum/","text":"Enum: VisitCategoryEnum A constrained set of enumerative values containing the OMOP values for visit categories. URI: VisitCategoryEnum Permissible Values Value Meaning Description INPATIENT OMOP:9201 Person visiting hospital, at a care stie, in bed, for duration of more than o... EMERGENCY_ROOM OMOP:9203 Person visiting dedicated healthcare institution for treating emergencies, at... EMERGENCY_ROOM_AND_INPATIENT OMOP:262 Person visiting ER followed by a subsequent Inpatient Visit, where Emergency ... NON_HOSPITAL_INSTITUTION OMOP:42898160 Person visiting dedicated institution for reasons of poor health, at a Care S... OUTPATIENT OMOP:9202 Person visiting dedicated ambulatory healthcare institution, at a Care Site, ... HOME OMOP:581476 Provider visiting Person, without a Care Site, within one day, delivering ser... TELEHEALTH OMOP:5083 Patient engages with Provider through communication media PHARMACY OMOP:581458 Person visiting pharmacy for dispensing of Drug, at a Care Site, within one d... LABORATORY OMOP:32036 Patient visiting dedicated institution, at a Care Site, within one day, for t... AMBULANCE OMOP:581478 Person using transportation service for the purpose of initiating one of the ... CASE_MANAGEMENT OMOP:38004193 Person interacting with healthcare system, without a Care Site, within a day,... Slots Name Description visit_category A value representing the kind (or category) of visit, like inpatient or outpa... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VisitCategoryEnum description: A constrained set of enumerative values containing the OMOP values for visit categories. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: INPATIENT: text: INPATIENT description: Person visiting hospital, at a care stie, in bed, for duration of more than one day, with physicians and other Providers permanently available to deliver service around the clock meaning: OMOP:9201 EMERGENCY_ROOM: text: EMERGENCY_ROOM description: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within one day, with physicians and Providers permanently available to deliver service around the clock meaning: OMOP:9203 EMERGENCY_ROOM_AND_INPATIENT: text: EMERGENCY_ROOM_AND_INPATIENT description: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of hospital, and transition from the ER to other hospital departments is undefined meaning: OMOP:262 NON_HOSPITAL_INSTITUTION: text: NON_HOSPITAL_INSTITUTION description: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock meaning: OMOP:42898160 OUTPATIENT: text: OUTPATIENT description: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, without bed, with physicians or medical Providers delivering service during Visit meaning: OMOP:9202 HOME: text: HOME description: Provider visiting Person, without a Care Site, within one day, delivering service meaning: OMOP:581476 TELEHEALTH: text: TELEHEALTH description: Patient engages with Provider through communication media meaning: OMOP:5083 PHARMACY: text: PHARMACY description: Person visiting pharmacy for dispensing of Drug, at a Care Site, within one day meaning: OMOP:581458 LABORATORY: text: LABORATORY description: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a Measurement. meaning: OMOP:32036 AMBULANCE: text: AMBULANCE description: Person using transportation service for the purpose of initiating one of the other Visits, without a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service meaning: OMOP:581478 CASE_MANAGEMENT: text: CASE_MANAGEMENT description: Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes meaning: OMOP:38004193","title":"Enum: VisitCategoryEnum"},{"location":"VisitCategoryEnum/#enum-visitcategoryenum","text":"A constrained set of enumerative values containing the OMOP values for visit categories. URI: VisitCategoryEnum","title":"Enum: VisitCategoryEnum"},{"location":"VisitCategoryEnum/#permissible-values","text":"Value Meaning Description INPATIENT OMOP:9201 Person visiting hospital, at a care stie, in bed, for duration of more than o... EMERGENCY_ROOM OMOP:9203 Person visiting dedicated healthcare institution for treating emergencies, at... EMERGENCY_ROOM_AND_INPATIENT OMOP:262 Person visiting ER followed by a subsequent Inpatient Visit, where Emergency ... NON_HOSPITAL_INSTITUTION OMOP:42898160 Person visiting dedicated institution for reasons of poor health, at a Care S... OUTPATIENT OMOP:9202 Person visiting dedicated ambulatory healthcare institution, at a Care Site, ... HOME OMOP:581476 Provider visiting Person, without a Care Site, within one day, delivering ser... TELEHEALTH OMOP:5083 Patient engages with Provider through communication media PHARMACY OMOP:581458 Person visiting pharmacy for dispensing of Drug, at a Care Site, within one d... LABORATORY OMOP:32036 Patient visiting dedicated institution, at a Care Site, within one day, for t... AMBULANCE OMOP:581478 Person using transportation service for the purpose of initiating one of the ... CASE_MANAGEMENT OMOP:38004193 Person interacting with healthcare system, without a Care Site, within a day,...","title":"Permissible Values"},{"location":"VisitCategoryEnum/#slots","text":"Name Description visit_category A value representing the kind (or category) of visit, like inpatient or outpa...","title":"Slots"},{"location":"VisitCategoryEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VisitCategoryEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VisitCategoryEnum/#linkml-source","text":"name: VisitCategoryEnum description: A constrained set of enumerative values containing the OMOP values for visit categories. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: INPATIENT: text: INPATIENT description: Person visiting hospital, at a care stie, in bed, for duration of more than one day, with physicians and other Providers permanently available to deliver service around the clock meaning: OMOP:9201 EMERGENCY_ROOM: text: EMERGENCY_ROOM description: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within one day, with physicians and Providers permanently available to deliver service around the clock meaning: OMOP:9203 EMERGENCY_ROOM_AND_INPATIENT: text: EMERGENCY_ROOM_AND_INPATIENT description: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of hospital, and transition from the ER to other hospital departments is undefined meaning: OMOP:262 NON_HOSPITAL_INSTITUTION: text: NON_HOSPITAL_INSTITUTION description: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock meaning: OMOP:42898160 OUTPATIENT: text: OUTPATIENT description: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, without bed, with physicians or medical Providers delivering service during Visit meaning: OMOP:9202 HOME: text: HOME description: Provider visiting Person, without a Care Site, within one day, delivering service meaning: OMOP:581476 TELEHEALTH: text: TELEHEALTH description: Patient engages with Provider through communication media meaning: OMOP:5083 PHARMACY: text: PHARMACY description: Person visiting pharmacy for dispensing of Drug, at a Care Site, within one day meaning: OMOP:581458 LABORATORY: text: LABORATORY description: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a Measurement. meaning: OMOP:32036 AMBULANCE: text: AMBULANCE description: Person using transportation service for the purpose of initiating one of the other Visits, without a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service meaning: OMOP:581478 CASE_MANAGEMENT: text: CASE_MANAGEMENT description: Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes meaning: OMOP:38004193","title":"LinkML Source"},{"location":"VisitProvenanceEnum/","text":"Enum: VisitProvenanceEnum A constrained set of enumerative values containing the OMOP values for visit provenance. URI: VisitProvenanceEnum Permissible Values Value Meaning Description CASE_REPORT_FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM_AUTHORIZATION OMOP:32811 Claim authorization CLAIM_DISCHARGE_RECORD OMOP:32812 Claim discharge record CLAIM_ENROLMENT_RECORD OMOP:32813 Claim enrolment record COST_RECORD OMOP:32814 Cost record DEATH_CERTIFICATE OMOP:32815 Death Certificate DENTAL_CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR_PATHOLOGY_REPORT OMOP:32835 EHR Pathology report EHR_ADMINISTRATION_RECORD OMOP:32818 EHR administration record EHR_ADMISSION_NOTE OMOP:32819 EHR admission note EHR_ANCILLARY_REPORT OMOP:32820 EHR ancillary report EHR_BILLING_RECORD OMOP:32821 EHR billing record EHR_CHIEF_COMPLAINT OMOP:32822 EHR chief complaint EHR_DISCHARGE_RECORD OMOP:32823 EHR discharge record EHR_DISCHARGE_SUMMARY OMOP:32824 EHR discharge summary EHR_DISPENSING_RECORD OMOP:32825 EHR dispensing record EHR_EMERGENCY_ROOM_NOTE OMOP:32826 EHR emergency room note EHR_ENCOUNTER_RECORD OMOP:32827 EHR encounter record EHR_EPISODE_RECORD OMOP:32828 EHR episode record EHR_INPATIENT_NOTE OMOP:32829 EHR inpatient note EHR_MEDICATION_LIST OMOP:32830 EHR medication list EHR_NOTE OMOP:32831 EHR note EHR_NURSING_REPORT OMOP:32832 EHR nursing report EHR_ORDER OMOP:32833 EHR order EHR_OUTPATIENT_NOTE OMOP:32834 EHR outpatient note EHR_PHYSICAL_EXAMINATION OMOP:32836 EHR physical examination EHR_PLANNED_DISPENSING_RECORD OMOP:32837 EHR planned dispensing record EHR_PRESCRIPTION OMOP:32838 EHR prescription EHR_PRESCRIPTION_ISSUE_RECORD OMOP:32839 EHR prescription issue record EHR_PROBLEM_LIST OMOP:32840 EHR problem list EHR_RADIOLOGY_REPORT OMOP:32841 EHR radiology report EHR_REFERRAL_RECORD OMOP:32842 EHR referral record EXTERNAL_CDM_INSTANCE OMOP:32843 External CDM instance FACILITY_CLAIM OMOP:32844 Facility claim FACILITY_CLAIM_DETAIL OMOP:32845 Facility claim detail FACILITY_CLAIM_HEADER OMOP:32846 Facility claim header GEOGRAPHIC_ISOLATION_RECORD OMOP:32847 Geographic isolation record GOVERNMENT_REPORT OMOP:32848 Government report HEALTH_INFORMATION_EXCHANGE_RECORD OMOP:32849 Health Information Exchange record HEALTH_RISK_ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE_PROFESSIONAL_FILLED_SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL_COST OMOP:32852 Hospital cost INPATIENT_CLAIM OMOP:32853 Inpatient claim INPATIENT_CLAIM_DETAIL OMOP:32854 Inpatient claim detail INPATIENT_CLAIM_HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL_ORDER_RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT_CLAIM OMOP:32859 Outpatient claim OUTPATIENT_CLAIM_DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT_CLAIM_HEADER OMOP:32861 Outpatient claim header PATIENT_FILLED_SURVEY OMOP:32862 Patient filled survey PATIENT_OR_PAYER_PAID_RECORD OMOP:32863 Patient or payer paid record PATIENT_REPORTED_COST OMOP:32864 Patient reported cost PATIENT_SELF-REPORT OMOP:32865 Patient self-report PATIENT_SELF-TESTED OMOP:705183 Patient self-tested PAYER_SYSTEM_RECORD_(PAID_PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) OMOP:32867 Payer system record (primary payer) PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY_CLAIM OMOP:32869 Pharmacy claim POINT_OF_CARE/EXPRESS_LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION_TIME_PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL_CLAIM OMOP:32871 Professional claim PROFESSIONAL_CLAIM_DETAIL OMOP:32872 Professional claim detail PROFESSIONAL_CLAIM_HEADER OMOP:32873 Professional claim header PROVIDER_CHARGE_LIST_PRICE OMOP:32874 Provider charge list price PROVIDER_FINANCIAL_SYSTEM OMOP:32875 Provider financial system PROVIDER_INCURRED_COST_RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION_RECORD OMOP:32877 Randomization record REFERENCE_LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD_ALGORITHM OMOP:32880 Standard algorithm STANDARD_ALGORITHM_FROM_EHR OMOP:32882 Standard algorithm from EHR STANDARD_ALGORITHM_FROM_CLAIMS OMOP:32881 Standard algorithm from claims SURVEY OMOP:32883 Survey US_SOCIAL_SECURITY_DEATH_MASTER_FILE OMOP:32885 US Social Security Death Master File URGENT_LAB OMOP:32884 Urgent lab VISION_CLAIM OMOP:32886 Vision claim Slots Name Description visit_provenance A value representing the provenance of the visit record, or where the record ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VisitProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for visit provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE_REPORT_FORM: text: CASE_REPORT_FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM_AUTHORIZATION: text: CLAIM_AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM_DISCHARGE_RECORD: text: CLAIM_DISCHARGE_RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM_ENROLMENT_RECORD: text: CLAIM_ENROLMENT_RECORD description: Claim enrolment record meaning: OMOP:32813 COST_RECORD: text: COST_RECORD description: Cost record meaning: OMOP:32814 DEATH_CERTIFICATE: text: DEATH_CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL_CLAIM: text: DENTAL_CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR_PATHOLOGY_REPORT: text: EHR_PATHOLOGY_REPORT description: EHR Pathology report meaning: OMOP:32835 EHR_ADMINISTRATION_RECORD: text: EHR_ADMINISTRATION_RECORD description: EHR administration record meaning: OMOP:32818 EHR_ADMISSION_NOTE: text: EHR_ADMISSION_NOTE description: EHR admission note meaning: OMOP:32819 EHR_ANCILLARY_REPORT: text: EHR_ANCILLARY_REPORT description: EHR ancillary report meaning: OMOP:32820 EHR_BILLING_RECORD: text: EHR_BILLING_RECORD description: EHR billing record meaning: OMOP:32821 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR_DISCHARGE_RECORD: text: EHR_DISCHARGE_RECORD description: EHR discharge record meaning: OMOP:32823 EHR_DISCHARGE_SUMMARY: text: EHR_DISCHARGE_SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR_DISPENSING_RECORD: text: EHR_DISPENSING_RECORD description: EHR dispensing record meaning: OMOP:32825 EHR_EMERGENCY_ROOM_NOTE: text: EHR_EMERGENCY_ROOM_NOTE description: EHR emergency room note meaning: OMOP:32826 EHR_ENCOUNTER_RECORD: text: EHR_ENCOUNTER_RECORD description: EHR encounter record meaning: OMOP:32827 EHR_EPISODE_RECORD: text: EHR_EPISODE_RECORD description: EHR episode record meaning: OMOP:32828 EHR_INPATIENT_NOTE: text: EHR_INPATIENT_NOTE description: EHR inpatient note meaning: OMOP:32829 EHR_MEDICATION_LIST: text: EHR_MEDICATION_LIST description: EHR medication list meaning: OMOP:32830 EHR_NOTE: text: EHR_NOTE description: EHR note meaning: OMOP:32831 EHR_NURSING_REPORT: text: EHR_NURSING_REPORT description: EHR nursing report meaning: OMOP:32832 EHR_ORDER: text: EHR_ORDER description: EHR order meaning: OMOP:32833 EHR_OUTPATIENT_NOTE: text: EHR_OUTPATIENT_NOTE description: EHR outpatient note meaning: OMOP:32834 EHR_PHYSICAL_EXAMINATION: text: EHR_PHYSICAL_EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR_PLANNED_DISPENSING_RECORD: text: EHR_PLANNED_DISPENSING_RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR_PRESCRIPTION: text: EHR_PRESCRIPTION description: EHR prescription meaning: OMOP:32838 EHR_PRESCRIPTION_ISSUE_RECORD: text: EHR_PRESCRIPTION_ISSUE_RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR_PROBLEM_LIST: text: EHR_PROBLEM_LIST description: EHR problem list meaning: OMOP:32840 EHR_RADIOLOGY_REPORT: text: EHR_RADIOLOGY_REPORT description: EHR radiology report meaning: OMOP:32841 EHR_REFERRAL_RECORD: text: EHR_REFERRAL_RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL_CDM_INSTANCE: text: EXTERNAL_CDM_INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY_CLAIM: text: FACILITY_CLAIM description: Facility claim meaning: OMOP:32844 FACILITY_CLAIM_DETAIL: text: FACILITY_CLAIM_DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY_CLAIM_HEADER: text: FACILITY_CLAIM_HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC_ISOLATION_RECORD: text: GEOGRAPHIC_ISOLATION_RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT_REPORT: text: GOVERNMENT_REPORT description: Government report meaning: OMOP:32848 HEALTH_INFORMATION_EXCHANGE_RECORD: text: HEALTH_INFORMATION_EXCHANGE_RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH_RISK_ASSESSMENT: text: HEALTH_RISK_ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE_PROFESSIONAL_FILLED_SURVEY: text: HEALTHCARE_PROFESSIONAL_FILLED_SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL_COST: text: HOSPITAL_COST description: Hospital cost meaning: OMOP:32852 INPATIENT_CLAIM: text: INPATIENT_CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT_CLAIM_DETAIL: text: INPATIENT_CLAIM_DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT_CLAIM_HEADER: text: INPATIENT_CLAIM_HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL_ORDER_RECORD: text: MAIL_ORDER_RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT_CLAIM: text: OUTPATIENT_CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT_CLAIM_DETAIL: text: OUTPATIENT_CLAIM_DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT_CLAIM_HEADER: text: OUTPATIENT_CLAIM_HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT_FILLED_SURVEY: text: PATIENT_FILLED_SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT_OR_PAYER_PAID_RECORD: text: PATIENT_OR_PAYER_PAID_RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT_REPORTED_COST: text: PATIENT_REPORTED_COST description: Patient reported cost meaning: OMOP:32864 PATIENT_SELF-REPORT: text: PATIENT_SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT_SELF-TESTED: text: PATIENT_SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER_SYSTEM_RECORD_(PAID_PREMIUM): text: PAYER_SYSTEM_RECORD_(PAID_PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER_SYSTEM_RECORD_(PRIMARY_PAYER): text: PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER_SYSTEM_RECORD_(SECONDARY_PAYER): text: PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY_CLAIM: text: PHARMACY_CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT_OF_CARE/EXPRESS_LAB: text: POINT_OF_CARE/EXPRESS_LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION_TIME_PERIOD: text: PRE-QUALIFICATION_TIME_PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL_CLAIM: text: PROFESSIONAL_CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL_CLAIM_DETAIL: text: PROFESSIONAL_CLAIM_DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL_CLAIM_HEADER: text: PROFESSIONAL_CLAIM_HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER_CHARGE_LIST_PRICE: text: PROVIDER_CHARGE_LIST_PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER_FINANCIAL_SYSTEM: text: PROVIDER_FINANCIAL_SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER_INCURRED_COST_RECORD: text: PROVIDER_INCURRED_COST_RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION_RECORD: text: RANDOMIZATION_RECORD description: Randomization record meaning: OMOP:32877 REFERENCE_LAB: text: REFERENCE_LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD_ALGORITHM: text: STANDARD_ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD_ALGORITHM_FROM_EHR: text: STANDARD_ALGORITHM_FROM_EHR description: Standard algorithm from EHR meaning: OMOP:32882 STANDARD_ALGORITHM_FROM_CLAIMS: text: STANDARD_ALGORITHM_FROM_CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 US_SOCIAL_SECURITY_DEATH_MASTER_FILE: text: US_SOCIAL_SECURITY_DEATH_MASTER_FILE description: US Social Security Death Master File meaning: OMOP:32885 URGENT_LAB: text: URGENT_LAB description: Urgent lab meaning: OMOP:32884 VISION_CLAIM: text: VISION_CLAIM description: Vision claim meaning: OMOP:32886","title":"Enum: VisitProvenanceEnum"},{"location":"VisitProvenanceEnum/#enum-visitprovenanceenum","text":"A constrained set of enumerative values containing the OMOP values for visit provenance. URI: VisitProvenanceEnum","title":"Enum: VisitProvenanceEnum"},{"location":"VisitProvenanceEnum/#permissible-values","text":"Value Meaning Description CASE_REPORT_FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM_AUTHORIZATION OMOP:32811 Claim authorization CLAIM_DISCHARGE_RECORD OMOP:32812 Claim discharge record CLAIM_ENROLMENT_RECORD OMOP:32813 Claim enrolment record COST_RECORD OMOP:32814 Cost record DEATH_CERTIFICATE OMOP:32815 Death Certificate DENTAL_CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR_PATHOLOGY_REPORT OMOP:32835 EHR Pathology report EHR_ADMINISTRATION_RECORD OMOP:32818 EHR administration record EHR_ADMISSION_NOTE OMOP:32819 EHR admission note EHR_ANCILLARY_REPORT OMOP:32820 EHR ancillary report EHR_BILLING_RECORD OMOP:32821 EHR billing record EHR_CHIEF_COMPLAINT OMOP:32822 EHR chief complaint EHR_DISCHARGE_RECORD OMOP:32823 EHR discharge record EHR_DISCHARGE_SUMMARY OMOP:32824 EHR discharge summary EHR_DISPENSING_RECORD OMOP:32825 EHR dispensing record EHR_EMERGENCY_ROOM_NOTE OMOP:32826 EHR emergency room note EHR_ENCOUNTER_RECORD OMOP:32827 EHR encounter record EHR_EPISODE_RECORD OMOP:32828 EHR episode record EHR_INPATIENT_NOTE OMOP:32829 EHR inpatient note EHR_MEDICATION_LIST OMOP:32830 EHR medication list EHR_NOTE OMOP:32831 EHR note EHR_NURSING_REPORT OMOP:32832 EHR nursing report EHR_ORDER OMOP:32833 EHR order EHR_OUTPATIENT_NOTE OMOP:32834 EHR outpatient note EHR_PHYSICAL_EXAMINATION OMOP:32836 EHR physical examination EHR_PLANNED_DISPENSING_RECORD OMOP:32837 EHR planned dispensing record EHR_PRESCRIPTION OMOP:32838 EHR prescription EHR_PRESCRIPTION_ISSUE_RECORD OMOP:32839 EHR prescription issue record EHR_PROBLEM_LIST OMOP:32840 EHR problem list EHR_RADIOLOGY_REPORT OMOP:32841 EHR radiology report EHR_REFERRAL_RECORD OMOP:32842 EHR referral record EXTERNAL_CDM_INSTANCE OMOP:32843 External CDM instance FACILITY_CLAIM OMOP:32844 Facility claim FACILITY_CLAIM_DETAIL OMOP:32845 Facility claim detail FACILITY_CLAIM_HEADER OMOP:32846 Facility claim header GEOGRAPHIC_ISOLATION_RECORD OMOP:32847 Geographic isolation record GOVERNMENT_REPORT OMOP:32848 Government report HEALTH_INFORMATION_EXCHANGE_RECORD OMOP:32849 Health Information Exchange record HEALTH_RISK_ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE_PROFESSIONAL_FILLED_SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL_COST OMOP:32852 Hospital cost INPATIENT_CLAIM OMOP:32853 Inpatient claim INPATIENT_CLAIM_DETAIL OMOP:32854 Inpatient claim detail INPATIENT_CLAIM_HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL_ORDER_RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT_CLAIM OMOP:32859 Outpatient claim OUTPATIENT_CLAIM_DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT_CLAIM_HEADER OMOP:32861 Outpatient claim header PATIENT_FILLED_SURVEY OMOP:32862 Patient filled survey PATIENT_OR_PAYER_PAID_RECORD OMOP:32863 Patient or payer paid record PATIENT_REPORTED_COST OMOP:32864 Patient reported cost PATIENT_SELF-REPORT OMOP:32865 Patient self-report PATIENT_SELF-TESTED OMOP:705183 Patient self-tested PAYER_SYSTEM_RECORD_(PAID_PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) OMOP:32867 Payer system record (primary payer) PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY_CLAIM OMOP:32869 Pharmacy claim POINT_OF_CARE/EXPRESS_LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION_TIME_PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL_CLAIM OMOP:32871 Professional claim PROFESSIONAL_CLAIM_DETAIL OMOP:32872 Professional claim detail PROFESSIONAL_CLAIM_HEADER OMOP:32873 Professional claim header PROVIDER_CHARGE_LIST_PRICE OMOP:32874 Provider charge list price PROVIDER_FINANCIAL_SYSTEM OMOP:32875 Provider financial system PROVIDER_INCURRED_COST_RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION_RECORD OMOP:32877 Randomization record REFERENCE_LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD_ALGORITHM OMOP:32880 Standard algorithm STANDARD_ALGORITHM_FROM_EHR OMOP:32882 Standard algorithm from EHR STANDARD_ALGORITHM_FROM_CLAIMS OMOP:32881 Standard algorithm from claims SURVEY OMOP:32883 Survey US_SOCIAL_SECURITY_DEATH_MASTER_FILE OMOP:32885 US Social Security Death Master File URGENT_LAB OMOP:32884 Urgent lab VISION_CLAIM OMOP:32886 Vision claim","title":"Permissible Values"},{"location":"VisitProvenanceEnum/#slots","text":"Name Description visit_provenance A value representing the provenance of the visit record, or where the record ...","title":"Slots"},{"location":"VisitProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VisitProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VisitProvenanceEnum/#linkml-source","text":"name: VisitProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for visit provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE_REPORT_FORM: text: CASE_REPORT_FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM_AUTHORIZATION: text: CLAIM_AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM_DISCHARGE_RECORD: text: CLAIM_DISCHARGE_RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM_ENROLMENT_RECORD: text: CLAIM_ENROLMENT_RECORD description: Claim enrolment record meaning: OMOP:32813 COST_RECORD: text: COST_RECORD description: Cost record meaning: OMOP:32814 DEATH_CERTIFICATE: text: DEATH_CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL_CLAIM: text: DENTAL_CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR_PATHOLOGY_REPORT: text: EHR_PATHOLOGY_REPORT description: EHR Pathology report meaning: OMOP:32835 EHR_ADMINISTRATION_RECORD: text: EHR_ADMINISTRATION_RECORD description: EHR administration record meaning: OMOP:32818 EHR_ADMISSION_NOTE: text: EHR_ADMISSION_NOTE description: EHR admission note meaning: OMOP:32819 EHR_ANCILLARY_REPORT: text: EHR_ANCILLARY_REPORT description: EHR ancillary report meaning: OMOP:32820 EHR_BILLING_RECORD: text: EHR_BILLING_RECORD description: EHR billing record meaning: OMOP:32821 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR_DISCHARGE_RECORD: text: EHR_DISCHARGE_RECORD description: EHR discharge record meaning: OMOP:32823 EHR_DISCHARGE_SUMMARY: text: EHR_DISCHARGE_SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR_DISPENSING_RECORD: text: EHR_DISPENSING_RECORD description: EHR dispensing record meaning: OMOP:32825 EHR_EMERGENCY_ROOM_NOTE: text: EHR_EMERGENCY_ROOM_NOTE description: EHR emergency room note meaning: OMOP:32826 EHR_ENCOUNTER_RECORD: text: EHR_ENCOUNTER_RECORD description: EHR encounter record meaning: OMOP:32827 EHR_EPISODE_RECORD: text: EHR_EPISODE_RECORD description: EHR episode record meaning: OMOP:32828 EHR_INPATIENT_NOTE: text: EHR_INPATIENT_NOTE description: EHR inpatient note meaning: OMOP:32829 EHR_MEDICATION_LIST: text: EHR_MEDICATION_LIST description: EHR medication list meaning: OMOP:32830 EHR_NOTE: text: EHR_NOTE description: EHR note meaning: OMOP:32831 EHR_NURSING_REPORT: text: EHR_NURSING_REPORT description: EHR nursing report meaning: OMOP:32832 EHR_ORDER: text: EHR_ORDER description: EHR order meaning: OMOP:32833 EHR_OUTPATIENT_NOTE: text: EHR_OUTPATIENT_NOTE description: EHR outpatient note meaning: OMOP:32834 EHR_PHYSICAL_EXAMINATION: text: EHR_PHYSICAL_EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR_PLANNED_DISPENSING_RECORD: text: EHR_PLANNED_DISPENSING_RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR_PRESCRIPTION: text: EHR_PRESCRIPTION description: EHR prescription meaning: OMOP:32838 EHR_PRESCRIPTION_ISSUE_RECORD: text: EHR_PRESCRIPTION_ISSUE_RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR_PROBLEM_LIST: text: EHR_PROBLEM_LIST description: EHR problem list meaning: OMOP:32840 EHR_RADIOLOGY_REPORT: text: EHR_RADIOLOGY_REPORT description: EHR radiology report meaning: OMOP:32841 EHR_REFERRAL_RECORD: text: EHR_REFERRAL_RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL_CDM_INSTANCE: text: EXTERNAL_CDM_INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY_CLAIM: text: FACILITY_CLAIM description: Facility claim meaning: OMOP:32844 FACILITY_CLAIM_DETAIL: text: FACILITY_CLAIM_DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY_CLAIM_HEADER: text: FACILITY_CLAIM_HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC_ISOLATION_RECORD: text: GEOGRAPHIC_ISOLATION_RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT_REPORT: text: GOVERNMENT_REPORT description: Government report meaning: OMOP:32848 HEALTH_INFORMATION_EXCHANGE_RECORD: text: HEALTH_INFORMATION_EXCHANGE_RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH_RISK_ASSESSMENT: text: HEALTH_RISK_ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE_PROFESSIONAL_FILLED_SURVEY: text: HEALTHCARE_PROFESSIONAL_FILLED_SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL_COST: text: HOSPITAL_COST description: Hospital cost meaning: OMOP:32852 INPATIENT_CLAIM: text: INPATIENT_CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT_CLAIM_DETAIL: text: INPATIENT_CLAIM_DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT_CLAIM_HEADER: text: INPATIENT_CLAIM_HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL_ORDER_RECORD: text: MAIL_ORDER_RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT_CLAIM: text: OUTPATIENT_CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT_CLAIM_DETAIL: text: OUTPATIENT_CLAIM_DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT_CLAIM_HEADER: text: OUTPATIENT_CLAIM_HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT_FILLED_SURVEY: text: PATIENT_FILLED_SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT_OR_PAYER_PAID_RECORD: text: PATIENT_OR_PAYER_PAID_RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT_REPORTED_COST: text: PATIENT_REPORTED_COST description: Patient reported cost meaning: OMOP:32864 PATIENT_SELF-REPORT: text: PATIENT_SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT_SELF-TESTED: text: PATIENT_SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER_SYSTEM_RECORD_(PAID_PREMIUM): text: PAYER_SYSTEM_RECORD_(PAID_PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER_SYSTEM_RECORD_(PRIMARY_PAYER): text: PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER_SYSTEM_RECORD_(SECONDARY_PAYER): text: PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY_CLAIM: text: PHARMACY_CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT_OF_CARE/EXPRESS_LAB: text: POINT_OF_CARE/EXPRESS_LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION_TIME_PERIOD: text: PRE-QUALIFICATION_TIME_PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL_CLAIM: text: PROFESSIONAL_CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL_CLAIM_DETAIL: text: PROFESSIONAL_CLAIM_DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL_CLAIM_HEADER: text: PROFESSIONAL_CLAIM_HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER_CHARGE_LIST_PRICE: text: PROVIDER_CHARGE_LIST_PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER_FINANCIAL_SYSTEM: text: PROVIDER_FINANCIAL_SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER_INCURRED_COST_RECORD: text: PROVIDER_INCURRED_COST_RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION_RECORD: text: RANDOMIZATION_RECORD description: Randomization record meaning: OMOP:32877 REFERENCE_LAB: text: REFERENCE_LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD_ALGORITHM: text: STANDARD_ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD_ALGORITHM_FROM_EHR: text: STANDARD_ALGORITHM_FROM_EHR description: Standard algorithm from EHR meaning: OMOP:32882 STANDARD_ALGORITHM_FROM_CLAIMS: text: STANDARD_ALGORITHM_FROM_CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 US_SOCIAL_SECURITY_DEATH_MASTER_FILE: text: US_SOCIAL_SECURITY_DEATH_MASTER_FILE description: US Social Security Death Master File meaning: OMOP:32885 URGENT_LAB: text: URGENT_LAB description: Urgent lab meaning: OMOP:32884 VISION_CLAIM: text: VISION_CLAIM description: Vision claim meaning: OMOP:32886","title":"LinkML Source"},{"location":"VitalStatusEnum/","text":"Enum: VitalStatusEnum A constrained set of enumerative values containing the OMOP values for vital status. URI: VitalStatusEnum Permissible Values Value Meaning Description ALIVE OMOP:4230556 Showing characteristics of life; displaying signs of life DEAD OMOP:434489 The cessation of life Slots Name Description vital_status Coded value indicating the state or condition of being living or deceased; al... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VitalStatusEnum description: A constrained set of enumerative values containing the OMOP values for vital status. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIVE: text: ALIVE description: Showing characteristics of life; displaying signs of life. (NCIt) meaning: OMOP:4230556 DEAD: text: DEAD description: The cessation of life. (NCIt) meaning: OMOP:434489","title":"Enum: VitalStatusEnum"},{"location":"VitalStatusEnum/#enum-vitalstatusenum","text":"A constrained set of enumerative values containing the OMOP values for vital status. URI: VitalStatusEnum","title":"Enum: VitalStatusEnum"},{"location":"VitalStatusEnum/#permissible-values","text":"Value Meaning Description ALIVE OMOP:4230556 Showing characteristics of life; displaying signs of life DEAD OMOP:434489 The cessation of life","title":"Permissible Values"},{"location":"VitalStatusEnum/#slots","text":"Name Description vital_status Coded value indicating the state or condition of being living or deceased; al...","title":"Slots"},{"location":"VitalStatusEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VitalStatusEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VitalStatusEnum/#linkml-source","text":"name: VitalStatusEnum description: A constrained set of enumerative values containing the OMOP values for vital status. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIVE: text: ALIVE description: Showing characteristics of life; displaying signs of life. (NCIt) meaning: OMOP:4230556 DEAD: text: DEAD description: The cessation of life. (NCIt) meaning: OMOP:434489","title":"LinkML Source"},{"location":"about/","text":"BDCHM Model Overview This is a high-level class diagram of the core entities present in the BioData Catalyst Harmonized Model (BDCHM). classDiagram Participant \"1..*\" --> \"1\" Person : associated_person Demography \"1..*\" --> \"1\" Participant : associated_participant ResearchStudy \"1..*\" <-- \"1\" Participant : member_of_research_study ResearchStudy \"0..1\" <-- \"1\" ResearchStudy : part_of Visit \"0..*\" --> \"1\" Participant : associated_participant QuestionnaireResponse \"0..*\" --> \"1\" Visit : associated_visit QuestionnaireResponseItem \"1..*\" <-- \"1\" QuestionnaireResponse : items QuestionnaireResponseValue \"1\" <-- \"1\" QuestionnaireResponseItem : response_value QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireItem \"0..1\" <-- \"1\" QuestionnaireResponseItem : has_questionnaire_item Questionnaire \"1\" --> \"1..*\" QuestionnaireItem : items QuestionnaireItem \"1\" --> \"0..1\" QuestionnaireItem : part_of Condition \"0..*\" --> \"0..1\" Visit : associated_visit Condition \"0..*\" --> \"1\" Participant : associated_participant Person : id Person : identity Person : species Person : breed Person : year_of_birth Person : vital_status Person : age_at_death Person : cause_of_death Demography : id Demography : identity Demography : sex Demography : race Demography : ethnicity Participant : id Participant : identity Participant : description Participant : age_at_enrollment Participant : index_timepoint Participant : originating_site Participant : study_arm ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : sponsor ResearchStudy : date_started ResearchStudy : date_ended ResearchStudy : url ResearchStudy : research_project_type ResearchStudy : associated_timepoint ResearchStudy : principal_investigator ResearchStudy : principal_investigator Visit : id Visit : age_at_visit_start Visit : age_at_visit_end Visit : visit_category Visit : visit_provenance Questionnaire : id Questionnaire : identity Questionnaire : name Questionnaire : title Questionnaire : description Questionnaire : url Questionnaire : version Questionnaire : publisher Questionnaire : copyright Questionnaire : copyright_label Questionnaire : language QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : text QuestionnaireItem : code QuestionnaireResponse : id QuestionnaireResponse : age_at_response QuestionnaireResponseItem : id QuestionnaireResponseItem : text QuestionnaireResponseValue : type QuestionnaireResponseValue : name QuestionnaireResponseValueDecimal : value QuestionnaireResponseValueBoolean : value QuestionnaireResponseValueString : value Condition : id Condition : identity Condition : condition_concept Condition : age_at_condition_start Condition : age_at_condition_end Condition : condition_provenance Condition : condition_status Condition : relationship_to_participant","title":"About"},{"location":"about/#bdchm-model-overview","text":"This is a high-level class diagram of the core entities present in the BioData Catalyst Harmonized Model (BDCHM). classDiagram Participant \"1..*\" --> \"1\" Person : associated_person Demography \"1..*\" --> \"1\" Participant : associated_participant ResearchStudy \"1..*\" <-- \"1\" Participant : member_of_research_study ResearchStudy \"0..1\" <-- \"1\" ResearchStudy : part_of Visit \"0..*\" --> \"1\" Participant : associated_participant QuestionnaireResponse \"0..*\" --> \"1\" Visit : associated_visit QuestionnaireResponseItem \"1..*\" <-- \"1\" QuestionnaireResponse : items QuestionnaireResponseValue \"1\" <-- \"1\" QuestionnaireResponseItem : response_value QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireItem \"0..1\" <-- \"1\" QuestionnaireResponseItem : has_questionnaire_item Questionnaire \"1\" --> \"1..*\" QuestionnaireItem : items QuestionnaireItem \"1\" --> \"0..1\" QuestionnaireItem : part_of Condition \"0..*\" --> \"0..1\" Visit : associated_visit Condition \"0..*\" --> \"1\" Participant : associated_participant Person : id Person : identity Person : species Person : breed Person : year_of_birth Person : vital_status Person : age_at_death Person : cause_of_death Demography : id Demography : identity Demography : sex Demography : race Demography : ethnicity Participant : id Participant : identity Participant : description Participant : age_at_enrollment Participant : index_timepoint Participant : originating_site Participant : study_arm ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : sponsor ResearchStudy : date_started ResearchStudy : date_ended ResearchStudy : url ResearchStudy : research_project_type ResearchStudy : associated_timepoint ResearchStudy : principal_investigator ResearchStudy : principal_investigator Visit : id Visit : age_at_visit_start Visit : age_at_visit_end Visit : visit_category Visit : visit_provenance Questionnaire : id Questionnaire : identity Questionnaire : name Questionnaire : title Questionnaire : description Questionnaire : url Questionnaire : version Questionnaire : publisher Questionnaire : copyright Questionnaire : copyright_label Questionnaire : language QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : text QuestionnaireItem : code QuestionnaireResponse : id QuestionnaireResponse : age_at_response QuestionnaireResponseItem : id QuestionnaireResponseItem : text QuestionnaireResponseValue : type QuestionnaireResponseValue : name QuestionnaireResponseValueDecimal : value QuestionnaireResponseValueBoolean : value QuestionnaireResponseValueString : value Condition : id Condition : identity Condition : condition_concept Condition : age_at_condition_start Condition : age_at_condition_end Condition : condition_provenance Condition : condition_status Condition : relationship_to_participant","title":"BDCHM Model Overview"},{"location":"activity_type/","text":"Slot: activity_type URI: bdchm:activity_type Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no Properties Range: String Identifier and Mapping Information LinkML Source name: activity_type alias: activity_type domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: string","title":"Slot: activity_type"},{"location":"activity_type/#slot-activity_type","text":"URI: bdchm:activity_type","title":"Slot: activity_type"},{"location":"activity_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no","title":"Applicable Classes"},{"location":"activity_type/#properties","text":"Range: String","title":"Properties"},{"location":"activity_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"activity_type/#linkml-source","text":"name: activity_type alias: activity_type domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: string","title":"LinkML Source"},{"location":"additive/","text":"Slot: additive URI: bdchm:additive Applicable Classes Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no Properties Range: String Identifier and Mapping Information LinkML Source name: additive alias: additive domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: string","title":"Slot: additive"},{"location":"additive/#slot-additive","text":"URI: bdchm:additive","title":"Slot: additive"},{"location":"additive/#applicable-classes","text":"Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no","title":"Applicable Classes"},{"location":"additive/#properties","text":"Range: 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URI: bdchm:associated_person","title":"Slot: associated_person"},{"location":"associated_person/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no","title":"Applicable Classes"},{"location":"associated_person/#properties","text":"Range: Person","title":"Properties"},{"location":"associated_person/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"associated_person/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"associated_person/#linkml-source","text":"name: associated_person description: A reference to the Person that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_person domain_of: - Participant range: Person","title":"LinkML Source"},{"location":"associated_timepoint/","text":"Slot: associated_timepoint A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) URI: bdchm:associated_timepoint Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: TimePoint Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint","title":"Slot: associated_timepoint"},{"location":"associated_timepoint/#slot-associated_timepoint","text":"A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) URI: bdchm:associated_timepoint","title":"Slot: associated_timepoint"},{"location":"associated_timepoint/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"associated_timepoint/#properties","text":"Range: TimePoint Multivalued: True","title":"Properties"},{"location":"associated_timepoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"associated_timepoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"associated_timepoint/#linkml-source","text":"name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint","title":"LinkML Source"},{"location":"associated_visit/","text":"Slot: associated_visit URI: bdchm:associated_visit Applicable Classes Name Description Modifies Slot QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set... no Condition Conditions are records of a Person suggesting the presence of a disease or me... no Procedure Procedure contains records of activities or processes ordered by, or carried ... no DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no DimensionalObservation A structured object that describes a single data item about the physical dime... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no Observation A data structure with key (observation_type) and value (value) attributes tha... no Properties Range: String Identifier and Mapping Information LinkML Source name: associated_visit alias: associated_visit domain_of: - 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QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: string","title":"LinkML Source"},{"location":"bdchm/","text":"bdchm This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm","title":"bdchm"},{"location":"bdchm/#bdchm","text":"This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm","title":"bdchm"},{"location":"breed/","text":"Slot: breed A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). URI: bdchm:breed Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: VertebrateBreedEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum","title":"Slot: breed"},{"location":"breed/#slot-breed","text":"A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). URI: bdchm:breed","title":"Slot: breed"},{"location":"breed/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"breed/#properties","text":"Range: VertebrateBreedEnum","title":"Properties"},{"location":"breed/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"breed/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"breed/#linkml-source","text":"name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum","title":"LinkML Source"},{"location":"category/","text":"Slot: category URI: bdchm:category Applicable Classes Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no Properties Range: String Identifier and Mapping Information LinkML Source name: category alias: category domain_of: - ObservationSet - Observation range: string","title":"Slot: category"},{"location":"category/#slot-category","text":"URI: bdchm:category","title":"Slot: category"},{"location":"category/#applicable-classes","text":"Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no","title":"Applicable Classes"},{"location":"category/#properties","text":"Range: String","title":"Properties"},{"location":"category/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"category/#linkml-source","text":"name: category alias: category domain_of: - ObservationSet - Observation range: string","title":"LinkML Source"},{"location":"cause_of_death/","text":"Slot: cause_of_death Coded value indicating the circumstance or condition that results in the death of the individual. URI: bdchm:cause_of_death Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string","title":"Slot: cause_of_death"},{"location":"cause_of_death/#slot-cause_of_death","text":"Coded value indicating the circumstance or condition that results in the death of the individual. URI: bdchm:cause_of_death","title":"Slot: cause_of_death"},{"location":"cause_of_death/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"cause_of_death/#properties","text":"Range: String","title":"Properties"},{"location":"cause_of_death/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cause_of_death/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"cause_of_death/#linkml-source","text":"name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string","title":"LinkML Source"},{"location":"cellular_composition_type/","text":"Slot: cellular_composition_type A term describing the type of cell or cellular material comprising a specimen. URI: bdchm:cellular_composition_type Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: String Examples Value 2D Classical Conditionally Reprogrammed Cells Adherent Cell Line Bone Marrow Components Buccal Cells Buffy Coat Derived Cell Line Granulocytes Pleural Effusion Human Original Cells Liquid Suspension Cell Line Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false","title":"Slot: cellular_composition_type"},{"location":"cellular_composition_type/#slot-cellular_composition_type","text":"A term describing the type of cell or cellular material comprising a specimen. URI: bdchm:cellular_composition_type","title":"Slot: cellular_composition_type"},{"location":"cellular_composition_type/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"cellular_composition_type/#properties","text":"Range: String","title":"Properties"},{"location":"cellular_composition_type/#examples","text":"Value 2D Classical Conditionally Reprogrammed Cells Adherent Cell Line Bone Marrow Components Buccal Cells Buffy Coat Derived Cell Line Granulocytes Pleural Effusion Human Original Cells Liquid Suspension Cell Line","title":"Examples"},{"location":"cellular_composition_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cellular_composition_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"cellular_composition_type/#linkml-source","text":"name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false","title":"LinkML Source"},{"location":"code/","text":"Slot: code Corresponding concept for this item in a terminology URI: bdchm:code Applicable Classes Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string","title":"Slot: code"},{"location":"code/#slot-code","text":"Corresponding concept for this item in a terminology URI: bdchm:code","title":"Slot: code"},{"location":"code/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no","title":"Applicable Classes"},{"location":"code/#properties","text":"Range: String","title":"Properties"},{"location":"code/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"code/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"code/#linkml-source","text":"name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string","title":"LinkML Source"},{"location":"collection_method_type/","text":"Slot: collection_method_type The type of method applied in collecting a sample from its original source. URI: bdchm:collection_method_type Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: SpecimenCollectionMethodType Examples Value Anterior Resection of Rectum Ascites Drainage Excisional Biopsy Specimen Pooling Comments This attribute applies only when the Specimen.category = 'original'. 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URI: bdchm:collection_method_type","title":"Slot: collection_method_type"},{"location":"collection_method_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"collection_method_type/#properties","text":"Range: SpecimenCollectionMethodType","title":"Properties"},{"location":"collection_method_type/#examples","text":"Value Anterior Resection of Rectum Ascites Drainage Excisional Biopsy Specimen Pooling","title":"Examples"},{"location":"collection_method_type/#comments","text":"This attribute applies only when the Specimen.category = 'original'.","title":"Comments"},{"location":"collection_method_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"collection_method_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"collection_method_type/#linkml-source","text":"name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: SpecimenCollectionMethodType required: false","title":"LinkML Source"},{"location":"collection_site/","text":"Slot: collection_site The anatomic site from which a specimen was collected. URI: bdchm:collection_site Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: BodySite Examples Value Abdomen Abdominal Wall Acetabulum Comments This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false","title":"Slot: collection_site"},{"location":"collection_site/#slot-collection_site","text":"The anatomic site from which a specimen was collected. URI: bdchm:collection_site","title":"Slot: collection_site"},{"location":"collection_site/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"collection_site/#properties","text":"Range: BodySite","title":"Properties"},{"location":"collection_site/#examples","text":"Value Abdomen Abdominal Wall Acetabulum","title":"Examples"},{"location":"collection_site/#comments","text":"This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'.","title":"Comments"},{"location":"collection_site/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"collection_site/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"collection_site/#linkml-source","text":"name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false","title":"LinkML Source"},{"location":"condition_concept/","text":"Slot: condition_concept The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. URI: bdchm:condition_concept Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: ConditionConceptEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum","title":"Slot: condition_concept"},{"location":"condition_concept/#slot-condition_concept","text":"The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. URI: bdchm:condition_concept","title":"Slot: condition_concept"},{"location":"condition_concept/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"condition_concept/#properties","text":"Range: ConditionConceptEnum","title":"Properties"},{"location":"condition_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"condition_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"condition_concept/#linkml-source","text":"name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum","title":"LinkML Source"},{"location":"condition_provenance/","text":"Slot: condition_provenance A value representing the provenance of the Condition record URI: bdchm:condition_provenance Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: ProvenanceEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum","title":"Slot: condition_provenance"},{"location":"condition_provenance/#slot-condition_provenance","text":"A value representing the provenance of the Condition record URI: bdchm:condition_provenance","title":"Slot: condition_provenance"},{"location":"condition_provenance/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"condition_provenance/#properties","text":"Range: ProvenanceEnum","title":"Properties"},{"location":"condition_provenance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"condition_provenance/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"condition_provenance/#linkml-source","text":"name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum","title":"LinkML Source"},{"location":"condition_status/","text":"Slot: condition_status A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. URI: bdchm:condition_status Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: ConditionStatusEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum","title":"Slot: condition_status"},{"location":"condition_status/#slot-condition_status","text":"A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. URI: bdchm:condition_status","title":"Slot: condition_status"},{"location":"condition_status/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"condition_status/#properties","text":"Range: ConditionStatusEnum","title":"Properties"},{"location":"condition_status/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"condition_status/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"condition_status/#linkml-source","text":"name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum","title":"LinkML Source"},{"location":"consent_code/","text":"Slot: consent_code Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html URI: bdchm:consent_code Applicable Classes Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no Properties Range: DataUseEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum","title":"Slot: consent_code"},{"location":"consent_code/#slot-consent_code","text":"Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html URI: bdchm:consent_code","title":"Slot: consent_code"},{"location":"consent_code/#applicable-classes","text":"Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no","title":"Applicable Classes"},{"location":"consent_code/#properties","text":"Range: DataUseEnum","title":"Properties"},{"location":"consent_code/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"consent_code/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"consent_code/#linkml-source","text":"name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum","title":"LinkML Source"},{"location":"consents/","text":"Slot: consents URI: bdchm:consents Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information LinkML Source name: consents alias: consents domain_of: - Participant - ResearchStudy range: string","title":"Slot: consents"},{"location":"consents/#slot-consents","text":"URI: bdchm:consents","title":"Slot: consents"},{"location":"consents/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"consents/#properties","text":"Range: String","title":"Properties"},{"location":"consents/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"consents/#linkml-source","text":"name: consents alias: consents domain_of: - Participant - ResearchStudy range: string","title":"LinkML Source"},{"location":"contained_in/","text":"Slot: contained_in A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:contained_in Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenContainer Comments The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false","title":"Slot: contained_in"},{"location":"contained_in/#slot-contained_in","text":"A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:contained_in","title":"Slot: contained_in"},{"location":"contained_in/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"contained_in/#properties","text":"Range: SpecimenContainer","title":"Properties"},{"location":"contained_in/#comments","text":"The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity.","title":"Comments"},{"location":"contained_in/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"contained_in/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"contained_in/#linkml-source","text":"name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false","title":"LinkML Source"},{"location":"container/","text":"Slot: container A container in which the specimen is held or affixed during its storage. URI: bdchm:container Applicable Classes Name Description Modifies Slot SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no Properties Range: SpecimenContainer Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true","title":"Slot: container"},{"location":"container/#slot-container","text":"A container in which the specimen is held or affixed during its storage. URI: bdchm:container","title":"Slot: container"},{"location":"container/#applicable-classes","text":"Name Description Modifies Slot SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no","title":"Applicable Classes"},{"location":"container/#properties","text":"Range: SpecimenContainer Multivalued: True","title":"Properties"},{"location":"container/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"container/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"container/#linkml-source","text":"name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true","title":"LinkML Source"},{"location":"container_number/","text":"Slot: container_number Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) URI: bdchm:container_number Applicable Classes Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"Slot: container_number"},{"location":"container_number/#slot-container_number","text":"Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) URI: bdchm:container_number","title":"Slot: container_number"},{"location":"container_number/#applicable-classes","text":"Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no","title":"Applicable Classes"},{"location":"container_number/#properties","text":"Range: String","title":"Properties"},{"location":"container_number/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"container_number/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"container_number/#linkml-source","text":"name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"LinkML Source"},{"location":"container_type/","text":"Slot: container_type The kind of the container. URI: bdchm:container_type Applicable Classes Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no Properties Range: String Examples Value Capillary blood collection tube Sputum specimen container Cell culture flask Glass slide Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"Slot: container_type"},{"location":"container_type/#slot-container_type","text":"The kind of the container. URI: bdchm:container_type","title":"Slot: container_type"},{"location":"container_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no","title":"Applicable Classes"},{"location":"container_type/#properties","text":"Range: String","title":"Properties"},{"location":"container_type/#examples","text":"Value Capillary blood collection tube Sputum specimen container Cell culture flask Glass slide","title":"Examples"},{"location":"container_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"container_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"container_type/#linkml-source","text":"name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"LinkML Source"},{"location":"copyright/","text":"Slot: copyright Textual description of any use and/or publishing restrictions URI: bdchm:copyright Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: copyright"},{"location":"copyright/#slot-copyright","text":"Textual description of any use and/or publishing restrictions URI: bdchm:copyright","title":"Slot: copyright"},{"location":"copyright/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"copyright/#properties","text":"Range: String","title":"Properties"},{"location":"copyright/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"copyright/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"copyright/#linkml-source","text":"name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"copyright_label/","text":"Slot: copyright_label Copyright holder and year(s) URI: bdchm:copyright_label Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: copyright_label"},{"location":"copyright_label/#slot-copyright_label","text":"Copyright holder and year(s) URI: bdchm:copyright_label","title":"Slot: copyright_label"},{"location":"copyright_label/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"copyright_label/#properties","text":"Range: String","title":"Properties"},{"location":"copyright_label/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"copyright_label/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"copyright_label/#linkml-source","text":"name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"creation_activity/","text":"Slot: creation_activity The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. URI: bdchm:creation_activity Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenCreationActivity Comments Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false","title":"Slot: creation_activity"},{"location":"creation_activity/#slot-creation_activity","text":"The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. URI: bdchm:creation_activity","title":"Slot: creation_activity"},{"location":"creation_activity/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"creation_activity/#properties","text":"Range: SpecimenCreationActivity","title":"Properties"},{"location":"creation_activity/#comments","text":"Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it.","title":"Comments"},{"location":"creation_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"creation_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"creation_activity/#linkml-source","text":"name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false","title":"LinkML Source"},{"location":"data_category/","text":"Slot: data_category A broad categorization of the contents of the data file. URI: bdchm:data_category Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string","title":"Slot: data_category"},{"location":"data_category/#slot-data_category","text":"A broad categorization of the contents of the data file. URI: bdchm:data_category","title":"Slot: data_category"},{"location":"data_category/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"data_category/#properties","text":"Range: String","title":"Properties"},{"location":"data_category/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"data_category/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"data_category/#linkml-source","text":"name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"data_type/","text":"Slot: data_type The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary DCMI-TYPE . To describe the file format, physical medium, or dimensions of the resource, use the Format element. URI: bdchm:data_type Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Comments Called 'type' in Dublin Core. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string","title":"Slot: data_type"},{"location":"data_type/#slot-data_type","text":"The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary DCMI-TYPE . To describe the file format, physical medium, or dimensions of the resource, use the Format element. URI: bdchm:data_type","title":"Slot: data_type"},{"location":"data_type/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"data_type/#properties","text":"Range: String","title":"Properties"},{"location":"data_type/#comments","text":"Called 'type' in Dublin Core.","title":"Comments"},{"location":"data_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"data_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"data_type/#linkml-source","text":"name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"date_ended/","text":"Slot: date_ended URI: bdchm:date_ended Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: String Identifier and Mapping Information LinkML Source name: date_ended alias: date_ended domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"Slot: date_ended"},{"location":"date_ended/#slot-date_ended","text":"URI: bdchm:date_ended","title":"Slot: date_ended"},{"location":"date_ended/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"date_ended/#properties","text":"Range: String","title":"Properties"},{"location":"date_ended/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_ended/#linkml-source","text":"name: date_ended alias: date_ended domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"LinkML Source"},{"location":"date_started/","text":"Slot: date_started URI: bdchm:date_started Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: String Identifier and Mapping Information LinkML Source name: date_started alias: date_started domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"Slot: date_started"},{"location":"date_started/#slot-date_started","text":"URI: bdchm:date_started","title":"Slot: date_started"},{"location":"date_started/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"date_started/#properties","text":"Range: String","title":"Properties"},{"location":"date_started/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_started/#linkml-source","text":"name: date_started alias: date_started domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"LinkML Source"},{"location":"date_time/","text":"Slot: date_time An explicitly specified timepoint described in terms of a date and optionally a time on that date. URI: bdchm:date_time Applicable Classes Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no Properties Range: Datetime Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime","title":"Slot: date_time"},{"location":"date_time/#slot-date_time","text":"An explicitly specified timepoint described in terms of a date and optionally a time on that date. URI: bdchm:date_time","title":"Slot: date_time"},{"location":"date_time/#applicable-classes","text":"Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no","title":"Applicable Classes"},{"location":"date_time/#properties","text":"Range: Datetime","title":"Properties"},{"location":"date_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_time/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"date_time/#linkml-source","text":"name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime","title":"LinkML Source"},{"location":"days_supply/","text":"Slot: days_supply The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). URI: bdchm:days_supply Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no Properties Range: Integer Comments The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"Slot: days_supply"},{"location":"days_supply/#slot-days_supply","text":"The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). URI: bdchm:days_supply","title":"Slot: days_supply"},{"location":"days_supply/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"days_supply/#properties","text":"Range: Integer","title":"Properties"},{"location":"days_supply/#comments","text":"The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras.","title":"Comments"},{"location":"days_supply/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"days_supply/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"days_supply/#linkml-source","text":"name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"LinkML Source"},{"location":"derivation_method_type/","text":"Slot: derivation_method_type The type of method applied to derive a new specimen from an existing one. URI: bdchm:derivation_method_type Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: String Examples Value Vibratome Cryosectioning Tissuemolds Slidingmicrotome Sectioning Other Unknown NotReported Comments This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false","title":"Slot: derivation_method_type"},{"location":"derivation_method_type/#slot-derivation_method_type","text":"The type of method applied to derive a new specimen from an existing one. URI: bdchm:derivation_method_type","title":"Slot: derivation_method_type"},{"location":"derivation_method_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"derivation_method_type/#properties","text":"Range: String","title":"Properties"},{"location":"derivation_method_type/#examples","text":"Value Vibratome Cryosectioning Tissuemolds Slidingmicrotome Sectioning Other Unknown NotReported","title":"Examples"},{"location":"derivation_method_type/#comments","text":"This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'.","title":"Comments"},{"location":"derivation_method_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"derivation_method_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"derivation_method_type/#linkml-source","text":"name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false","title":"LinkML Source"},{"location":"derived_product/","text":"Slot: derived_product A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) URI: bdchm:derived_product Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: BiologicProduct Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true","title":"Slot: derived_product"},{"location":"derived_product/#slot-derived_product","text":"A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) URI: bdchm:derived_product","title":"Slot: derived_product"},{"location":"derived_product/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"derived_product/#properties","text":"Range: BiologicProduct Multivalued: True","title":"Properties"},{"location":"derived_product/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"derived_product/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"derived_product/#linkml-source","text":"name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true","title":"LinkML Source"},{"location":"description/","text":"Slot: description URI: bdchm:description Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no File Abstract class for various kinds of files no Document A collection of information intented to be understood together as a whole, an... no Specimen Any material taken as a sample from a biological entity (living or dead), or ... no BiologicProduct A living organism, or a metabolically active biological system such as a cell... no Properties Range: String Identifier and Mapping Information LinkML Source name: description alias: description domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string","title":"Slot: description"},{"location":"description/#slot-description","text":"URI: bdchm:description","title":"Slot: description"},{"location":"description/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no File Abstract class for various kinds of files no Document A collection of information intented to be understood together as a whole, an... no Specimen Any material taken as a sample from a biological entity (living or dead), or ... no BiologicProduct A living organism, or a metabolically active biological system such as a cell... no","title":"Applicable Classes"},{"location":"description/#properties","text":"Range: String","title":"Properties"},{"location":"description/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"description/#linkml-source","text":"name: description alias: description domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string","title":"LinkML Source"},{"location":"description_shortened/","text":"Slot: description_shortened An abbreviated description of a research program, project, or study. URI: bdchm:description_shortened Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"Slot: description_shortened"},{"location":"description_shortened/#slot-description_shortened","text":"An abbreviated description of a research program, project, or study. URI: bdchm:description_shortened","title":"Slot: description_shortened"},{"location":"description_shortened/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"description_shortened/#properties","text":"Range: String","title":"Properties"},{"location":"description_shortened/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"description_shortened/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"description_shortened/#linkml-source","text":"name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"LinkML Source"},{"location":"device_concept/","text":"Slot: device_concept The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. URI: bdchm:device_concept Applicable Classes Name Description Modifies Slot DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no Properties Range: DeviceExposureConceptEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum","title":"Slot: device_concept"},{"location":"device_concept/#slot-device_concept","text":"The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. URI: bdchm:device_concept","title":"Slot: device_concept"},{"location":"device_concept/#applicable-classes","text":"Name Description Modifies Slot DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no","title":"Applicable Classes"},{"location":"device_concept/#properties","text":"Range: DeviceExposureConceptEnum","title":"Properties"},{"location":"device_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"device_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"device_concept/#linkml-source","text":"name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum","title":"LinkML Source"},{"location":"dimensional_measures/","text":"Slot: dimensional_measures Observations about the current physical dimensions of an object (e.g. length, width, area). URI: bdchm:dimensional_measures Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: DimensionalObservationSet Comments Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false","title":"Slot: dimensional_measures"},{"location":"dimensional_measures/#slot-dimensional_measures","text":"Observations about the current physical dimensions of an object (e.g. length, width, area). URI: bdchm:dimensional_measures","title":"Slot: dimensional_measures"},{"location":"dimensional_measures/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"dimensional_measures/#properties","text":"Range: DimensionalObservationSet","title":"Properties"},{"location":"dimensional_measures/#comments","text":"Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object.","title":"Comments"},{"location":"dimensional_measures/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"dimensional_measures/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"dimensional_measures/#linkml-source","text":"name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false","title":"LinkML Source"},{"location":"document_type/","text":"Slot: document_type The high-level type of the document (e.g. 'publication', 'pathology report') URI: bdchm:document_type Applicable Classes Name Description Modifies Slot Document A collection of information intented to be understood together as a whole, an... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false","title":"Slot: document_type"},{"location":"document_type/#slot-document_type","text":"The high-level type of the document (e.g. 'publication', 'pathology report') URI: bdchm:document_type","title":"Slot: document_type"},{"location":"document_type/#applicable-classes","text":"Name Description Modifies Slot Document A collection of information intented to be understood together as a whole, an... no","title":"Applicable Classes"},{"location":"document_type/#properties","text":"Range: String","title":"Properties"},{"location":"document_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"document_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"document_type/#linkml-source","text":"name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false","title":"LinkML Source"},{"location":"drug_concept/","text":"Slot: drug_concept The coded value for a drug. From RxNorm. The syntax for the enum may need work. URI: bdchm:drug_concept Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no Properties Range: DrugExposureConceptEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum","title":"Slot: drug_concept"},{"location":"drug_concept/#slot-drug_concept","text":"The coded value for a drug. From RxNorm. The syntax for the enum may need work. URI: bdchm:drug_concept","title":"Slot: drug_concept"},{"location":"drug_concept/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"drug_concept/#properties","text":"Range: DrugExposureConceptEnum","title":"Properties"},{"location":"drug_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"drug_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"drug_concept/#linkml-source","text":"name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum","title":"LinkML Source"},{"location":"duration/","text":"Slot: duration URI: bdchm:duration Applicable Classes Name Description Modifies Slot SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: String Identifier and Mapping Information LinkML Source name: duration alias: duration domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"Slot: duration"},{"location":"duration/#slot-duration","text":"URI: bdchm:duration","title":"Slot: duration"},{"location":"duration/#applicable-classes","text":"Name Description Modifies Slot SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"duration/#properties","text":"Range: String","title":"Properties"},{"location":"duration/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"duration/#linkml-source","text":"name: duration alias: duration domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"LinkML Source"},{"location":"entries/","text":"Slot: entries URI: bdchm:entries Applicable Classes Name Description Modifies Slot ResearchStudyCollection A holder for ResearchStudy objects no Properties Range: ResearchStudy Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true","title":"Slot: entries"},{"location":"entries/#slot-entries","text":"URI: bdchm:entries","title":"Slot: entries"},{"location":"entries/#applicable-classes","text":"Name Description Modifies Slot ResearchStudyCollection A holder for ResearchStudy objects no","title":"Applicable Classes"},{"location":"entries/#properties","text":"Range: ResearchStudy Multivalued: True","title":"Properties"},{"location":"entries/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"entries/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"entries/#linkml-source","text":"name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true","title":"LinkML Source"},{"location":"ethnicity/","text":"Slot: ethnicity An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau URI: bdchm:ethnicity Applicable Classes Name Description Modifies Slot Demography Demographics about an individual or animal receiving care or other health-rel... no Properties Range: EthnicityEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum","title":"Slot: ethnicity"},{"location":"ethnicity/#slot-ethnicity","text":"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau URI: bdchm:ethnicity","title":"Slot: ethnicity"},{"location":"ethnicity/#applicable-classes","text":"Name Description Modifies Slot Demography Demographics about an individual or animal receiving care or other health-rel... no","title":"Applicable Classes"},{"location":"ethnicity/#properties","text":"Range: EthnicityEnum","title":"Properties"},{"location":"ethnicity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ethnicity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ethnicity/#linkml-source","text":"name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum","title":"LinkML Source"},{"location":"event_type/","text":"Slot: event_type An event that occurred at the point in time specified by this TimePoint. URI: bdchm:event_type Applicable Classes Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string","title":"Slot: event_type"},{"location":"event_type/#slot-event_type","text":"An event that occurred at the point in time specified by this TimePoint. URI: bdchm:event_type","title":"Slot: event_type"},{"location":"event_type/#applicable-classes","text":"Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no","title":"Applicable Classes"},{"location":"event_type/#properties","text":"Range: String","title":"Properties"},{"location":"event_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"event_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"event_type/#linkml-source","text":"name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string","title":"LinkML Source"},{"location":"exposure_provenance/","text":"Slot: exposure_provenance URI: bdchm:exposure_provenance Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no Properties Range: String Identifier and Mapping Information LinkML Source name: exposure_provenance alias: exposure_provenance domain_of: - DrugExposure - DeviceExposure range: string","title":"Slot: exposure_provenance"},{"location":"exposure_provenance/#slot-exposure_provenance","text":"URI: bdchm:exposure_provenance","title":"Slot: exposure_provenance"},{"location":"exposure_provenance/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no","title":"Applicable Classes"},{"location":"exposure_provenance/#properties","text":"Range: String","title":"Properties"},{"location":"exposure_provenance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"exposure_provenance/#linkml-source","text":"name: exposure_provenance alias: exposure_provenance domain_of: - DrugExposure - DeviceExposure range: string","title":"LinkML Source"},{"location":"file_name/","text":"Slot: file_name The name (or part of a name) of a file (of any type). URI: bdchm:file_name Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string","title":"Slot: file_name"},{"location":"file_name/#slot-file_name","text":"The name (or part of a name) of a file (of any type). URI: bdchm:file_name","title":"Slot: file_name"},{"location":"file_name/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"file_name/#properties","text":"Range: String","title":"Properties"},{"location":"file_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"file_name/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"file_name/#linkml-source","text":"name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"file_size/","text":"Slot: file_size The size of the data file (object) in bytes. URI: bdchm:file_size Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer","title":"Slot: file_size"},{"location":"file_size/#slot-file_size","text":"The size of the data file (object) in bytes. URI: bdchm:file_size","title":"Slot: file_size"},{"location":"file_size/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"file_size/#properties","text":"Range: Integer","title":"Properties"},{"location":"file_size/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"file_size/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"file_size/#linkml-source","text":"name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer","title":"LinkML Source"},{"location":"focus/","text":"Slot: focus URI: bdchm:focus Applicable Classes Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no Document A collection of information intented to be understood together as a whole, an... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no Properties Range: String Identifier and Mapping Information LinkML Source name: focus alias: focus domain_of: - Document - ObservationSet - Observation range: string","title":"Slot: focus"},{"location":"focus/#slot-focus","text":"URI: bdchm:focus","title":"Slot: focus"},{"location":"focus/#applicable-classes","text":"Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no Document A collection of information intented to be understood together as a whole, an... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no","title":"Applicable Classes"},{"location":"focus/#properties","text":"Range: String","title":"Properties"},{"location":"focus/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"focus/#linkml-source","text":"name: focus alias: focus domain_of: - Document - ObservationSet - Observation range: string","title":"LinkML Source"},{"location":"format/","text":"Slot: format The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). URI: bdchm:format Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string","title":"Slot: format"},{"location":"format/#slot-format","text":"The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). URI: bdchm:format","title":"Slot: format"},{"location":"format/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"format/#properties","text":"Range: String","title":"Properties"},{"location":"format/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"format/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"format/#linkml-source","text":"name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"growth_rate/","text":"Slot: growth_rate When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. URI: bdchm:growth_rate Applicable Classes Name Description Modifies Slot BiologicProduct A living organism, or a metabolically active biological system such as a cell... no Properties Range: String Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false","title":"Slot: growth_rate"},{"location":"growth_rate/#slot-growth_rate","text":"When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. URI: bdchm:growth_rate","title":"Slot: growth_rate"},{"location":"growth_rate/#applicable-classes","text":"Name Description Modifies Slot BiologicProduct A living organism, or a metabolically active biological system such as a cell... no","title":"Applicable Classes"},{"location":"growth_rate/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"growth_rate/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"growth_rate/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"growth_rate/#linkml-source","text":"name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false","title":"LinkML Source"},{"location":"has_questionnaire_item/","text":"Slot: has_questionnaire_item A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. URI: bdchm:has_questionnaire_item Applicable Classes Name Description Modifies Slot QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no Properties Range: QuestionnaireItem Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem","title":"Slot: has_questionnaire_item"},{"location":"has_questionnaire_item/#slot-has_questionnaire_item","text":"A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. URI: bdchm:has_questionnaire_item","title":"Slot: has_questionnaire_item"},{"location":"has_questionnaire_item/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no","title":"Applicable Classes"},{"location":"has_questionnaire_item/#properties","text":"Range: QuestionnaireItem","title":"Properties"},{"location":"has_questionnaire_item/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"has_questionnaire_item/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"has_questionnaire_item/#linkml-source","text":"name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem","title":"LinkML Source"},{"location":"id/","text":"Slot: id The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. 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The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id domain_of: - Entity range: uriorcurie required: true","title":"Slot: id"},{"location":"id/#slot-id","text":"The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. 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The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id domain_of: - Entity range: uriorcurie required: true","title":"LinkML Source"},{"location":"identity/","text":"Slot: identity A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. 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Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. 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Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. URI: schema:identifier","title":"Slot: identity"},{"location":"identity/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Demography Demographics about an individual or animal receiving care or other health-rel... no Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Organization A grouping of people or organizations with a common purpose such as a data co... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no Condition Conditions are records of a Person suggesting the presence of a disease or me... no Procedure Procedure contains records of activities or processes ordered by, or carried ... no DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no File Abstract class for various kinds of files no Document A collection of information intented to be understood together as a whole, an... no Specimen Any material taken as a sample from a biological entity (living or dead), or ... no BiologicProduct A living organism, or a metabolically active biological system such as a cell... no","title":"Applicable Classes"},{"location":"identity/#properties","text":"Range: Uriorcurie Multivalued: True","title":"Properties"},{"location":"identity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"identity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"identity/#linkml-source","text":"name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie","title":"LinkML Source"},{"location":"index_time_point/","text":"Slot: index_time_point Another TimePoint from which this point is offset. URI: bdchm:index_time_point Applicable Classes Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no Properties Range: TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_time_point owner: TimePoint domain_of: - TimePoint range: TimePoint","title":"Slot: index_time_point"},{"location":"index_time_point/#slot-index_time_point","text":"Another TimePoint from which this point is offset. URI: bdchm:index_time_point","title":"Slot: index_time_point"},{"location":"index_time_point/#applicable-classes","text":"Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no","title":"Applicable Classes"},{"location":"index_time_point/#properties","text":"Range: TimePoint","title":"Properties"},{"location":"index_time_point/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"index_time_point/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"index_time_point/#linkml-source","text":"name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_time_point owner: TimePoint domain_of: - TimePoint range: TimePoint","title":"LinkML Source"},{"location":"index_timepoint/","text":"Slot: index_timepoint The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. URI: bdchm:index_timepoint Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_timepoint owner: Participant domain_of: - Participant range: string","title":"Slot: index_timepoint"},{"location":"index_timepoint/#slot-index_timepoint","text":"The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. URI: bdchm:index_timepoint","title":"Slot: index_timepoint"},{"location":"index_timepoint/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no","title":"Applicable Classes"},{"location":"index_timepoint/#properties","text":"Range: String","title":"Properties"},{"location":"index_timepoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"index_timepoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"index_timepoint/#linkml-source","text":"name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_timepoint owner: Participant domain_of: - Participant range: string","title":"LinkML Source"},{"location":"items/","text":"Slot: items URI: bdchm:items Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set... no Properties Range: String Identifier and Mapping Information LinkML Source name: items alias: items domain_of: - Questionnaire - QuestionnaireResponse range: string","title":"Slot: items"},{"location":"items/#slot-items","text":"URI: bdchm:items","title":"Slot: items"},{"location":"items/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set... no","title":"Applicable Classes"},{"location":"items/#properties","text":"Range: String","title":"Properties"},{"location":"items/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"items/#linkml-source","text":"name: items alias: items domain_of: - Questionnaire - QuestionnaireResponse range: string","title":"LinkML Source"},{"location":"language/","text":"Slot: language The language(s) in which questions are presented. 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URI: bdchm:language","title":"Slot: language"},{"location":"language/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"language/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"language/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"language/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"language/#linkml-source","text":"name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: language owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"member_of_research_study/","text":"Slot: member_of_research_study A reference to the Study(s) of which this Participant is a member URI: bdchm:member_of_research_study Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no Properties Range: ResearchStudy Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: member_of_research_study owner: Participant domain_of: - 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Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: parent_specimen owner: Specimen domain_of: - Specimen range: Specimen required: false inlined: true inlined_as_list: true","title":"LinkML Source"},{"location":"part_of/","text":"Slot: part_of URI: bdchm:part_of Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no Properties Range: String Identifier and Mapping Information LinkML Source name: part_of alias: part_of domain_of: - ResearchStudy - QuestionnaireItem range: string","title":"Slot: part_of"},{"location":"part_of/#slot-part_of","text":"URI: bdchm:part_of","title":"Slot: part_of"},{"location":"part_of/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no","title":"Applicable Classes"},{"location":"part_of/#properties","text":"Range: String","title":"Properties"},{"location":"part_of/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"part_of/#linkml-source","text":"name: part_of alias: part_of domain_of: - ResearchStudy - QuestionnaireItem range: string","title":"LinkML Source"},{"location":"passage_number/","text":"Slot: passage_number When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. 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However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity.","title":"Comments"},{"location":"processing_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"processing_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"processing_activity/#linkml-source","text":"name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: processing_activity owner: Specimen domain_of: - Specimen range: SpecimenProcessingActivity required: false","title":"LinkML Source"},{"location":"product_type/","text":"Slot: product_type The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) URI: bdchm:product_type Applicable Classes Name Description Modifies Slot BiologicProduct A living organism, or a metabolically active biological system such as a cell... no Properties Range: String Examples Value cell line cell culture tissue culture organoid Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - 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value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false alias: product_type owner: BiologicProduct domain_of: - BiologicProduct range: string required: false","title":"LinkML Source"},{"location":"publisher/","text":"Slot: publisher Name of the publisher/steward (organization or individual) of this Questionnaire URI: bdchm:publisher Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: publisher owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: publisher"},{"location":"publisher/#slot-publisher","text":"Name of the publisher/steward (organization or individual) of this Questionnaire URI: bdchm:publisher","title":"Slot: publisher"},{"location":"publisher/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"publisher/#properties","text":"Range: String","title":"Properties"},{"location":"publisher/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"publisher/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"publisher/#linkml-source","text":"name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: publisher owner: Questionnaire domain_of: - 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crdch:enum_CRDCH_BodySite_qualifier multivalued: true alias: qualifier owner: BodySite domain_of: - BodySite range: string required: false","title":"Slot: qualifier"},{"location":"qualifier/#slot-qualifier","text":"A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') URI: bdchm:qualifier","title":"Slot: qualifier"},{"location":"qualifier/#applicable-classes","text":"Name Description Modifies Slot BodySite A site in the body of an organism, typically described in terms of an anatomi... no","title":"Applicable Classes"},{"location":"qualifier/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"qualifier/#examples","text":"Value left right bilateral","title":"Examples"},{"location":"qualifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"qualifier/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"qualifier/#linkml-source","text":"name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true alias: qualifier owner: BodySite domain_of: - BodySite range: string required: false","title":"LinkML Source"},{"location":"quality_measure/","text":"Slot: quality_measure An observation about characteristics of a specimen that are indicative of its quality or suitability for use. 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The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quality_measure owner: Specimen domain_of: - Specimen range: SpecimenQualityObservation required: false","title":"Slot: quality_measure"},{"location":"quality_measure/#slot-quality_measure","text":"An observation about characteristics of a specimen that are indicative of its quality or suitability for use. URI: bdchm:quality_measure","title":"Slot: quality_measure"},{"location":"quality_measure/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"quality_measure/#properties","text":"Range: SpecimenQualityObservation Multivalued: True","title":"Properties"},{"location":"quality_measure/#comments","text":"Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object.","title":"Comments"},{"location":"quality_measure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"quality_measure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"quality_measure/#linkml-source","text":"name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quality_measure owner: Specimen domain_of: - Specimen range: SpecimenQualityObservation required: false","title":"LinkML Source"},{"location":"quantity/","text":"Slot: quantity URI: bdchm:quantity Applicable Classes Name Description Modifies Slot Procedure Procedure contains records of activities or processes ordered by, or carried ... no DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no Properties Range: String Identifier and Mapping Information LinkML Source name: quantity alias: quantity domain_of: - Procedure - DrugExposure - DeviceExposure range: string","title":"Slot: quantity"},{"location":"quantity/#slot-quantity","text":"URI: bdchm:quantity","title":"Slot: quantity"},{"location":"quantity/#applicable-classes","text":"Name Description Modifies Slot Procedure Procedure contains records of activities or processes ordered by, or carried ... no DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no","title":"Applicable Classes"},{"location":"quantity/#properties","text":"Range: String","title":"Properties"},{"location":"quantity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"quantity/#linkml-source","text":"name: quantity alias: quantity domain_of: - Procedure - DrugExposure - DeviceExposure range: string","title":"LinkML Source"},{"location":"quantity_collected/","text":"Slot: quantity_collected The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) URI: bdchm:quantity_collected Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: Quantity Comments This attribute applies only when Specimen.category='initial sample'. 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The specific type of observation made is captured as data in the Observation object.","title":"Comments"},{"location":"quantity_measure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"quantity_measure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"quantity_measure/#linkml-source","text":"name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. 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URI: bdchm:refills","title":"Slot: refills"},{"location":"refills/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"refills/#properties","text":"Range: Integer","title":"Properties"},{"location":"refills/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"refills/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"refills/#linkml-source","text":"name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"LinkML Source"},{"location":"related_document/","text":"Slot: related_document A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) URI: bdchm:related_document Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: Document Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false","title":"Slot: related_document"},{"location":"related_document/#slot-related_document","text":"A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) URI: bdchm:related_document","title":"Slot: related_document"},{"location":"related_document/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"related_document/#properties","text":"Range: Document Multivalued: True","title":"Properties"},{"location":"related_document/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"related_document/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"related_document/#linkml-source","text":"name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false","title":"LinkML Source"},{"location":"relationship_to_participant/","text":"Slot: relationship_to_participant A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. 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If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') URI: bdchm:relationship_to_participant","title":"Slot: relationship_to_participant"},{"location":"relationship_to_participant/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"relationship_to_participant/#properties","text":"Range: String","title":"Properties"},{"location":"relationship_to_participant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"relationship_to_participant/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"relationship_to_participant/#linkml-source","text":"name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. 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If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string","title":"LinkML Source"},{"location":"research_project_type/","text":"Slot: research_project_type The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') URI: bdchm:research_project_type Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"Slot: research_project_type"},{"location":"research_project_type/#slot-research_project_type","text":"The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') URI: bdchm:research_project_type","title":"Slot: research_project_type"},{"location":"research_project_type/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"research_project_type/#properties","text":"Range: String","title":"Properties"},{"location":"research_project_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"research_project_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"research_project_type/#linkml-source","text":"name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - 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QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"LinkML Source"},{"location":"role/","text":"Slot: role A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) URI: bdchm:role Applicable Classes Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no Properties Range: String Multivalued: True Examples Value lysis buffer fixative mounting medium collection media Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - 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value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false","title":"LinkML Source"},{"location":"route_concept/","text":"Slot: route_concept Route of drug administration. 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URI: bdchm:route_concept","title":"Slot: route_concept"},{"location":"route_concept/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"route_concept/#properties","text":"Range: DrugRouteEnum","title":"Properties"},{"location":"route_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"route_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"route_concept/#linkml-source","text":"name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum","title":"LinkML Source"},{"location":"section_location/","text":"Slot: section_location The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) URI: bdchm:section_location Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SectionLocationEnum Examples Value Top Bottom Unknown Comments This attribute applies only to Specimens that are of type 'portion' or 'slide'. 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URI: bdchm:source_participant","title":"Slot: source_participant"},{"location":"source_participant/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"source_participant/#properties","text":"Range: Participant","title":"Properties"},{"location":"source_participant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"source_participant/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"source_participant/#linkml-source","text":"name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false","title":"LinkML Source"},{"location":"species/","text":"Slot: species The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). URI: bdchm:species Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: CellularOrganismSpeciesEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: species owner: Person domain_of: - Person range: CellularOrganismSpeciesEnum","title":"Slot: species"},{"location":"species/#slot-species","text":"The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). URI: bdchm:species","title":"Slot: species"},{"location":"species/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"species/#properties","text":"Range: CellularOrganismSpeciesEnum","title":"Properties"},{"location":"species/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"species/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"species/#linkml-source","text":"name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: species owner: Person domain_of: - Person range: CellularOrganismSpeciesEnum","title":"LinkML Source"},{"location":"specimen_order/","text":"Slot: specimen_order A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. URI: bdchm:specimen_order Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false","title":"Slot: specimen_order"},{"location":"specimen_order/#slot-specimen_order","text":"A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. URI: bdchm:specimen_order","title":"Slot: specimen_order"},{"location":"specimen_order/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"specimen_order/#properties","text":"Range: Integer","title":"Properties"},{"location":"specimen_order/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specimen_order/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"specimen_order/#linkml-source","text":"name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false","title":"LinkML Source"},{"location":"specimen_type/","text":"Slot: specimen_type The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: bdchm:specimen_type Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenTypeEnum Examples Value Fresh Specimen Portion Aliquot Analyte Slide Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false","title":"Slot: specimen_type"},{"location":"specimen_type/#slot-specimen_type","text":"The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: bdchm:specimen_type","title":"Slot: specimen_type"},{"location":"specimen_type/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"specimen_type/#properties","text":"Range: SpecimenTypeEnum","title":"Properties"},{"location":"specimen_type/#examples","text":"Value Fresh Specimen Portion Aliquot Analyte Slide","title":"Examples"},{"location":"specimen_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specimen_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"specimen_type/#linkml-source","text":"name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false","title":"LinkML Source"},{"location":"sponsor/","text":"Slot: sponsor An entity that is responsible for the initiation, management, and/or financing of a research project. URI: bdchm:sponsor Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"Slot: sponsor"},{"location":"sponsor/#slot-sponsor","text":"An entity that is responsible for the initiation, management, and/or financing of a research project. URI: bdchm:sponsor","title":"Slot: sponsor"},{"location":"sponsor/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"sponsor/#properties","text":"Range: String","title":"Properties"},{"location":"sponsor/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sponsor/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"sponsor/#linkml-source","text":"name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"LinkML Source"},{"location":"storage_activity/","text":"Slot: storage_activity An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. URI: bdchm:storage_activity Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenStorageActivity Multivalued: True Comments The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false","title":"Slot: storage_activity"},{"location":"storage_activity/#slot-storage_activity","text":"An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. URI: bdchm:storage_activity","title":"Slot: storage_activity"},{"location":"storage_activity/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"storage_activity/#properties","text":"Range: SpecimenStorageActivity Multivalued: True","title":"Properties"},{"location":"storage_activity/#comments","text":"The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions","title":"Comments"},{"location":"storage_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"storage_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"storage_activity/#linkml-source","text":"name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false","title":"LinkML Source"},{"location":"study_arm/","text":"Slot: study_arm The arm(s) of the study on which the Participant is enrolled URI: bdchm:study_arm Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no Properties Range: String Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string","title":"Slot: study_arm"},{"location":"study_arm/#slot-study_arm","text":"The arm(s) of the study on which the Participant is enrolled URI: bdchm:study_arm","title":"Slot: study_arm"},{"location":"study_arm/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no","title":"Applicable Classes"},{"location":"study_arm/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"study_arm/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"study_arm/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"study_arm/#linkml-source","text":"name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string","title":"LinkML Source"},{"location":"substance_quantity/","text":"Slot: substance_quantity The quantity of substance this instance stands for. URI: bdchm:substance_quantity Applicable Classes Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no Properties Range: Quantity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: substance_quantity owner: Substance domain_of: - Substance range: Quantity required: false","title":"Slot: substance_quantity"},{"location":"substance_quantity/#slot-substance_quantity","text":"The quantity of substance this instance stands for. URI: bdchm:substance_quantity","title":"Slot: substance_quantity"},{"location":"substance_quantity/#applicable-classes","text":"Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no","title":"Applicable Classes"},{"location":"substance_quantity/#properties","text":"Range: Quantity","title":"Properties"},{"location":"substance_quantity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"substance_quantity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"substance_quantity/#linkml-source","text":"name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: substance_quantity owner: Substance domain_of: - Substance range: Quantity required: false","title":"LinkML Source"},{"location":"substance_type/","text":"Slot: substance_type The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. URI: bdchm:substance_type Applicable Classes Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no Properties Range: String Examples Value toluene formalin DMEM Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false","title":"Slot: substance_type"},{"location":"substance_type/#slot-substance_type","text":"The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. URI: bdchm:substance_type","title":"Slot: substance_type"},{"location":"substance_type/#applicable-classes","text":"Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no","title":"Applicable Classes"},{"location":"substance_type/#properties","text":"Range: String","title":"Properties"},{"location":"substance_type/#examples","text":"Value toluene formalin DMEM","title":"Examples"},{"location":"substance_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"substance_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"substance_type/#linkml-source","text":"name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false","title":"LinkML Source"},{"location":"text/","text":"Slot: text URI: bdchm:text Applicable Classes Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no Properties Range: String Identifier and Mapping Information LinkML Source name: text alias: text domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string","title":"Slot: text"},{"location":"text/#slot-text","text":"URI: bdchm:text","title":"Slot: text"},{"location":"text/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no","title":"Applicable Classes"},{"location":"text/#properties","text":"Range: String","title":"Properties"},{"location":"text/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"text/#linkml-source","text":"name: text alias: text domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string","title":"LinkML Source"},{"location":"title/","text":"Slot: title Name for this Questionnaire (human friendly) URI: bdchm:title Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: title"},{"location":"title/#slot-title","text":"Name for this Questionnaire (human friendly) URI: bdchm:title","title":"Slot: title"},{"location":"title/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"title/#properties","text":"Range: String","title":"Properties"},{"location":"title/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"title/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"title/#linkml-source","text":"name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"transport_activity/","text":"Slot: transport_activity An activity through which the specimen is transported between locations. URI: bdchm:transport_activity Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenTransportActivity Multivalued: True Comments The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false","title":"Slot: transport_activity"},{"location":"transport_activity/#slot-transport_activity","text":"An activity through which the specimen is transported between locations. URI: bdchm:transport_activity","title":"Slot: transport_activity"},{"location":"transport_activity/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"transport_activity/#properties","text":"Range: SpecimenTransportActivity Multivalued: True","title":"Properties"},{"location":"transport_activity/#comments","text":"The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time.","title":"Comments"},{"location":"transport_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"transport_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"transport_activity/#linkml-source","text":"name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false","title":"LinkML Source"},{"location":"transport_destination/","text":"Slot: transport_destination An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. URI: bdchm:transport_destination Applicable Classes Name Description Modifies Slot SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: Organization Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false","title":"Slot: transport_destination"},{"location":"transport_destination/#slot-transport_destination","text":"An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. URI: bdchm:transport_destination","title":"Slot: transport_destination"},{"location":"transport_destination/#applicable-classes","text":"Name Description Modifies Slot SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"transport_destination/#properties","text":"Range: Organization","title":"Properties"},{"location":"transport_destination/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"transport_destination/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"transport_destination/#linkml-source","text":"name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false","title":"LinkML Source"},{"location":"transport_origin/","text":"Slot: transport_origin An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. URI: bdchm:transport_origin Applicable Classes Name Description Modifies Slot SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: Organization Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_origin owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false","title":"Slot: transport_origin"},{"location":"transport_origin/#slot-transport_origin","text":"An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. URI: bdchm:transport_origin","title":"Slot: transport_origin"},{"location":"transport_origin/#applicable-classes","text":"Name Description Modifies Slot SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"transport_origin/#properties","text":"Range: Organization","title":"Properties"},{"location":"transport_origin/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"transport_origin/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"transport_origin/#linkml-source","text":"name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_origin owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false","title":"LinkML Source"},{"location":"type/","text":"Slot: type URI: bdchm:type Applicable Classes Name Description Modifies Slot QuestionnaireResponseValue Single-valued answer to the question no QuestionnaireResponseValueDecimal Single-valued decimal answer to the question no QuestionnaireResponseValueBoolean Single-valued boolean answer to the question no QuestionnaireResponseValueInteger Single-valued integer answer to the question no QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question no QuestionnaireResponseValueString Single-valued string answer to the question no ObservationValue Single-valued observation valueholiding slot no ObservationValueDecimal Single-valued decimal observation no ObservationValueInteger Single-valued integer observation no ObservationValueBoolean Single-valued boolean observation no ObservationValueString Single-valued string observation no ObservationValueQuantity Single-valued Quantity observation no Properties Range: String Identifier and Mapping Information LinkML Source name: type alias: type domain_of: - QuestionnaireResponseValue - ObservationValue range: string","title":"Slot: type"},{"location":"type/#slot-type","text":"URI: bdchm:type","title":"Slot: type"},{"location":"type/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireResponseValue Single-valued answer to the question no QuestionnaireResponseValueDecimal Single-valued decimal answer to the question no QuestionnaireResponseValueBoolean Single-valued boolean answer to the question no QuestionnaireResponseValueInteger Single-valued integer answer to the question no QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question no QuestionnaireResponseValueString Single-valued string answer to the question no ObservationValue Single-valued observation valueholiding slot no ObservationValueDecimal Single-valued decimal observation no ObservationValueInteger Single-valued integer observation no ObservationValueBoolean Single-valued boolean observation no ObservationValueString Single-valued string observation no ObservationValueQuantity Single-valued Quantity observation no","title":"Applicable Classes"},{"location":"type/#properties","text":"Range: String","title":"Properties"},{"location":"type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"type/#linkml-source","text":"name: type alias: type domain_of: - QuestionnaireResponseValue - ObservationValue range: string","title":"LinkML Source"},{"location":"unit/","text":"Slot: unit A coded or free text (in the .text field) representation of the unit. URI: bdchm:unit Applicable Classes Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no Properties Range: UnitOfMeasurementEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false","title":"Slot: unit"},{"location":"unit/#slot-unit","text":"A coded or free text (in the .text field) representation of the unit. URI: bdchm:unit","title":"Slot: unit"},{"location":"unit/#applicable-classes","text":"Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no","title":"Applicable Classes"},{"location":"unit/#properties","text":"Range: UnitOfMeasurementEnum","title":"Properties"},{"location":"unit/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"unit/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"unit/#linkml-source","text":"name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false","title":"LinkML Source"},{"location":"uri/","text":"Slot: uri A unique identifier or url for identifying or locating the file. URI: bdchm:uri Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: Uriorcurie Comments Not included in the Gen3 Core Metadata or Dublin Core. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: uri description: A unique identifier or url for identifying or locating the file. comments: - Not included in the Gen3 Core Metadata or Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: uri owner: File domain_of: - File range: uriorcurie","title":"Slot: uri"},{"location":"uri/#slot-uri","text":"A unique identifier or url for identifying or locating the file. URI: bdchm:uri","title":"Slot: uri"},{"location":"uri/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"uri/#properties","text":"Range: Uriorcurie","title":"Properties"},{"location":"uri/#comments","text":"Not included in the Gen3 Core Metadata or Dublin Core.","title":"Comments"},{"location":"uri/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"uri/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"uri/#linkml-source","text":"name: uri description: A unique identifier or url for identifying or locating the file. comments: - Not included in the Gen3 Core Metadata or Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: uri owner: File domain_of: - File range: uriorcurie","title":"LinkML Source"},{"location":"url/","text":"Slot: url URI: bdchm:url Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Document A collection of information intented to be understood together as a whole, an... no Properties Range: String Identifier and Mapping Information LinkML Source name: url alias: url domain_of: - ResearchStudy - Questionnaire - Document range: string","title":"Slot: url"},{"location":"url/#slot-url","text":"URI: bdchm:url","title":"Slot: url"},{"location":"url/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Document A collection of information intented to be understood together as a whole, an... no","title":"Applicable Classes"},{"location":"url/#properties","text":"Range: String","title":"Properties"},{"location":"url/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"url/#linkml-source","text":"name: url alias: url domain_of: - ResearchStudy - Questionnaire - Document range: string","title":"LinkML Source"},{"location":"valid_from/","text":"Slot: valid_from The point in time from which the consent record is valid. URI: bdchm:valid_from Applicable Classes Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no Properties Range: TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint","title":"Slot: valid_from"},{"location":"valid_from/#slot-valid_from","text":"The point in time from which the consent record is valid. URI: bdchm:valid_from","title":"Slot: valid_from"},{"location":"valid_from/#applicable-classes","text":"Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no","title":"Applicable Classes"},{"location":"valid_from/#properties","text":"Range: TimePoint","title":"Properties"},{"location":"valid_from/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"valid_from/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"valid_from/#linkml-source","text":"name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint","title":"LinkML Source"},{"location":"valid_to/","text":"Slot: valid_to The point in time after which the consent record is invalid. URI: bdchm:valid_to Applicable Classes Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no Properties Range: TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint","title":"Slot: valid_to"},{"location":"valid_to/#slot-valid_to","text":"The point in time after which the consent record is invalid. URI: bdchm:valid_to","title":"Slot: valid_to"},{"location":"valid_to/#applicable-classes","text":"Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no","title":"Applicable Classes"},{"location":"valid_to/#properties","text":"Range: TimePoint","title":"Properties"},{"location":"valid_to/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"valid_to/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"valid_to/#linkml-source","text":"name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint","title":"LinkML Source"},{"location":"value/","text":"Slot: value A general slot to hold a value. URI: bdchm:value Applicable Classes Name Description Modifies Slot QuestionnaireResponseValue Single-valued answer to the question no ObservationValue Single-valued observation valueholiding slot no QuestionnaireResponseValueDecimal Single-valued decimal answer to the question yes QuestionnaireResponseValueBoolean Single-valued boolean answer to the question yes QuestionnaireResponseValueInteger Single-valued integer answer to the question yes QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question yes QuestionnaireResponseValueString Single-valued string answer to the question yes DimensionalObservation A structured object that describes a single data item about the physical dime... yes SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... yes SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... yes Observation A data structure with key (observation_type) and value (value) attributes tha... no ObservationValueDecimal Single-valued decimal observation yes ObservationValueInteger Single-valued integer observation yes ObservationValueBoolean Single-valued boolean observation yes ObservationValueString Single-valued string observation yes ObservationValueQuantity Single-valued Quantity observation yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Slot: value"},{"location":"value/#slot-value","text":"A general slot to hold a value. URI: bdchm:value","title":"Slot: value"},{"location":"value/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireResponseValue Single-valued answer to the question no ObservationValue Single-valued observation valueholiding slot no QuestionnaireResponseValueDecimal Single-valued decimal answer to the question yes QuestionnaireResponseValueBoolean Single-valued boolean answer to the question yes QuestionnaireResponseValueInteger Single-valued integer answer to the question yes QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question yes QuestionnaireResponseValueString Single-valued string answer to the question yes DimensionalObservation A structured object that describes a single data item about the physical dime... yes SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... yes SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... yes Observation A data structure with key (observation_type) and value (value) attributes tha... no ObservationValueDecimal Single-valued decimal observation yes ObservationValueInteger Single-valued integer observation yes ObservationValueBoolean Single-valued boolean observation yes ObservationValueString Single-valued string observation yes ObservationValueQuantity Single-valued Quantity observation yes","title":"Applicable Classes"},{"location":"value/#properties","text":"Range: String","title":"Properties"},{"location":"value/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"value/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"value/#linkml-source","text":"name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"LinkML Source"},{"location":"value_concept/","text":"Slot: value_concept A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") URI: bdchm:value_concept Applicable Classes Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false","title":"Slot: value_concept"},{"location":"value_concept/#slot-value_concept","text":"A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") URI: bdchm:value_concept","title":"Slot: value_concept"},{"location":"value_concept/#applicable-classes","text":"Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no","title":"Applicable Classes"},{"location":"value_concept/#properties","text":"Range: String","title":"Properties"},{"location":"value_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"value_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"value_concept/#linkml-source","text":"name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false","title":"LinkML Source"},{"location":"value_decimal/","text":"Slot: value_decimal An amount, in the given units (if specified) URI: bdchm:value_decimal Applicable Classes Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no Properties Range: Decimal Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false","title":"Slot: value_decimal"},{"location":"value_decimal/#slot-value_decimal","text":"An amount, in the given units (if specified) URI: bdchm:value_decimal","title":"Slot: value_decimal"},{"location":"value_decimal/#applicable-classes","text":"Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no","title":"Applicable Classes"},{"location":"value_decimal/#properties","text":"Range: Decimal","title":"Properties"},{"location":"value_decimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"value_decimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"value_decimal/#linkml-source","text":"name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false","title":"LinkML Source"},{"location":"version/","text":"Slot: version The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. URI: bdchm:version Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: version"},{"location":"version/#slot-version","text":"The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. URI: bdchm:version","title":"Slot: version"},{"location":"version/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"version/#properties","text":"Range: String","title":"Properties"},{"location":"version/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"version/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"version/#linkml-source","text":"name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"visit_category/","text":"Slot: visit_category A value representing the kind (or category) of visit, like inpatient or outpatient. URI: bdchm:visit_category Applicable Classes Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no Properties Range: VisitCategoryEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum","title":"Slot: visit_category"},{"location":"visit_category/#slot-visit_category","text":"A value representing the kind (or category) of visit, like inpatient or outpatient. URI: bdchm:visit_category","title":"Slot: visit_category"},{"location":"visit_category/#applicable-classes","text":"Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no","title":"Applicable Classes"},{"location":"visit_category/#properties","text":"Range: VisitCategoryEnum","title":"Properties"},{"location":"visit_category/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"visit_category/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"visit_category/#linkml-source","text":"name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum","title":"LinkML Source"},{"location":"visit_provenance/","text":"Slot: visit_provenance A value representing the provenance of the visit record, or where the record comes from. URI: bdchm:visit_provenance Applicable Classes Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no Properties Range: VisitProvenanceEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum","title":"Slot: visit_provenance"},{"location":"visit_provenance/#slot-visit_provenance","text":"A value representing the provenance of the visit record, or where the record comes from. URI: bdchm:visit_provenance","title":"Slot: visit_provenance"},{"location":"visit_provenance/#applicable-classes","text":"Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no","title":"Applicable Classes"},{"location":"visit_provenance/#properties","text":"Range: VisitProvenanceEnum","title":"Properties"},{"location":"visit_provenance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"visit_provenance/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"visit_provenance/#linkml-source","text":"name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum","title":"LinkML Source"},{"location":"vital_status/","text":"Slot: vital_status Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. URI: bdchm:vital_status Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: VitalStatusEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum","title":"Slot: vital_status"},{"location":"vital_status/#slot-vital_status","text":"Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. URI: bdchm:vital_status","title":"Slot: vital_status"},{"location":"vital_status/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"vital_status/#properties","text":"Range: VitalStatusEnum","title":"Properties"},{"location":"vital_status/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"vital_status/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"vital_status/#linkml-source","text":"name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum","title":"LinkML Source"},{"location":"year_of_birth/","text":"Slot: year_of_birth Numeric value to represent the calendar year in which an individual was born. URI: bdchm:year_of_birth Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_birth owner: Person domain_of: - Person range: integer","title":"Slot: year_of_birth"},{"location":"year_of_birth/#slot-year_of_birth","text":"Numeric value to represent the calendar year in which an individual was born. 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URI: bdchm:year_of_death Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_death owner: Person domain_of: - Person range: integer","title":"Slot: year_of_death"},{"location":"year_of_death/#slot-year_of_death","text":"Numeric value to represent the calendar year in which an individual died. 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+{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"","text":"BioData Catalyst Harmonized Model (bdchm) This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm Name: bdchm Classes Class Description Entity Any resource that has its own identifier BiologicProduct A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. BodySite A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. Condition Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. Consent An entity that can be used to capture consent code and other relevant data about consent for a study. Demography Demographics about an individual or animal receiving care or other health-related services. DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. Document A collection of information intented to be understood together as a whole, and codified in human-readable form. DrugExposure DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. File Abstract class for various kinds of files. Subclasses may be defined for specific file types. Observation A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. DimensionalObservation A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. ObservationSet A structured object to hold related Observations in a set. DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). Organization A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. Participant A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. Person Administrative information about an individual or animal receiving care or other health-related services. Procedure Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] Quantity A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. Questionnaire A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) ResearchStudy A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. Specimen Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) SpecimenCreationActivity The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. SpecimenTransportActivity An activity through which a specimen is transported between locations or organizations. Substance A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. TimePoint A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. Visit Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) ObservationValue Single-valued observation valueholiding slot ObservationValueBoolean Single-valued boolean observation ObservationValueDecimal Single-valued decimal observation ObservationValueInteger Single-valued integer observation ObservationValueQuantity Single-valued Quantity observation ObservationValueString Single-valued string observation QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) QuestionnaireResponseValue Single-valued answer to the question. (FHIR) QuestionnaireResponseValueBoolean Single-valued boolean answer to the question QuestionnaireResponseValueDecimal Single-valued decimal answer to the question QuestionnaireResponseValueInteger Single-valued integer answer to the question QuestionnaireResponseValueString Single-valued string answer to the question QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question ResearchStudyCollection A holder for ResearchStudy objects TimePeriod A period of time between a start and end time point. Slots Slot Description activity_type The high-level type of creation activity additive A material substance added to the container (typically to support the primary... age_at_condition_end The Participant's age (expressed in days) when the condition was recorded as ... age_at_condition_start The Participant's age (expressed in days) when the condition was first record... age_at_death The age of an individual at the time of death, expressed in days since birth age_at_enrollment The age in days when the Participant enrolled on the ResearchStudy age_at_exposure_end The Participant's age (expressed in days) at the exposure end date, if availa... age_at_exposure_start The Participant's age (expressed in days) at the exposure start date age_at_observation The Participant's age (expressed in days) when the Observation was made age_at_procedure The Participant's age (expressed in days) when the procedure was performed age_at_response The age (in days) of the Participant when the QuestionnaireResponse was captu... age_at_visit_end The age of the Participant (in days) at the end of the Visit age_at_visit_start The age of the Participant (in days) at the start of the Visit alias A secondary name for the organization such as a short name or abbreviation (e analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... associated_participant A reference to the Participant that is associated with this record associated_person A reference to the Person that is associated with this record associated_timepoint A collection of timepoint observations that are relevant to research projects... associated_visit A reference to the Visit during which this QuestionnaireResponse was captured breed A label given to a group of animals homogeneous in appearance and other chara... category The general category of observation set described cause_of_death Coded value indicating the circumstance or condition that results in the deat... cellular_composition_type A term describing the type of cell or cellular material comprising a specimen code Corresponding concept for this item in a terminology collection_method_type The type of method applied in collecting a sample from its original source collection_site The anatomic site from which a specimen was collected condition_concept The coded value for the presence of a disease or medical condition stated as ... condition_provenance A value representing the provenance of the Condition record condition_status A value indicating whether the medical condition described in this record is ... consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ... consents Data Use Restrictions that are used to indicate permissions/restrictions for ... contained_in A physical container in which a specimen is presently held or attached - as ... container A container in which the specimen is held or affixed during its storage container_number Informal number by which the container is referenced or identified (e container_type The kind of the container copyright Textual description of any use and/or publishing restrictions copyright_label Copyright holder and year(s) creation_activity The activity through which a specimen was created, by removing material from ... data_category A broad categorization of the contents of the data file data_type The nature or genre of the resource date_ended The date when the research project ended date_started The date when the research project began date_time An explicitly specified timepoint described in terms of a date and optionally... days_supply The number of days of supply of the medication as recorded in the original pr... derivation_method_type The type of method applied to derive a new specimen from an existing one derived_from A File from which this File is derived derived_product A 'living' biologically active product that was derived from the specimen (e description A free text field to capture additional info/explanation about the research s... description_shortened An abbreviated description of a research program, project, or study device_concept The coded value for a device dimensional_measures Observations about the current physical dimensions of an object (e document_type The high-level type of the document (e drug_concept The coded value for a drug duration The length of time over which the activity was performed entries ethnicity An individual's self-described social and cultural grouping, specifically whe... event_type An event that occurred at the point in time specified by this TimePoint exposure_provenance A value representing the provenance of the DrugExposure record file_location A unique identifier or url for identifying or locating the file file_name The name (or part of a name) of a file (of any type) file_size The size of the data file (object) in bytes focus The entity that the report is primarily about format The file format, physical medium, or dimensions of the resource growth_rate When the specimen an actively growing model system, such as a cell or tissue ... has_questionnaire_item A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... id The 'logical' identifier of the entity within the system of record identity A 'business' identifier or accession number for the entity, typically as prov... index_time_point Another TimePoint from which this point is offset index_timepoint The text term used to describe the reference or anchor date used for date obf... items A collection of QuestionnaireItem objects which encapsulate the question bein... language The language(s) in which questions are presented md5sum The 128-bit hash value expressed as a 32 digit hexadecimal number used as a f... member_of_research_study A reference to the Study(s) of which this Participant is a member method_type A specific type of method or procedure performed to process the specimen name An unabridged name of a research program, project, or study name_shortened An abbreviated name of a research program, project, or study observation_type The type of Observation being represented (e observations A set of one or more observations offset_from_index A quantity of time that, together with the index date or event, can be used t... organization_type The type of the organization (e originating_site The Organization through which a subject was enrolled on a ResearchStudy parent_container A larger container of which this container is a part (e parent_specimen An existing specimen from which the specimen of interest was directly derived... part_of A reference to a parent ResearchStudy (e passage_number When the specimen an actively growing model system, such as a cell or tissue ... performed_by The organization or group that performed the activity period_end When a period of time ended period_start When a period of time started principal_investigator The investigator or investigators leading a project procedure_concept The coded value that describes the procedure, derived from OMOP codes procedure_provenance A value representing the provenance of the Procedure record processing_activity An activity that modifies the physical structure, composition, or state of a ... product_type The high level type of model system (e publisher Name of the publisher/steward (organization or individual) of this Questionna... qualifier A qualifier that further refines or specifies the location of the body site -... quality_measure An observation about characteristics of a specimen that are indicative of its... quantity The quantity of procedures ordered or administered quantity_collected The quantity of material in the specimen as originally collected from its ori... quantity_measure An observation related to the present quantity of a specimen - e race An arbitrary classification of a taxonomic group that is a division of a spec... refills Intended refills at time of the prescription related_document A reference to an external document that is about or related to the specimen ... relationship_to_participant A value indicating the relationship between the Participant to which the Cond... research_project_type The 'type' of ResearchStudy represented (e response_value role A role played by the substance in a particular application (e route_concept Route of drug administration section_location The location in a parent specimen from which a section/portion was excised (e sex The biologic character or quality that distinguishes male and female from one... sig This is the verbatim instruction for the drug as written by the provider site A term describing any site in the body source_material_type The general kind of material from which the specimen was derived source_participant A specific Subject from which the specimen was directly or indirectly derived species The scientific binomial name for the species of the Person (e specimen_order A numeric value that represents the sequential order of this creation activit... specimen_type The high-level type of the specimen, based on its derivation provenance (i sponsor An entity that is responsible for the initiation, management, and/or financin... storage_activity An activity that results in the storage or maintenance of a specimen in a par... study_arm The arm(s) of the study on which the Participant is enrolled substance_quantity The quantity of substance this instance stands for substance_type The specific type of the substance - at as granular a level as possible text Name for group or question text title Name for this Questionnaire (human friendly) transport_activity An activity through which the specimen is transported between locations transport_destination An organization (facility, site, lab, etc) to which the specimen is delivered... transport_origin An organization (facility, site, lab, etc) from which the specimen was transp... type unit A coded or free text (in the url A URL address for a resource that provides information about a research progr... valid_from The point in time from which the consent record is valid valid_to The point in time after which the consent record is invalid value A general slot to hold a value value_concept A coded value representing a quantity (e value_decimal An amount, in the given units (if specified) version The identifier that is used to identify this version of the questionnaire whe... visit_category A value representing the kind (or category) of visit, like inpatient or outpa... visit_provenance A value representing the provenance of the visit record, or where the record ... vital_status Coded value indicating the state or condition of being living or deceased; al... year_of_birth Numeric value to represent the calendar year in which an individual was born year_of_death Numeric value to represent the calendar year in which an individual died Enumerations Enumeration Description AnalyteTypeEnum CellularOrganismSpeciesEnum A constrained set of enumerative values containing the NCBITaxon values for c... ConditionConceptEnum A constrained set of enumerative values containing both the MONDO values for ... ConditionStatusEnum A constrained set of enumerative values indicating whether a Condition is pre... DataUseEnum A constrained set of enumerative values drawn from the Data Use Ontology (DUO... DeviceExposureConceptEnum Device codes from SNOMED DeviceExposureProvenanceEnum Source of device exposure record DrugExposureConceptEnum Drug codes from RxNorm DrugExposureProvenanceEnum Source of drug exposure record DrugRouteEnum Routes of drug administration EthnicityEnum A constrained set of enumerative values containing the United States Office o... HpoPhenotypicAbnormalityEnum A constrained set of enumerative values containing the HPO values for phenoty... MondoHumanDiseaseEnum A constrained set of enumerative values containing the MONDO values for human... ProcedureConceptEnum Procedure codes from OMOP ProvenanceEnum A constrained set of enumerative values containing the OMOP values for proven... RaceEnum A constrained set of enumerative values containing the United States Office o... SectionLocationEnum The location in a parent specimen from which a section/portion was excised SexEnum A constrained set of enumerative values containing the OMOP values for sex SourceMaterialTypeEnum SpecimenCollectionMethodType SpecimenCreationActivityTypeEnum The high-level type of activity through which the specimen was generated (i SpecimenProcessingActivityTypeEnum The high-level type of processing activity performed SpecimenQualityObservationMethodEnum A type of method used in determining the quantity of a specimen SpecimenQualityObservationTypeEnum Types of measurements that reflect the quality of a specimen or its suitabili... SpecimenQuantityObservationTypeEnum Measures related to the quantity of a specimen or analyte it currently contai... SpecimenTypeEnum A high-level type of specimen, based on its derivation provenance (i UnitOfMeasurementEnum Standard units of measurement from the [Units of Measurement (UOM) ontology](... VertebrateBreedEnum A constrained set of enumerative values containing the VBO values for vertebr... VisitCategoryEnum A constrained set of enumerative values containing the OMOP values for visit ... VisitProvenanceEnum A constrained set of enumerative values containing the OMOP values for visit ... VitalStatusEnum A constrained set of enumerative values containing the OMOP values for vital ... Types Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... 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URI: https://w3id.org/nhlbidatastage/bdchm Name: bdchm","title":"BioData Catalyst Harmonized Model (bdchm)"},{"location":"#classes","text":"Class Description Entity Any resource that has its own identifier BiologicProduct A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. BodySite A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. Condition Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. Consent An entity that can be used to capture consent code and other relevant data about consent for a study. Demography Demographics about an individual or animal receiving care or other health-related services. DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. Document A collection of information intented to be understood together as a whole, and codified in human-readable form. DrugExposure DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. File Abstract class for various kinds of files. Subclasses may be defined for specific file types. Observation A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. DimensionalObservation A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. ObservationSet A structured object to hold related Observations in a set. DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). Organization A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. Participant A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. Person Administrative information about an individual or animal receiving care or other health-related services. Procedure Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] Quantity A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. Questionnaire A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) ResearchStudy A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. Specimen Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) SpecimenCreationActivity The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. SpecimenTransportActivity An activity through which a specimen is transported between locations or organizations. Substance A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. TimePoint A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. Visit Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) ObservationValue Single-valued observation valueholiding slot ObservationValueBoolean Single-valued boolean observation ObservationValueDecimal Single-valued decimal observation ObservationValueInteger Single-valued integer observation ObservationValueQuantity Single-valued Quantity observation ObservationValueString Single-valued string observation QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) QuestionnaireResponseValue Single-valued answer to the question. (FHIR) QuestionnaireResponseValueBoolean Single-valued boolean answer to the question QuestionnaireResponseValueDecimal Single-valued decimal answer to the question QuestionnaireResponseValueInteger Single-valued integer answer to the question QuestionnaireResponseValueString Single-valued string answer to the question QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question ResearchStudyCollection A holder for ResearchStudy objects TimePeriod A period of time between a start and end time point.","title":"Classes"},{"location":"#slots","text":"Slot Description activity_type The high-level type of creation activity additive A material substance added to the container (typically to support the primary... age_at_condition_end The Participant's age (expressed in days) when the condition was recorded as ... age_at_condition_start The Participant's age (expressed in days) when the condition was first record... age_at_death The age of an individual at the time of death, expressed in days since birth age_at_enrollment The age in days when the Participant enrolled on the ResearchStudy age_at_exposure_end The Participant's age (expressed in days) at the exposure end date, if availa... age_at_exposure_start The Participant's age (expressed in days) at the exposure start date age_at_observation The Participant's age (expressed in days) when the Observation was made age_at_procedure The Participant's age (expressed in days) when the procedure was performed age_at_response The age (in days) of the Participant when the QuestionnaireResponse was captu... age_at_visit_end The age of the Participant (in days) at the end of the Visit age_at_visit_start The age of the Participant (in days) at the start of the Visit alias A secondary name for the organization such as a short name or abbreviation (e analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... associated_participant A reference to the Participant that is associated with this record associated_person A reference to the Person that is associated with this record associated_timepoint A collection of timepoint observations that are relevant to research projects... associated_visit A reference to the Visit during which this QuestionnaireResponse was captured breed A label given to a group of animals homogeneous in appearance and other chara... category The general category of observation set described cause_of_death Coded value indicating the circumstance or condition that results in the deat... cellular_composition_type A term describing the type of cell or cellular material comprising a specimen code Corresponding concept for this item in a terminology collection_method_type The type of method applied in collecting a sample from its original source collection_site The anatomic site from which a specimen was collected condition_concept The coded value for the presence of a disease or medical condition stated as ... condition_provenance A value representing the provenance of the Condition record condition_status A value indicating whether the medical condition described in this record is ... consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ... consents Data Use Restrictions that are used to indicate permissions/restrictions for ... contained_in A physical container in which a specimen is presently held or attached - as ... container A container in which the specimen is held or affixed during its storage container_number Informal number by which the container is referenced or identified (e container_type The kind of the container copyright Textual description of any use and/or publishing restrictions copyright_label Copyright holder and year(s) creation_activity The activity through which a specimen was created, by removing material from ... data_category A broad categorization of the contents of the data file data_type The nature or genre of the resource date_ended The date when the research project ended date_started The date when the research project began date_time An explicitly specified timepoint described in terms of a date and optionally... days_supply The number of days of supply of the medication as recorded in the original pr... derivation_method_type The type of method applied to derive a new specimen from an existing one derived_from A File from which this File is derived derived_product A 'living' biologically active product that was derived from the specimen (e description A free text field to capture additional info/explanation about the research s... description_shortened An abbreviated description of a research program, project, or study device_concept The coded value for a device dimensional_measures Observations about the current physical dimensions of an object (e document_type The high-level type of the document (e drug_concept The coded value for a drug duration The length of time over which the activity was performed entries ethnicity An individual's self-described social and cultural grouping, specifically whe... event_type An event that occurred at the point in time specified by this TimePoint exposure_provenance A value representing the provenance of the DrugExposure record file_location A unique identifier or url for identifying or locating the file file_name The name (or part of a name) of a file (of any type) file_size The size of the data file (object) in bytes focus The entity that the report is primarily about format The file format, physical medium, or dimensions of the resource growth_rate When the specimen an actively growing model system, such as a cell or tissue ... has_questionnaire_item A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... id The 'logical' identifier of the entity within the system of record identity A 'business' identifier or accession number for the entity, typically as prov... index_time_point Another TimePoint from which this point is offset index_timepoint The text term used to describe the reference or anchor date used for date obf... items A collection of QuestionnaireItem objects which encapsulate the question bein... language The language(s) in which questions are presented md5sum The 128-bit hash value expressed as a 32 digit hexadecimal number used as a f... member_of_research_study A reference to the Study(s) of which this Participant is a member method_type A specific type of method or procedure performed to process the specimen name An unabridged name of a research program, project, or study name_shortened An abbreviated name of a research program, project, or study observation_type The type of Observation being represented (e observations A set of one or more observations offset_from_index A quantity of time that, together with the index date or event, can be used t... organization_type The type of the organization (e originating_site The Organization through which a subject was enrolled on a ResearchStudy parent_container A larger container of which this container is a part (e parent_specimen An existing specimen from which the specimen of interest was directly derived... part_of A reference to a parent ResearchStudy (e passage_number When the specimen an actively growing model system, such as a cell or tissue ... performed_by The organization or group that performed the activity period_end When a period of time ended period_start When a period of time started principal_investigator The investigator or investigators leading a project procedure_concept The coded value that describes the procedure, derived from OMOP codes procedure_provenance A value representing the provenance of the Procedure record processing_activity An activity that modifies the physical structure, composition, or state of a ... product_type The high level type of model system (e publisher Name of the publisher/steward (organization or individual) of this Questionna... qualifier A qualifier that further refines or specifies the location of the body site -... quality_measure An observation about characteristics of a specimen that are indicative of its... quantity The quantity of procedures ordered or administered quantity_collected The quantity of material in the specimen as originally collected from its ori... quantity_measure An observation related to the present quantity of a specimen - e race An arbitrary classification of a taxonomic group that is a division of a spec... refills Intended refills at time of the prescription related_document A reference to an external document that is about or related to the specimen ... relationship_to_participant A value indicating the relationship between the Participant to which the Cond... research_project_type The 'type' of ResearchStudy represented (e response_value role A role played by the substance in a particular application (e route_concept Route of drug administration section_location The location in a parent specimen from which a section/portion was excised (e sex The biologic character or quality that distinguishes male and female from one... sig This is the verbatim instruction for the drug as written by the provider site A term describing any site in the body source_material_type The general kind of material from which the specimen was derived source_participant A specific Subject from which the specimen was directly or indirectly derived species The scientific binomial name for the species of the Person (e specimen_order A numeric value that represents the sequential order of this creation activit... specimen_type The high-level type of the specimen, based on its derivation provenance (i sponsor An entity that is responsible for the initiation, management, and/or financin... storage_activity An activity that results in the storage or maintenance of a specimen in a par... study_arm The arm(s) of the study on which the Participant is enrolled substance_quantity The quantity of substance this instance stands for substance_type The specific type of the substance - at as granular a level as possible text Name for group or question text title Name for this Questionnaire (human friendly) transport_activity An activity through which the specimen is transported between locations transport_destination An organization (facility, site, lab, etc) to which the specimen is delivered... transport_origin An organization (facility, site, lab, etc) from which the specimen was transp... type unit A coded or free text (in the url A URL address for a resource that provides information about a research progr... valid_from The point in time from which the consent record is valid valid_to The point in time after which the consent record is invalid value A general slot to hold a value value_concept A coded value representing a quantity (e value_decimal An amount, in the given units (if specified) version The identifier that is used to identify this version of the questionnaire whe... visit_category A value representing the kind (or category) of visit, like inpatient or outpa... visit_provenance A value representing the provenance of the visit record, or where the record ... vital_status Coded value indicating the state or condition of being living or deceased; al... year_of_birth Numeric value to represent the calendar year in which an individual was born year_of_death Numeric value to represent the calendar year in which an individual died","title":"Slots"},{"location":"#enumerations","text":"Enumeration Description AnalyteTypeEnum CellularOrganismSpeciesEnum A constrained set of enumerative values containing the NCBITaxon values for c... ConditionConceptEnum A constrained set of enumerative values containing both the MONDO values for ... ConditionStatusEnum A constrained set of enumerative values indicating whether a Condition is pre... DataUseEnum A constrained set of enumerative values drawn from the Data Use Ontology (DUO... DeviceExposureConceptEnum Device codes from SNOMED DeviceExposureProvenanceEnum Source of device exposure record DrugExposureConceptEnum Drug codes from RxNorm DrugExposureProvenanceEnum Source of drug exposure record DrugRouteEnum Routes of drug administration EthnicityEnum A constrained set of enumerative values containing the United States Office o... HpoPhenotypicAbnormalityEnum A constrained set of enumerative values containing the HPO values for phenoty... MondoHumanDiseaseEnum A constrained set of enumerative values containing the MONDO values for human... ProcedureConceptEnum Procedure codes from OMOP ProvenanceEnum A constrained set of enumerative values containing the OMOP values for proven... RaceEnum A constrained set of enumerative values containing the United States Office o... SectionLocationEnum The location in a parent specimen from which a section/portion was excised SexEnum A constrained set of enumerative values containing the OMOP values for sex SourceMaterialTypeEnum SpecimenCollectionMethodType SpecimenCreationActivityTypeEnum The high-level type of activity through which the specimen was generated (i SpecimenProcessingActivityTypeEnum The high-level type of processing activity performed SpecimenQualityObservationMethodEnum A type of method used in determining the quantity of a specimen SpecimenQualityObservationTypeEnum Types of measurements that reflect the quality of a specimen or its suitabili... SpecimenQuantityObservationTypeEnum Measures related to the quantity of a specimen or analyte it currently contai... SpecimenTypeEnum A high-level type of specimen, based on its derivation provenance (i UnitOfMeasurementEnum Standard units of measurement from the [Units of Measurement (UOM) ontology](... VertebrateBreedEnum A constrained set of enumerative values containing the VBO values for vertebr... VisitCategoryEnum A constrained set of enumerative values containing the OMOP values for visit ... VisitProvenanceEnum A constrained set of enumerative values containing the OMOP values for visit ... VitalStatusEnum A constrained set of enumerative values containing the OMOP values for vital ...","title":"Enumerations"},{"location":"#types","text":"Type Description Boolean A binary (true or false) value Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... Double A real number that conforms to the xsd:double specification Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Uri a complete URI Uriorcurie a URI or a CURIE","title":"Types"},{"location":"#subsets","text":"Subset Description","title":"Subsets"},{"location":"AnalyteTypeEnum/","text":"Enum: AnalyteTypeEnum URI: AnalyteTypeEnum Permissible Values Value Meaning Description FFPE DNA None Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA None Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA None Total RNA None Total Ribonucleic Acid Repli-G X (Qiagen) DNA None Repli-G X (Qiagen) DNA RNA None Ribonucleic Acid Repli-G Pooled (Qiagen) DNA None REPLI-g Pooled DNA DNA None DNA EBV Immortalized Normal None Normal Epstein-Barr Virus Immortalization FFPE RNA None Formalin-Fixed Paraffin-Embedded RNA Protein None Protein Nuclei RNA None cfDNA None Slots Name Description analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: AnalyteTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FFPE DNA: text: FFPE DNA description: Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA: text: Repli-G (Qiagen) DNA description: Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA: text: GenomePlex (Rubicon) Amplified DNA Total RNA: text: Total RNA description: Total Ribonucleic Acid Repli-G X (Qiagen) DNA: text: Repli-G X (Qiagen) DNA description: Repli-G X (Qiagen) DNA RNA: text: RNA description: Ribonucleic Acid Repli-G Pooled (Qiagen) DNA: text: Repli-G Pooled (Qiagen) DNA description: REPLI-g Pooled DNA DNA: text: DNA description: DNA EBV Immortalized Normal: text: EBV Immortalized Normal description: Normal Epstein-Barr Virus Immortalization FFPE RNA: text: FFPE RNA description: Formalin-Fixed Paraffin-Embedded RNA Protein: text: Protein description: Protein Nuclei RNA: text: Nuclei RNA cfDNA: text: cfDNA","title":"Enum: AnalyteTypeEnum"},{"location":"AnalyteTypeEnum/#enum-analytetypeenum","text":"URI: AnalyteTypeEnum","title":"Enum: AnalyteTypeEnum"},{"location":"AnalyteTypeEnum/#permissible-values","text":"Value Meaning Description FFPE DNA None Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA None Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA None Total RNA None Total Ribonucleic Acid Repli-G X (Qiagen) DNA None Repli-G X (Qiagen) DNA RNA None Ribonucleic Acid Repli-G Pooled (Qiagen) DNA None REPLI-g Pooled DNA DNA None DNA EBV Immortalized Normal None Normal Epstein-Barr Virus Immortalization FFPE RNA None Formalin-Fixed Paraffin-Embedded RNA Protein None Protein Nuclei RNA None cfDNA None","title":"Permissible Values"},{"location":"AnalyteTypeEnum/#slots","text":"Name Description analyte_type For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th...","title":"Slots"},{"location":"AnalyteTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"AnalyteTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"AnalyteTypeEnum/#linkml-source","text":"name: AnalyteTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FFPE DNA: text: FFPE DNA description: Formalin-Fixed Paraffin-Embedded DNA Repli-G (Qiagen) DNA: text: Repli-G (Qiagen) DNA description: Repli-G (Qiagen) DNA GenomePlex (Rubicon) Amplified DNA: text: GenomePlex (Rubicon) Amplified DNA Total RNA: text: Total RNA description: Total Ribonucleic Acid Repli-G X (Qiagen) DNA: text: Repli-G X (Qiagen) DNA description: Repli-G X (Qiagen) DNA RNA: text: RNA description: Ribonucleic Acid Repli-G Pooled (Qiagen) DNA: text: Repli-G Pooled (Qiagen) DNA description: REPLI-g Pooled DNA DNA: text: DNA description: DNA EBV Immortalized Normal: text: EBV Immortalized Normal description: Normal Epstein-Barr Virus Immortalization FFPE RNA: text: FFPE RNA description: Formalin-Fixed Paraffin-Embedded RNA Protein: text: Protein description: Protein Nuclei RNA: text: Nuclei RNA cfDNA: text: cfDNA","title":"LinkML Source"},{"location":"BiologicProduct/","text":"Class: BiologicProduct A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. URI: bdchm:BiologicProduct classDiagram class BiologicProduct Entity <|-- BiologicProduct BiologicProduct : description BiologicProduct : growth_rate BiologicProduct : id BiologicProduct : identity BiologicProduct : passage_number BiologicProduct : product_type Inheritance Entity BiologicProduct Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the model syst... direct product_type 0..1 String The high level type of model system (e direct passage_number 0..* Integer When the specimen an actively growing model system, such as a cell or tissue ... direct growth_rate 0..* String When the specimen an actively growing model system, such as a cell or tissue ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen derived_product range BiologicProduct Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:BiologicProduct native bdchm:BiologicProduct LinkML Source Direct name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string required: false Induced name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: BiologicProduct domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false alias: product_type owner: BiologicProduct domain_of: - BiologicProduct range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: passage_number owner: BiologicProduct domain_of: - BiologicProduct range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: BiologicProduct domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BiologicProduct domain_of: - Entity range: uriorcurie required: true","title":"Class: BiologicProduct"},{"location":"BiologicProduct/#class-biologicproduct","text":"A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. URI: bdchm:BiologicProduct classDiagram class BiologicProduct Entity <|-- BiologicProduct BiologicProduct : description BiologicProduct : growth_rate BiologicProduct : id BiologicProduct : identity BiologicProduct : passage_number BiologicProduct : product_type","title":"Class: BiologicProduct"},{"location":"BiologicProduct/#inheritance","text":"Entity BiologicProduct","title":"Inheritance"},{"location":"BiologicProduct/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the model syst... direct product_type 0..1 String The high level type of model system (e direct passage_number 0..* Integer When the specimen an actively growing model system, such as a cell or tissue ... direct growth_rate 0..* String When the specimen an actively growing model system, such as a cell or tissue ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"BiologicProduct/#usages","text":"used by used in type used Specimen derived_product range BiologicProduct","title":"Usages"},{"location":"BiologicProduct/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"BiologicProduct/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"BiologicProduct/#mappings","text":"Mapping Type Mapped Value self bdchm:BiologicProduct native bdchm:BiologicProduct","title":"Mappings"},{"location":"BiologicProduct/#linkml-source","text":"","title":"LinkML Source"},{"location":"BiologicProduct/#direct","text":"name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string required: false","title":"Direct"},{"location":"BiologicProduct/#induced","text":"name: BiologicProduct description: A living organism, or a metabolically active biological system such as a cell culture, tissue culture, or organoid that is maintained or propagated in vitro. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the model system from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: BiologicProduct domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false product_type: name: product_type description: The high level type of model system (e.g. cell line, cell culture, tissue culture, organoid) examples: - value: cell line - value: cell culture - value: tissue culture - value: organoid from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BiologicProduct_product_type multivalued: false alias: product_type owner: BiologicProduct domain_of: - BiologicProduct range: string required: false passage_number: name: passage_number description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its passage number. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: passage_number owner: BiologicProduct domain_of: - BiologicProduct range: integer required: false growth_rate: name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: BiologicProduct domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BiologicProduct domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"BodySite/","text":"Class: BodySite A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. URI: bdchm:BodySite classDiagram class BodySite Entity <|-- BodySite BodySite : id BodySite : qualifier BodySite : site Inheritance Entity BodySite Slots Name Cardinality and Range Description Inheritance site 1..1 String A term describing any site in the body direct qualifier 0..* String A qualifier that further refines or specifies the location of the body site -... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used SpecimenCreationActivity collection_site range BodySite Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:BodySite native bdchm:BodySite LinkML Source Direct name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true range: string required: false Induced name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false alias: site owner: BodySite domain_of: - BodySite range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true alias: qualifier owner: BodySite domain_of: - BodySite range: string required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BodySite domain_of: - Entity range: uriorcurie required: true","title":"Class: BodySite"},{"location":"BodySite/#class-bodysite","text":"A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. URI: bdchm:BodySite classDiagram class BodySite Entity <|-- BodySite BodySite : id BodySite : qualifier BodySite : site","title":"Class: BodySite"},{"location":"BodySite/#inheritance","text":"Entity BodySite","title":"Inheritance"},{"location":"BodySite/#slots","text":"Name Cardinality and Range Description Inheritance site 1..1 String A term describing any site in the body direct qualifier 0..* String A qualifier that further refines or specifies the location of the body site -... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"BodySite/#usages","text":"used by used in type used SpecimenCreationActivity collection_site range BodySite","title":"Usages"},{"location":"BodySite/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"BodySite/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"BodySite/#mappings","text":"Mapping Type Mapped Value self bdchm:BodySite native bdchm:BodySite","title":"Mappings"},{"location":"BodySite/#linkml-source","text":"","title":"LinkML Source"},{"location":"BodySite/#direct","text":"name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true range: string required: false","title":"Direct"},{"location":"BodySite/#induced","text":"name: BodySite description: A site in the body of an organism, typically described in terms of an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). But body sites as defined here may include non-canonical sites, such as an implanted medical device. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: site: name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false alias: site owner: BodySite domain_of: - BodySite range: string required: true qualifier: name: qualifier description: A qualifier that further refines or specifies the location of the body site - e.g. to indicate laterality, upper v. lower, containment in some other anatomical structure (e.g. 'blood' contained in the 'hepatic vein') examples: - value: left - value: right - value: bilateral from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_qualifier multivalued: true alias: qualifier owner: BodySite domain_of: - BodySite range: string required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: BodySite domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Boolean/","text":"Type: Boolean A binary (true or false) value URI: xsd:boolean base : Bool uri : xsd:boolean repr : bool Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Boolean"},{"location":"Boolean/#type-boolean","text":"A binary (true or false) value URI: xsd:boolean base : Bool uri : xsd:boolean repr : bool","title":"Type: Boolean"},{"location":"Boolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Boolean/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"CellularOrganismSpeciesEnum/","text":"Enum: CellularOrganismSpeciesEnum A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. URI: CellularOrganismSpeciesEnum This is a dynamic enum Slots Name Description species The scientific binomial name for the species of the Person (e Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: CellularOrganismSpeciesEnum description: A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:ncbitaxon source_nodes: - ncbitaxon:131567 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: CellularOrganismSpeciesEnum"},{"location":"CellularOrganismSpeciesEnum/#enum-cellularorganismspeciesenum","text":"A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. URI: CellularOrganismSpeciesEnum This is a dynamic enum","title":"Enum: CellularOrganismSpeciesEnum"},{"location":"CellularOrganismSpeciesEnum/#slots","text":"Name Description species The scientific binomial name for the species of the Person (e","title":"Slots"},{"location":"CellularOrganismSpeciesEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"CellularOrganismSpeciesEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"CellularOrganismSpeciesEnum/#linkml-source","text":"name: CellularOrganismSpeciesEnum description: A constrained set of enumerative values containing the NCBITaxon values for cellular organisms. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:ncbitaxon source_nodes: - ncbitaxon:131567 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Condition/","text":"Class: Condition _Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. _ URI: bdchm:Condition classDiagram class Condition Entity <|-- Condition Condition : age_at_condition_end Condition : age_at_condition_start Condition : associated_participant Condition --> Participant : associated_participant Condition : associated_visit Condition --> Visit : associated_visit Condition : condition_concept Condition --> ConditionConceptEnum : condition_concept Condition : condition_provenance Condition --> ProvenanceEnum : condition_provenance Condition : condition_status Condition --> ConditionStatusEnum : condition_status Condition : id Condition : identity Condition : relationship_to_participant Inheritance Entity Condition Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct condition_concept 0..1 ConditionConceptEnum The coded value for the presence of a disease or medical condition stated as ... direct age_at_condition_start 0..1 Integer The Participant's age (expressed in days) when the condition was first record... direct age_at_condition_end 0..1 Integer The Participant's age (expressed in days) when the condition was recorded as ... direct condition_provenance 0..1 ProvenanceEnum A value representing the provenance of the Condition record direct condition_status 0..1 ConditionStatusEnum A value indicating whether the medical condition described in this record is ... direct relationship_to_participant 0..1 String A value indicating the relationship between the Participant to which the Cond... direct associated_participant 0..1 Participant A reference to the Participant to which the Condition is attributed direct associated_visit 0..1 Visit A reference to the Visit during which this Condition was recorded direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Condition native bdchm:Condition LinkML Source Direct name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit Induced name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_start owner: Condition domain_of: - Condition range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_end owner: Condition domain_of: - Condition range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Condition domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Condition domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Condition domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Condition domain_of: - Entity range: uriorcurie required: true","title":"Class: Condition"},{"location":"Condition/#class-condition","text":"_Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. _ URI: bdchm:Condition classDiagram class Condition Entity <|-- Condition Condition : age_at_condition_end Condition : age_at_condition_start Condition : associated_participant Condition --> Participant : associated_participant Condition : associated_visit Condition --> Visit : associated_visit Condition : condition_concept Condition --> ConditionConceptEnum : condition_concept Condition : condition_provenance Condition --> ProvenanceEnum : condition_provenance Condition : condition_status Condition --> ConditionStatusEnum : condition_status Condition : id Condition : identity Condition : relationship_to_participant","title":"Class: Condition"},{"location":"Condition/#inheritance","text":"Entity Condition","title":"Inheritance"},{"location":"Condition/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct condition_concept 0..1 ConditionConceptEnum The coded value for the presence of a disease or medical condition stated as ... direct age_at_condition_start 0..1 Integer The Participant's age (expressed in days) when the condition was first record... direct age_at_condition_end 0..1 Integer The Participant's age (expressed in days) when the condition was recorded as ... direct condition_provenance 0..1 ProvenanceEnum A value representing the provenance of the Condition record direct condition_status 0..1 ConditionStatusEnum A value indicating whether the medical condition described in this record is ... direct relationship_to_participant 0..1 String A value indicating the relationship between the Participant to which the Cond... direct associated_participant 0..1 Participant A reference to the Participant to which the Condition is attributed direct associated_visit 0..1 Visit A reference to the Visit during which this Condition was recorded direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Condition/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Condition/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Condition/#mappings","text":"Mapping Type Mapped Value self bdchm:Condition native bdchm:Condition","title":"Mappings"},{"location":"Condition/#linkml-source","text":"","title":"LinkML Source"},{"location":"Condition/#direct","text":"name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit","title":"Direct"},{"location":"Condition/#induced","text":"name: Condition description: 'Conditions are records of a Person suggesting the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, which is either observed by a Provider or reported by the patient. Conditions are recorded in different sources and levels of standardization. ' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: condition_concept: name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum age_at_condition_start: name: age_at_condition_start description: The Participant's age (expressed in days) when the condition was first recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_start owner: Condition domain_of: - Condition range: integer unit: ucum_code: d age_at_condition_end: name: age_at_condition_end description: The Participant's age (expressed in days) when the condition was recorded as having been resolved. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_condition_end owner: Condition domain_of: - Condition range: integer unit: ucum_code: d condition_provenance: name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum condition_status: name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum relationship_to_participant: name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string associated_participant: name: associated_participant description: A reference to the Participant to which the Condition is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Condition domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Condition was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Condition domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Condition domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Condition domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ConditionConceptEnum/","text":"Enum: ConditionConceptEnum A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. URI: ConditionConceptEnum This is a dynamic enum Slots Name Description condition_concept The coded value for the presence of a disease or medical condition stated as ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ConditionConceptEnum description: A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 inherits: - MondoHumanDiseaseEnum - HpoPhenotypicAbnormalityEnum","title":"Enum: ConditionConceptEnum"},{"location":"ConditionConceptEnum/#enum-conditionconceptenum","text":"A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. URI: ConditionConceptEnum This is a dynamic enum","title":"Enum: ConditionConceptEnum"},{"location":"ConditionConceptEnum/#slots","text":"Name Description condition_concept The coded value for the presence of a disease or medical condition stated as ...","title":"Slots"},{"location":"ConditionConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ConditionConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ConditionConceptEnum/#linkml-source","text":"name: ConditionConceptEnum description: A constrained set of enumerative values containing both the MONDO values for human diseases and the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 inherits: - MondoHumanDiseaseEnum - HpoPhenotypicAbnormalityEnum","title":"LinkML Source"},{"location":"ConditionStatusEnum/","text":"Enum: ConditionStatusEnum A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. URI: ConditionStatusEnum Permissible Values Value Meaning Description PRESENT None The condition is/was present in the patient ABSENT None The condition is/was absent in the patient UNKNOWN None The condition is/was of unknown status in the patient Slots Name Description condition_status A value indicating whether the medical condition described in this record is ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ConditionStatusEnum description: A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: PRESENT: text: PRESENT description: The condition is/was present in the patient. ABSENT: text: ABSENT description: The condition is/was absent in the patient. UNKNOWN: text: UNKNOWN description: The condition is/was of unknown status in the patient.","title":"Enum: ConditionStatusEnum"},{"location":"ConditionStatusEnum/#enum-conditionstatusenum","text":"A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. URI: ConditionStatusEnum","title":"Enum: ConditionStatusEnum"},{"location":"ConditionStatusEnum/#permissible-values","text":"Value Meaning Description PRESENT None The condition is/was present in the patient ABSENT None The condition is/was absent in the patient UNKNOWN None The condition is/was of unknown status in the patient","title":"Permissible Values"},{"location":"ConditionStatusEnum/#slots","text":"Name Description condition_status A value indicating whether the medical condition described in this record is ...","title":"Slots"},{"location":"ConditionStatusEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ConditionStatusEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ConditionStatusEnum/#linkml-source","text":"name: ConditionStatusEnum description: A constrained set of enumerative values indicating whether a Condition is present, absent, or its status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: PRESENT: text: PRESENT description: The condition is/was present in the patient. ABSENT: text: ABSENT description: The condition is/was absent in the patient. UNKNOWN: text: UNKNOWN description: The condition is/was of unknown status in the patient.","title":"LinkML Source"},{"location":"Consent/","text":"Class: Consent An entity that can be used to capture consent code and other relevant data about consent for a study. URI: bdchm:Consent classDiagram class Consent Entity <|-- Consent Consent : consent_code Consent --> DataUseEnum : consent_code Consent : id Consent : valid_from Consent --> TimePoint : valid_from Consent : valid_to Consent --> TimePoint : valid_to Inheritance Entity Consent Slots Name Cardinality and Range Description Inheritance consent_code 0..1 DataUseEnum Data Use Restrictions that are used to indicate permissions/restrictions for ... direct valid_from 0..1 TimePoint The point in time from which the consent record is valid direct valid_to 0..1 TimePoint The point in time after which the consent record is invalid direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant consents range Consent ResearchStudy consents range Consent Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Consent native bdchm:Consent LinkML Source Direct name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint Induced name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Consent domain_of: - Entity range: uriorcurie required: true","title":"Class: Consent"},{"location":"Consent/#class-consent","text":"An entity that can be used to capture consent code and other relevant data about consent for a study. URI: bdchm:Consent classDiagram class Consent Entity <|-- Consent Consent : consent_code Consent --> DataUseEnum : consent_code Consent : id Consent : valid_from Consent --> TimePoint : valid_from Consent : valid_to Consent --> TimePoint : valid_to","title":"Class: Consent"},{"location":"Consent/#inheritance","text":"Entity Consent","title":"Inheritance"},{"location":"Consent/#slots","text":"Name Cardinality and Range Description Inheritance consent_code 0..1 DataUseEnum Data Use Restrictions that are used to indicate permissions/restrictions for ... direct valid_from 0..1 TimePoint The point in time from which the consent record is valid direct valid_to 0..1 TimePoint The point in time after which the consent record is invalid direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Consent/#usages","text":"used by used in type used Participant consents range Consent ResearchStudy consents range Consent","title":"Usages"},{"location":"Consent/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Consent/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Consent/#mappings","text":"Mapping Type Mapped Value self bdchm:Consent native bdchm:Consent","title":"Mappings"},{"location":"Consent/#linkml-source","text":"","title":"LinkML Source"},{"location":"Consent/#direct","text":"name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint","title":"Direct"},{"location":"Consent/#induced","text":"name: Consent description: An entity that can be used to capture consent code and other relevant data about consent for a study. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: consent_code: name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum valid_from: name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint valid_to: name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Consent domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Curie/","text":"Type: Curie a compact URI URI: xsd:string base : Curie uri : xsd:string repr : str Comments in RDF serializations this MUST be expanded to a URI in non-RDF serializations MAY be serialized as the compact representation Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Curie"},{"location":"Curie/#type-curie","text":"a compact URI URI: xsd:string base : Curie uri : xsd:string repr : str","title":"Type: Curie"},{"location":"Curie/#comments","text":"in RDF serializations this MUST be expanded to a URI in non-RDF serializations MAY be serialized as the compact representation","title":"Comments"},{"location":"Curie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Curie/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DataUseEnum/","text":"Enum: DataUseEnum A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. URI: DataUseEnum Permissible Values Value Meaning Description GRU DUO:0000042 This data use permission indicates that use is allowed for general research u... HMB DUO:0000006 This data use permission indicates that use is allowed for health/medical/bio... DS DUO:0000007 This data use permission indicates that use is allowed provided it is related... NPUNCU DUO:0000018 This data use modifier indicates that use of the data is limited to not-for-p... IRB DUO:0000021 This data use modifier indicates that the requestor must provide documentatio... Slots Name Description consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DataUseEnum description: A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: GRU: text: GRU description: 'This data use permission indicates that use is allowed for general research use for any research purpose. This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.' meaning: DUO:0000042 HMB: text: HMB description: This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. meaning: DUO:0000006 DS: text: DS description: This data use permission indicates that use is allowed provided it is related to the specified disease. This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms. meaning: DUO:0000007 NPUNCU: text: NPUNCU description: This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. meaning: DUO:0000018 IRB: text: IRB description: This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. meaning: DUO:0000021","title":"Enum: DataUseEnum"},{"location":"DataUseEnum/#enum-datauseenum","text":"A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. URI: DataUseEnum","title":"Enum: DataUseEnum"},{"location":"DataUseEnum/#permissible-values","text":"Value Meaning Description GRU DUO:0000042 This data use permission indicates that use is allowed for general research u... HMB DUO:0000006 This data use permission indicates that use is allowed for health/medical/bio... DS DUO:0000007 This data use permission indicates that use is allowed provided it is related... NPUNCU DUO:0000018 This data use modifier indicates that use of the data is limited to not-for-p... IRB DUO:0000021 This data use modifier indicates that the requestor must provide documentatio...","title":"Permissible Values"},{"location":"DataUseEnum/#slots","text":"Name Description consent_code Data Use Restrictions that are used to indicate permissions/restrictions for ...","title":"Slots"},{"location":"DataUseEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DataUseEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DataUseEnum/#linkml-source","text":"name: DataUseEnum description: A constrained set of enumerative values drawn from the Data Use Ontology (DUO). The DUO is an ontology which represent data use conditions. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: GRU: text: GRU description: 'This data use permission indicates that use is allowed for general research use for any research purpose. This includes but is not limited to: health/medical/biomedical purposes, fundamental biology research, the study of population origins or ancestry, statistical methods and algorithms development, and social-sciences research.' meaning: DUO:0000042 HMB: text: HMB description: This data use permission indicates that use is allowed for health/medical/biomedical purposes; does not include the study of population origins or ancestry. meaning: DUO:0000006 DS: text: DS description: This data use permission indicates that use is allowed provided it is related to the specified disease. This term should be coupled with a term describing a disease from an ontology to specify the disease the restriction applies to. DUO recommends MONDO be used, to provide the basis for automated evaluation. For more information see https://github.com/EBISPOT/DUO/blob/master/MONDO_Overview.md Other resources, such as the Disease Ontology, HPO, SNOMED-CT or others, can also be used. When those other resources are being used, this may require an extra mapping step to leverage automated matching algorithms. meaning: DUO:0000007 NPUNCU: text: NPUNCU description: This data use modifier indicates that use of the data is limited to not-for-profit organizations and not-for-profit use, non-commercial use. meaning: DUO:0000018 IRB: text: IRB description: This data use modifier indicates that the requestor must provide documentation of local IRB/ERB approval. meaning: DUO:0000021","title":"LinkML Source"},{"location":"Date/","text":"Type: Date a date (year, month and day) in an idealized calendar URI: xsd:date base : XSDDate uri : xsd:date repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Date"},{"location":"Date/#type-date","text":"a date (year, month and day) in an idealized calendar URI: xsd:date base : XSDDate uri : xsd:date repr : str","title":"Type: Date"},{"location":"Date/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Date/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DateOrDatetime/","text":"Type: DateOrDatetime Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#type-dateordatetime","text":"Either a date or a datetime URI: linkml:DateOrDatetime base : str uri : linkml:DateOrDatetime repr : str","title":"Type: DateOrDatetime"},{"location":"DateOrDatetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DateOrDatetime/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Datetime/","text":"Type: Datetime The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Datetime"},{"location":"Datetime/#type-datetime","text":"The combination of a date and time URI: xsd:dateTime base : XSDDateTime uri : xsd:dateTime repr : str","title":"Type: Datetime"},{"location":"Datetime/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Datetime/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Decimal/","text":"Type: Decimal A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Decimal"},{"location":"Decimal/#type-decimal","text":"A real number with arbitrary precision that conforms to the xsd:decimal specification URI: xsd:decimal base : Decimal uri : xsd:decimal","title":"Type: Decimal"},{"location":"Decimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Decimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Demography/","text":"Class: Demography Demographics about an individual or animal receiving care or other health-related services. URI: bdchm:Demography classDiagram class Demography Entity <|-- Demography Demography : associated_participant Demography --> Participant : associated_participant Demography : ethnicity Demography --> EthnicityEnum : ethnicity Demography : id Demography : identity Demography : race Demography --> RaceEnum : race Demography : sex Demography --> SexEnum : sex Inheritance Entity Demography Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct associated_participant 0..1 Participant A reference to the Participant that is associated with this record direct sex 0..1 SexEnum The biologic character or quality that distinguishes male and female from one... direct ethnicity 0..1 EthnicityEnum An individual's self-described social and cultural grouping, specifically whe... direct race 0..1 RaceEnum An arbitrary classification of a taxonomic group that is a division of a spec... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Demography native bdchm:Demography LinkML Source Direct name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity - associated_participant attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: RaceEnum Induced name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sex owner: Demography domain_of: - Demography range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: race owner: Demography domain_of: - Demography range: RaceEnum identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Demography domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie associated_participant: name: associated_participant description: A reference to the Participant that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_participant owner: Demography domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Demography domain_of: - Entity range: uriorcurie required: true","title":"Class: Demography"},{"location":"Demography/#class-demography","text":"Demographics about an individual or animal receiving care or other health-related services. URI: bdchm:Demography classDiagram class Demography Entity <|-- Demography Demography : associated_participant Demography --> Participant : associated_participant Demography : ethnicity Demography --> EthnicityEnum : ethnicity Demography : id Demography : identity Demography : race Demography --> RaceEnum : race Demography : sex Demography --> SexEnum : sex","title":"Class: Demography"},{"location":"Demography/#inheritance","text":"Entity Demography","title":"Inheritance"},{"location":"Demography/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct associated_participant 0..1 Participant A reference to the Participant that is associated with this record direct sex 0..1 SexEnum The biologic character or quality that distinguishes male and female from one... direct ethnicity 0..1 EthnicityEnum An individual's self-described social and cultural grouping, specifically whe... direct race 0..1 RaceEnum An arbitrary classification of a taxonomic group that is a division of a spec... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Demography/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Demography/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Demography/#mappings","text":"Mapping Type Mapped Value self bdchm:Demography native bdchm:Demography","title":"Mappings"},{"location":"Demography/#linkml-source","text":"","title":"LinkML Source"},{"location":"Demography/#direct","text":"name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity - associated_participant attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: RaceEnum","title":"Direct"},{"location":"Demography/#induced","text":"name: Demography description: Demographics about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: sex: name: sex description: The biologic character or quality that distinguishes male and female from one another as expressed by analysis of the person's gonadal, morphologic (internal and external), chromosomal, and hormonal characteristics. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sex owner: Demography domain_of: - Demography range: SexEnum ethnicity: name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum race: name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: race owner: Demography domain_of: - Demography range: RaceEnum identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Demography domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie associated_participant: name: associated_participant description: A reference to the Participant that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_participant owner: Demography domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Demography domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DeviceExposure/","text":"Class: DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. URI: bdchm:DeviceExposure classDiagram class DeviceExposure Entity <|-- DeviceExposure DeviceExposure : age_at_exposure_end DeviceExposure : age_at_exposure_start DeviceExposure : associated_participant DeviceExposure --> Participant : associated_participant DeviceExposure : associated_visit DeviceExposure --> Visit : associated_visit DeviceExposure : device_concept DeviceExposure --> DeviceExposureConceptEnum : device_concept DeviceExposure : exposure_provenance DeviceExposure --> DeviceExposureProvenanceEnum : exposure_provenance DeviceExposure : id DeviceExposure : identity DeviceExposure : quantity Inheritance Entity DeviceExposure Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct device_concept 0..1 DeviceExposureConceptEnum The coded value for a device direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DeviceExposureProvenanceEnum A value representing the provenance of the DeviceExposure record direct quantity 0..1 Float Amount of device used direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DeviceExposure native bdchm:DeviceExposure LinkML Source Direct name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false Induced name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_start owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_end owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: exposure_provenance owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DeviceExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DeviceExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DeviceExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DeviceExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DeviceExposure domain_of: - Entity range: uriorcurie required: true","title":"Class: DeviceExposure"},{"location":"DeviceExposure/#class-deviceexposure","text":"DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. URI: bdchm:DeviceExposure classDiagram class DeviceExposure Entity <|-- DeviceExposure DeviceExposure : age_at_exposure_end DeviceExposure : age_at_exposure_start DeviceExposure : associated_participant DeviceExposure --> Participant : associated_participant DeviceExposure : associated_visit DeviceExposure --> Visit : associated_visit DeviceExposure : device_concept DeviceExposure --> DeviceExposureConceptEnum : device_concept DeviceExposure : exposure_provenance DeviceExposure --> DeviceExposureProvenanceEnum : exposure_provenance DeviceExposure : id DeviceExposure : identity DeviceExposure : quantity","title":"Class: DeviceExposure"},{"location":"DeviceExposure/#inheritance","text":"Entity DeviceExposure","title":"Inheritance"},{"location":"DeviceExposure/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct device_concept 0..1 DeviceExposureConceptEnum The coded value for a device direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DeviceExposureProvenanceEnum A value representing the provenance of the DeviceExposure record direct quantity 0..1 Float Amount of device used direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DeviceExposure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DeviceExposure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DeviceExposure/#mappings","text":"Mapping Type Mapped Value self bdchm:DeviceExposure native bdchm:DeviceExposure","title":"Mappings"},{"location":"DeviceExposure/#linkml-source","text":"","title":"LinkML Source"},{"location":"DeviceExposure/#direct","text":"name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false","title":"Direct"},{"location":"DeviceExposure/#induced","text":"name: DeviceExposure description: DeviceExposures are records of a Person suggesting exposure to a foreign object. The source is typically physical objects used in procedures, measurements, or observations. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: device_concept: name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_start owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: age_at_exposure_end owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DeviceExposure record. From OMOP Device Types. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: exposure_provenance owner: DeviceExposure domain_of: - DrugExposure - DeviceExposure range: DeviceExposureProvenanceEnum quantity: name: quantity description: Amount of device used. If not present in source, default to 1. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DeviceExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DeviceExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DeviceExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DeviceExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DeviceExposure domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DeviceExposureConceptEnum/","text":"Enum: DeviceExposureConceptEnum Device codes from SNOMED. URI: DeviceExposureConceptEnum This is a dynamic enum Slots Name Description device_concept The coded value for a device See Also https://bioregistry.io/registry/snomedct https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html https://www.nlm.nih.gov/healthit/snomedct/index.html urn:oid:2.16.840.1.113883.6.96 Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DeviceExposureConceptEnum description: Device codes from SNOMED. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/snomedct - https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html - https://www.nlm.nih.gov/healthit/snomedct/index.html - urn:oid:2.16.840.1.113883.6.96 rank: 1000 reachable_from: source_ontology: bioregistry:snomedct","title":"Enum: DeviceExposureConceptEnum"},{"location":"DeviceExposureConceptEnum/#enum-deviceexposureconceptenum","text":"Device codes from SNOMED. URI: DeviceExposureConceptEnum This is a dynamic enum","title":"Enum: DeviceExposureConceptEnum"},{"location":"DeviceExposureConceptEnum/#slots","text":"Name Description device_concept The coded value for a device","title":"Slots"},{"location":"DeviceExposureConceptEnum/#see-also","text":"https://bioregistry.io/registry/snomedct https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html https://www.nlm.nih.gov/healthit/snomedct/index.html urn:oid:2.16.840.1.113883.6.96","title":"See Also"},{"location":"DeviceExposureConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DeviceExposureConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DeviceExposureConceptEnum/#linkml-source","text":"name: DeviceExposureConceptEnum description: Device codes from SNOMED. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/snomedct - https://terminology.hl7.org/3.1.0/CodeSystem-v3-snomed-CT.html - https://www.nlm.nih.gov/healthit/snomedct/index.html - urn:oid:2.16.840.1.113883.6.96 rank: 1000 reachable_from: source_ontology: bioregistry:snomedct","title":"LinkML Source"},{"location":"DeviceExposureProvenanceEnum/","text":"Enum: DeviceExposureProvenanceEnum Source of device exposure record URI: DeviceExposureProvenanceEnum Permissible Values Value Meaning Description CASE REPORT FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM AUTHORIZATION OMOP:32811 Claim authorization CLAIM DISCHARGE RECORD OMOP:32812 Claim discharge record CLAIM ENROLMENT RECORD OMOP:32813 Claim enrolment record COST RECORD OMOP:32814 Cost record DEATH CERTIFICATE OMOP:32815 Death Certificate DENTAL CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR ADMINISTRATION RECORD OMOP:32818 EHR administration record EHR ADMISSION NOTE OMOP:32819 EHR admission note EHR ANCILLARY REPORT OMOP:32820 EHR ancillary report EHR BILLING RECORD OMOP:32821 EHR billing record EHR CHIEF COMPLAINT OMOP:32822 EHR chief complaint EHR DISCHARGE RECORD OMOP:32823 EHR discharge record EHR DISCHARGE SUMMARY OMOP:32824 EHR discharge summary EHR DISPENSING RECORD OMOP:32825 EHR dispensing record EHR EMERGENCY ROOM NOTE OMOP:32826 EHR emergency room note EHR ENCOUNTER RECORD OMOP:32827 EHR encounter record EHR EPISODE RECORD OMOP:32828 EHR episode record EHR INPATIENT NOTE OMOP:32829 EHR inpatient note EHR MEDICATION LIST OMOP:32830 EHR medication list EHR NOTE OMOP:32831 EHR note EHR NURSING REPORT OMOP:32832 EHR nursing report EHR ORDER OMOP:32833 EHR order EHR OUTPATIENT NOTE OMOP:32834 EHR outpatient note EHR PATHOLOGY REPORT OMOP:32835 EHR Pathology report EHR PHYSICAL EXAMINATION OMOP:32836 EHR physical examination EHR PLANNED DISPENSING RECORD OMOP:32837 EHR planned dispensing record EHR PERSCRIPTION OMOP:32838 EHR prescription EHR PERSCRIPTION ISSUE RECORD OMOP:32839 EHR prescription issue record EHR PROBLEM LIST OMOP:32840 EHR problem list EHR RADIOLOGY REPORT OMOP:32841 EHR radiology report EHR REFERRAL RECORD OMOP:32842 EHR referral record EXTERNAL CDM INSTANCE OMOP:32843 External CDM instance FACILITY CLAIM OMOP:32844 Facility claim FACILITY CLAIM DETAIL OMOP:32845 Facility claim detail FACILITY CLAIM HEADER OMOP:32846 Facility claim header GEOGRAPHIC ISOLATION RECORD OMOP:32847 Geographic isolation record GOVERNMENT REPORT OMOP:32848 Government report HEALTH INFORMATION EXCHANGE RECORD OMOP:32849 Health Information Exchange record HEALTH RISK ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE PROFESSIONAL FILLED SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL COST OMOP:32852 Hospital cost INPATIENT CLAIM OMOP:32853 Inpatient claim INPATIENT CLAIM DETAIL OMOP:32854 Inpatient claim detail INPATIENT CLAIM HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL ORDER RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT CLAIM OMOP:32859 Outpatient claim OUTPATIENT CLAIM DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT CLAIM HEADER OMOP:32861 Outpatient claim header PATIENT FILLED SURVEY OMOP:32862 Patient filled survey PATIENT OR PAYER PAID RECORD OMOP:32863 Patient or payer paid record PATIENT REPORTED COST OMOP:32864 Patient reported cost PATIENT SELF-REPORT OMOP:32865 Patient self-report PATIENT SELF-TESTED OMOP:705183 Patient self-tested PAYER SYSTEM RECORD (PAID PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER SYSTEM RECORD (PRIMARY PAYER) OMOP:32867 Payer system record (primary payer) PAYER SYSTEM RECORD (SECONDARY PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY CLAIM OMOP:32869 Pharmacy claim POINT OF CARE/EXPRESS LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION TIME PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL CLAIM OMOP:32871 Professional claim PROFESSIONAL CLAIM DETAIL OMOP:32872 Professional claim detail PROFESSIONAL CLAIM HEADER OMOP:32873 Professional claim header PROVIDER CHARGE LIST PRICE OMOP:32874 Provider charge list price PROVIDER FINANCIAL SYSTEM OMOP:32875 Provider financial system PROVIDER INCURRED COST RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION RECORD OMOP:32877 Randomization record REFERENCE LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD ALGORITHM OMOP:32880 Standard algorithm STANDARD ALGORITHM FROM CLAIMS OMOP:32881 Standard algorithm from claims STANDARD ALGORITHM FROM EHR OMOP:32882 Standard algorithm from EHR SURVEY OMOP:32883 Survey URGENT LAB OMOP:32884 Urgent lab US SOCIAL SECURITY DEATH MASTER FILE OMOP:32885 US Social Security Death Master File VISION CLAIM OMOP:32886 Vision claim Comments Taken from OMOP Type Concept Domain Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DeviceExposureProvenanceEnum description: Source of device exposure record comments: - Taken from OMOP Type Concept Domain from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE REPORT FORM: text: CASE REPORT FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM AUTHORIZATION: text: CLAIM AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM DISCHARGE RECORD: text: CLAIM DISCHARGE RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM ENROLMENT RECORD: text: CLAIM ENROLMENT RECORD description: Claim enrolment record meaning: OMOP:32813 COST RECORD: text: COST RECORD description: Cost record meaning: OMOP:32814 DEATH CERTIFICATE: text: DEATH CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL CLAIM: text: DENTAL CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR ADMINISTRATION RECORD: text: EHR ADMINISTRATION RECORD description: EHR administration record meaning: OMOP:32818 EHR ADMISSION NOTE: text: EHR ADMISSION NOTE description: EHR admission note meaning: OMOP:32819 EHR ANCILLARY REPORT: text: EHR ANCILLARY REPORT description: EHR ancillary report meaning: OMOP:32820 EHR BILLING RECORD: text: EHR BILLING RECORD description: EHR billing record meaning: OMOP:32821 EHR CHIEF COMPLAINT: text: EHR CHIEF COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR DISCHARGE RECORD: text: EHR DISCHARGE RECORD description: EHR discharge record meaning: OMOP:32823 EHR DISCHARGE SUMMARY: text: EHR DISCHARGE SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR DISPENSING RECORD: text: EHR DISPENSING RECORD description: EHR dispensing record meaning: OMOP:32825 EHR EMERGENCY ROOM NOTE: text: EHR EMERGENCY ROOM NOTE description: EHR emergency room note meaning: OMOP:32826 EHR ENCOUNTER RECORD: text: EHR ENCOUNTER RECORD description: EHR encounter record meaning: OMOP:32827 EHR EPISODE RECORD: text: EHR EPISODE RECORD description: EHR episode record meaning: OMOP:32828 EHR INPATIENT NOTE: text: EHR INPATIENT NOTE description: EHR inpatient note meaning: OMOP:32829 EHR MEDICATION LIST: text: EHR MEDICATION LIST description: EHR medication list meaning: OMOP:32830 EHR NOTE: text: EHR NOTE description: EHR note meaning: OMOP:32831 EHR NURSING REPORT: text: EHR NURSING REPORT description: EHR nursing report meaning: OMOP:32832 EHR ORDER: text: EHR ORDER description: EHR order meaning: OMOP:32833 EHR OUTPATIENT NOTE: text: EHR OUTPATIENT NOTE description: EHR outpatient note meaning: OMOP:32834 EHR PATHOLOGY REPORT: text: EHR PATHOLOGY REPORT description: EHR Pathology report meaning: OMOP:32835 EHR PHYSICAL EXAMINATION: text: EHR PHYSICAL EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR PLANNED DISPENSING RECORD: text: EHR PLANNED DISPENSING RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR PERSCRIPTION: text: EHR PERSCRIPTION description: EHR prescription meaning: OMOP:32838 EHR PERSCRIPTION ISSUE RECORD: text: EHR PERSCRIPTION ISSUE RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR PROBLEM LIST: text: EHR PROBLEM LIST description: EHR problem list meaning: OMOP:32840 EHR RADIOLOGY REPORT: text: EHR RADIOLOGY REPORT description: EHR radiology report meaning: OMOP:32841 EHR REFERRAL RECORD: text: EHR REFERRAL RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL CDM INSTANCE: text: EXTERNAL CDM INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY CLAIM: text: FACILITY CLAIM description: Facility claim meaning: OMOP:32844 FACILITY CLAIM DETAIL: text: FACILITY CLAIM DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY CLAIM HEADER: text: FACILITY CLAIM HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC ISOLATION RECORD: text: GEOGRAPHIC ISOLATION RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT REPORT: text: GOVERNMENT REPORT description: Government report meaning: OMOP:32848 HEALTH INFORMATION EXCHANGE RECORD: text: HEALTH INFORMATION EXCHANGE RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH RISK ASSESSMENT: text: HEALTH RISK ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE PROFESSIONAL FILLED SURVEY: text: HEALTHCARE PROFESSIONAL FILLED SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL COST: text: HOSPITAL COST description: Hospital cost meaning: OMOP:32852 INPATIENT CLAIM: text: INPATIENT CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT CLAIM DETAIL: text: INPATIENT CLAIM DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT CLAIM HEADER: text: INPATIENT CLAIM HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL ORDER RECORD: text: MAIL ORDER RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT CLAIM: text: OUTPATIENT CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT CLAIM DETAIL: text: OUTPATIENT CLAIM DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT CLAIM HEADER: text: OUTPATIENT CLAIM HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT FILLED SURVEY: text: PATIENT FILLED SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT OR PAYER PAID RECORD: text: PATIENT OR PAYER PAID RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT REPORTED COST: text: PATIENT REPORTED COST description: Patient reported cost meaning: OMOP:32864 PATIENT SELF-REPORT: text: PATIENT SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT SELF-TESTED: text: PATIENT SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER SYSTEM RECORD (PAID PREMIUM): text: PAYER SYSTEM RECORD (PAID PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER SYSTEM RECORD (PRIMARY PAYER): text: PAYER SYSTEM RECORD (PRIMARY PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER SYSTEM RECORD (SECONDARY PAYER): text: PAYER SYSTEM RECORD (SECONDARY PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY CLAIM: text: PHARMACY CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT OF CARE/EXPRESS LAB: text: POINT OF CARE/EXPRESS LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION TIME PERIOD: text: PRE-QUALIFICATION TIME PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL CLAIM: text: PROFESSIONAL CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL CLAIM DETAIL: text: PROFESSIONAL CLAIM DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL CLAIM HEADER: text: PROFESSIONAL CLAIM HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER CHARGE LIST PRICE: text: PROVIDER CHARGE LIST PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER FINANCIAL SYSTEM: text: PROVIDER FINANCIAL SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER INCURRED COST RECORD: text: PROVIDER INCURRED COST RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION RECORD: text: RANDOMIZATION RECORD description: Randomization record meaning: OMOP:32877 REFERENCE LAB: text: REFERENCE LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD ALGORITHM: text: STANDARD ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD ALGORITHM FROM CLAIMS: text: STANDARD ALGORITHM FROM CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 STANDARD ALGORITHM FROM EHR: text: STANDARD ALGORITHM FROM EHR description: Standard algorithm from EHR meaning: OMOP:32882 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 URGENT LAB: text: URGENT LAB description: Urgent lab meaning: OMOP:32884 US SOCIAL SECURITY DEATH MASTER FILE: text: US SOCIAL SECURITY DEATH MASTER FILE description: US Social Security Death Master File meaning: OMOP:32885 VISION CLAIM: text: VISION CLAIM description: Vision claim meaning: OMOP:32886","title":"Enum: DeviceExposureProvenanceEnum"},{"location":"DeviceExposureProvenanceEnum/#enum-deviceexposureprovenanceenum","text":"Source of device exposure record URI: DeviceExposureProvenanceEnum","title":"Enum: DeviceExposureProvenanceEnum"},{"location":"DeviceExposureProvenanceEnum/#permissible-values","text":"Value Meaning Description CASE REPORT FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM AUTHORIZATION OMOP:32811 Claim authorization CLAIM DISCHARGE RECORD OMOP:32812 Claim discharge record CLAIM ENROLMENT RECORD OMOP:32813 Claim enrolment record COST RECORD OMOP:32814 Cost record DEATH CERTIFICATE OMOP:32815 Death Certificate DENTAL CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR ADMINISTRATION RECORD OMOP:32818 EHR administration record EHR ADMISSION NOTE OMOP:32819 EHR admission note EHR ANCILLARY REPORT OMOP:32820 EHR ancillary report EHR BILLING RECORD OMOP:32821 EHR billing record EHR CHIEF COMPLAINT OMOP:32822 EHR chief complaint EHR DISCHARGE RECORD OMOP:32823 EHR discharge record EHR DISCHARGE SUMMARY OMOP:32824 EHR discharge summary EHR DISPENSING RECORD OMOP:32825 EHR dispensing record EHR EMERGENCY ROOM NOTE OMOP:32826 EHR emergency room note EHR ENCOUNTER RECORD OMOP:32827 EHR encounter record EHR EPISODE RECORD OMOP:32828 EHR episode record EHR INPATIENT NOTE OMOP:32829 EHR inpatient note EHR MEDICATION LIST OMOP:32830 EHR medication list EHR NOTE OMOP:32831 EHR note EHR NURSING REPORT OMOP:32832 EHR nursing report EHR ORDER OMOP:32833 EHR order EHR OUTPATIENT NOTE OMOP:32834 EHR outpatient note EHR PATHOLOGY REPORT OMOP:32835 EHR Pathology report EHR PHYSICAL EXAMINATION OMOP:32836 EHR physical examination EHR PLANNED DISPENSING RECORD OMOP:32837 EHR planned dispensing record EHR PERSCRIPTION OMOP:32838 EHR prescription EHR PERSCRIPTION ISSUE RECORD OMOP:32839 EHR prescription issue record EHR PROBLEM LIST OMOP:32840 EHR problem list EHR RADIOLOGY REPORT OMOP:32841 EHR radiology report EHR REFERRAL RECORD OMOP:32842 EHR referral record EXTERNAL CDM INSTANCE OMOP:32843 External CDM instance FACILITY CLAIM OMOP:32844 Facility claim FACILITY CLAIM DETAIL OMOP:32845 Facility claim detail FACILITY CLAIM HEADER OMOP:32846 Facility claim header GEOGRAPHIC ISOLATION RECORD OMOP:32847 Geographic isolation record GOVERNMENT REPORT OMOP:32848 Government report HEALTH INFORMATION EXCHANGE RECORD OMOP:32849 Health Information Exchange record HEALTH RISK ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE PROFESSIONAL FILLED SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL COST OMOP:32852 Hospital cost INPATIENT CLAIM OMOP:32853 Inpatient claim INPATIENT CLAIM DETAIL OMOP:32854 Inpatient claim detail INPATIENT CLAIM HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL ORDER RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT CLAIM OMOP:32859 Outpatient claim OUTPATIENT CLAIM DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT CLAIM HEADER OMOP:32861 Outpatient claim header PATIENT FILLED SURVEY OMOP:32862 Patient filled survey PATIENT OR PAYER PAID RECORD OMOP:32863 Patient or payer paid record PATIENT REPORTED COST OMOP:32864 Patient reported cost PATIENT SELF-REPORT OMOP:32865 Patient self-report PATIENT SELF-TESTED OMOP:705183 Patient self-tested PAYER SYSTEM RECORD (PAID PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER SYSTEM RECORD (PRIMARY PAYER) OMOP:32867 Payer system record (primary payer) PAYER SYSTEM RECORD (SECONDARY PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY CLAIM OMOP:32869 Pharmacy claim POINT OF CARE/EXPRESS LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION TIME PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL CLAIM OMOP:32871 Professional claim PROFESSIONAL CLAIM DETAIL OMOP:32872 Professional claim detail PROFESSIONAL CLAIM HEADER OMOP:32873 Professional claim header PROVIDER CHARGE LIST PRICE OMOP:32874 Provider charge list price PROVIDER FINANCIAL SYSTEM OMOP:32875 Provider financial system PROVIDER INCURRED COST RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION RECORD OMOP:32877 Randomization record REFERENCE LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD ALGORITHM OMOP:32880 Standard algorithm STANDARD ALGORITHM FROM CLAIMS OMOP:32881 Standard algorithm from claims STANDARD ALGORITHM FROM EHR OMOP:32882 Standard algorithm from EHR SURVEY OMOP:32883 Survey URGENT LAB OMOP:32884 Urgent lab US SOCIAL SECURITY DEATH MASTER FILE OMOP:32885 US Social Security Death Master File VISION CLAIM OMOP:32886 Vision claim","title":"Permissible Values"},{"location":"DeviceExposureProvenanceEnum/#comments","text":"Taken from OMOP Type Concept Domain","title":"Comments"},{"location":"DeviceExposureProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DeviceExposureProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DeviceExposureProvenanceEnum/#linkml-source","text":"name: DeviceExposureProvenanceEnum description: Source of device exposure record comments: - Taken from OMOP Type Concept Domain from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE REPORT FORM: text: CASE REPORT FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM AUTHORIZATION: text: CLAIM AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM DISCHARGE RECORD: text: CLAIM DISCHARGE RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM ENROLMENT RECORD: text: CLAIM ENROLMENT RECORD description: Claim enrolment record meaning: OMOP:32813 COST RECORD: text: COST RECORD description: Cost record meaning: OMOP:32814 DEATH CERTIFICATE: text: DEATH CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL CLAIM: text: DENTAL CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR ADMINISTRATION RECORD: text: EHR ADMINISTRATION RECORD description: EHR administration record meaning: OMOP:32818 EHR ADMISSION NOTE: text: EHR ADMISSION NOTE description: EHR admission note meaning: OMOP:32819 EHR ANCILLARY REPORT: text: EHR ANCILLARY REPORT description: EHR ancillary report meaning: OMOP:32820 EHR BILLING RECORD: text: EHR BILLING RECORD description: EHR billing record meaning: OMOP:32821 EHR CHIEF COMPLAINT: text: EHR CHIEF COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR DISCHARGE RECORD: text: EHR DISCHARGE RECORD description: EHR discharge record meaning: OMOP:32823 EHR DISCHARGE SUMMARY: text: EHR DISCHARGE SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR DISPENSING RECORD: text: EHR DISPENSING RECORD description: EHR dispensing record meaning: OMOP:32825 EHR EMERGENCY ROOM NOTE: text: EHR EMERGENCY ROOM NOTE description: EHR emergency room note meaning: OMOP:32826 EHR ENCOUNTER RECORD: text: EHR ENCOUNTER RECORD description: EHR encounter record meaning: OMOP:32827 EHR EPISODE RECORD: text: EHR EPISODE RECORD description: EHR episode record meaning: OMOP:32828 EHR INPATIENT NOTE: text: EHR INPATIENT NOTE description: EHR inpatient note meaning: OMOP:32829 EHR MEDICATION LIST: text: EHR MEDICATION LIST description: EHR medication list meaning: OMOP:32830 EHR NOTE: text: EHR NOTE description: EHR note meaning: OMOP:32831 EHR NURSING REPORT: text: EHR NURSING REPORT description: EHR nursing report meaning: OMOP:32832 EHR ORDER: text: EHR ORDER description: EHR order meaning: OMOP:32833 EHR OUTPATIENT NOTE: text: EHR OUTPATIENT NOTE description: EHR outpatient note meaning: OMOP:32834 EHR PATHOLOGY REPORT: text: EHR PATHOLOGY REPORT description: EHR Pathology report meaning: OMOP:32835 EHR PHYSICAL EXAMINATION: text: EHR PHYSICAL EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR PLANNED DISPENSING RECORD: text: EHR PLANNED DISPENSING RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR PERSCRIPTION: text: EHR PERSCRIPTION description: EHR prescription meaning: OMOP:32838 EHR PERSCRIPTION ISSUE RECORD: text: EHR PERSCRIPTION ISSUE RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR PROBLEM LIST: text: EHR PROBLEM LIST description: EHR problem list meaning: OMOP:32840 EHR RADIOLOGY REPORT: text: EHR RADIOLOGY REPORT description: EHR radiology report meaning: OMOP:32841 EHR REFERRAL RECORD: text: EHR REFERRAL RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL CDM INSTANCE: text: EXTERNAL CDM INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY CLAIM: text: FACILITY CLAIM description: Facility claim meaning: OMOP:32844 FACILITY CLAIM DETAIL: text: FACILITY CLAIM DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY CLAIM HEADER: text: FACILITY CLAIM HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC ISOLATION RECORD: text: GEOGRAPHIC ISOLATION RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT REPORT: text: GOVERNMENT REPORT description: Government report meaning: OMOP:32848 HEALTH INFORMATION EXCHANGE RECORD: text: HEALTH INFORMATION EXCHANGE RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH RISK ASSESSMENT: text: HEALTH RISK ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE PROFESSIONAL FILLED SURVEY: text: HEALTHCARE PROFESSIONAL FILLED SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL COST: text: HOSPITAL COST description: Hospital cost meaning: OMOP:32852 INPATIENT CLAIM: text: INPATIENT CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT CLAIM DETAIL: text: INPATIENT CLAIM DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT CLAIM HEADER: text: INPATIENT CLAIM HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL ORDER RECORD: text: MAIL ORDER RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT CLAIM: text: OUTPATIENT CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT CLAIM DETAIL: text: OUTPATIENT CLAIM DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT CLAIM HEADER: text: OUTPATIENT CLAIM HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT FILLED SURVEY: text: PATIENT FILLED SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT OR PAYER PAID RECORD: text: PATIENT OR PAYER PAID RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT REPORTED COST: text: PATIENT REPORTED COST description: Patient reported cost meaning: OMOP:32864 PATIENT SELF-REPORT: text: PATIENT SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT SELF-TESTED: text: PATIENT SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER SYSTEM RECORD (PAID PREMIUM): text: PAYER SYSTEM RECORD (PAID PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER SYSTEM RECORD (PRIMARY PAYER): text: PAYER SYSTEM RECORD (PRIMARY PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER SYSTEM RECORD (SECONDARY PAYER): text: PAYER SYSTEM RECORD (SECONDARY PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY CLAIM: text: PHARMACY CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT OF CARE/EXPRESS LAB: text: POINT OF CARE/EXPRESS LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION TIME PERIOD: text: PRE-QUALIFICATION TIME PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL CLAIM: text: PROFESSIONAL CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL CLAIM DETAIL: text: PROFESSIONAL CLAIM DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL CLAIM HEADER: text: PROFESSIONAL CLAIM HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER CHARGE LIST PRICE: text: PROVIDER CHARGE LIST PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER FINANCIAL SYSTEM: text: PROVIDER FINANCIAL SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER INCURRED COST RECORD: text: PROVIDER INCURRED COST RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION RECORD: text: RANDOMIZATION RECORD description: Randomization record meaning: OMOP:32877 REFERENCE LAB: text: REFERENCE LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD ALGORITHM: text: STANDARD ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD ALGORITHM FROM CLAIMS: text: STANDARD ALGORITHM FROM CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 STANDARD ALGORITHM FROM EHR: text: STANDARD ALGORITHM FROM EHR description: Standard algorithm from EHR meaning: OMOP:32882 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 URGENT LAB: text: URGENT LAB description: Urgent lab meaning: OMOP:32884 US SOCIAL SECURITY DEATH MASTER FILE: text: US SOCIAL SECURITY DEATH MASTER FILE description: US Social Security Death Master File meaning: OMOP:32885 VISION CLAIM: text: VISION CLAIM description: Vision claim meaning: OMOP:32886","title":"LinkML Source"},{"location":"DimensionalObservation/","text":"Class: DimensionalObservation A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. URI: bdchm:DimensionalObservation classDiagram class DimensionalObservation Observation <|-- DimensionalObservation DimensionalObservation : age_at_observation DimensionalObservation : associated_participant DimensionalObservation --> Participant : associated_participant DimensionalObservation : associated_visit DimensionalObservation --> Visit : associated_visit DimensionalObservation : category DimensionalObservation : focus DimensionalObservation --> Entity : focus DimensionalObservation : id DimensionalObservation : method_type DimensionalObservation : observation_type DimensionalObservation : performed_by DimensionalObservation --> Organization : performed_by DimensionalObservation : value DimensionalObservation --> ObservationValueQuantity : value Inheritance Entity Observation DimensionalObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used DimensionalObservationSet observations range DimensionalObservation Comments At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DimensionalObservation native bdchm:DimensionalObservation LinkML Source Direct name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true Induced name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: DimensionalObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: DimensionalObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: DimensionalObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: DimensionalObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: DimensionalObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DimensionalObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: DimensionalObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservation domain_of: - Entity range: uriorcurie required: true","title":"Class: DimensionalObservation"},{"location":"DimensionalObservation/#class-dimensionalobservation","text":"A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. URI: bdchm:DimensionalObservation classDiagram class DimensionalObservation Observation <|-- DimensionalObservation DimensionalObservation : age_at_observation DimensionalObservation : associated_participant DimensionalObservation --> Participant : associated_participant DimensionalObservation : associated_visit DimensionalObservation --> Visit : associated_visit DimensionalObservation : category DimensionalObservation : focus DimensionalObservation --> Entity : focus DimensionalObservation : id DimensionalObservation : method_type DimensionalObservation : observation_type DimensionalObservation : performed_by DimensionalObservation --> Organization : performed_by DimensionalObservation : value DimensionalObservation --> ObservationValueQuantity : value","title":"Class: DimensionalObservation"},{"location":"DimensionalObservation/#inheritance","text":"Entity Observation DimensionalObservation","title":"Inheritance"},{"location":"DimensionalObservation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DimensionalObservation/#usages","text":"used by used in type used DimensionalObservationSet observations range DimensionalObservation","title":"Usages"},{"location":"DimensionalObservation/#comments","text":"At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data.","title":"Comments"},{"location":"DimensionalObservation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DimensionalObservation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DimensionalObservation/#mappings","text":"Mapping Type Mapped Value self bdchm:DimensionalObservation native bdchm:DimensionalObservation","title":"Mappings"},{"location":"DimensionalObservation/#linkml-source","text":"","title":"LinkML Source"},{"location":"DimensionalObservation/#direct","text":"name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true","title":"Direct"},{"location":"DimensionalObservation/#induced","text":"name: DimensionalObservation description: A structured object that describes a single data item about the physical dimensions of an entity (e.g. length width, area), as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: DimensionalObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: DimensionalObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: DimensionalObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: DimensionalObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: DimensionalObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DimensionalObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: DimensionalObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DimensionalObservationSet/","text":"Class: DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). URI: bdchm:DimensionalObservationSet classDiagram class DimensionalObservationSet ObservationSet <|-- DimensionalObservationSet DimensionalObservationSet : associated_participant DimensionalObservationSet --> Participant : associated_participant DimensionalObservationSet : category DimensionalObservationSet : focus DimensionalObservationSet --> Entity : focus DimensionalObservationSet : id DimensionalObservationSet : method_type DimensionalObservationSet : observations DimensionalObservationSet --> DimensionalObservation : observations DimensionalObservationSet : performed_by DimensionalObservationSet --> Organization : performed_by Inheritance Entity ObservationSet DimensionalObservationSet Slots Name Cardinality and Range Description Inheritance observations 0..* DimensionalObservation A set of one or more observations ObservationSet category 0..1 String The general category of observation set described ObservationSet focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... ObservationSet associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) ObservationSet method_type 0..* String The type of method used in generating the ObservationSet ObservationSet performed_by 0..1 Organization The organization or group that performed the observation activity ObservationSet id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen dimensional_measures range DimensionalObservationSet Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DimensionalObservationSet native bdchm:DimensionalObservationSet LinkML Source Direct name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation Induced name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation attributes: observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: DimensionalObservationSet domain_of: - ObservationSet range: DimensionalObservation category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: DimensionalObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: DimensionalObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: DimensionalObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Class: DimensionalObservationSet"},{"location":"DimensionalObservationSet/#class-dimensionalobservationset","text":"A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). URI: bdchm:DimensionalObservationSet classDiagram class DimensionalObservationSet ObservationSet <|-- DimensionalObservationSet DimensionalObservationSet : associated_participant DimensionalObservationSet --> Participant : associated_participant DimensionalObservationSet : category DimensionalObservationSet : focus DimensionalObservationSet --> Entity : focus DimensionalObservationSet : id DimensionalObservationSet : method_type DimensionalObservationSet : observations DimensionalObservationSet --> DimensionalObservation : observations DimensionalObservationSet : performed_by DimensionalObservationSet --> Organization : performed_by","title":"Class: DimensionalObservationSet"},{"location":"DimensionalObservationSet/#inheritance","text":"Entity ObservationSet DimensionalObservationSet","title":"Inheritance"},{"location":"DimensionalObservationSet/#slots","text":"Name Cardinality and Range Description Inheritance observations 0..* DimensionalObservation A set of one or more observations ObservationSet category 0..1 String The general category of observation set described ObservationSet focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... ObservationSet associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) ObservationSet method_type 0..* String The type of method used in generating the ObservationSet ObservationSet performed_by 0..1 Organization The organization or group that performed the observation activity ObservationSet id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DimensionalObservationSet/#usages","text":"used by used in type used Specimen dimensional_measures range DimensionalObservationSet","title":"Usages"},{"location":"DimensionalObservationSet/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DimensionalObservationSet/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DimensionalObservationSet/#mappings","text":"Mapping Type Mapped Value self bdchm:DimensionalObservationSet native bdchm:DimensionalObservationSet","title":"Mappings"},{"location":"DimensionalObservationSet/#linkml-source","text":"","title":"LinkML Source"},{"location":"DimensionalObservationSet/#direct","text":"name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation","title":"Direct"},{"location":"DimensionalObservationSet/#induced","text":"name: DimensionalObservationSet description: A set of one or more discrete observations about the physical dimensions of an object (e.g. length, width, area). from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationSet slot_usage: observations: name: observations domain_of: - ObservationSet range: DimensionalObservation attributes: observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: DimensionalObservationSet domain_of: - ObservationSet range: DimensionalObservation category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: DimensionalObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: DimensionalObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: DimensionalObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: DimensionalObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: DimensionalObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DimensionalObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Document/","text":"Class: Document A collection of information intented to be understood together as a whole, and codified in human-readable form. URI: bdchm:Document classDiagram class Document Entity <|-- Document Document : description Document : document_type Document : focus Document --> Entity : focus Document : id Document : identity Document : url Inheritance Entity Document Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct document_type 0..1 String The high-level type of the document (e direct description 0..1 String A free text description or summary of the report direct focus 0..1 Entity The entity that the report is primarily about direct url 0..* String A URL/web address where the document can be accessed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen related_document range Document Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Document native bdchm:Document LinkML Source Direct name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true Induced name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Document domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: focus owner: Document domain_of: - Document - ObservationSet - Observation range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: url owner: Document domain_of: - ResearchStudy - Questionnaire - Document range: string required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Document domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Document domain_of: - Entity range: uriorcurie required: true","title":"Class: Document"},{"location":"Document/#class-document","text":"A collection of information intented to be understood together as a whole, and codified in human-readable form. URI: bdchm:Document classDiagram class Document Entity <|-- Document Document : description Document : document_type Document : focus Document --> Entity : focus Document : id Document : identity Document : url","title":"Class: Document"},{"location":"Document/#inheritance","text":"Entity Document","title":"Inheritance"},{"location":"Document/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct document_type 0..1 String The high-level type of the document (e direct description 0..1 String A free text description or summary of the report direct focus 0..1 Entity The entity that the report is primarily about direct url 0..* String A URL/web address where the document can be accessed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Document/#usages","text":"used by used in type used Specimen related_document range Document","title":"Usages"},{"location":"Document/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Document/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Document/#mappings","text":"Mapping Type Mapped Value self bdchm:Document native bdchm:Document","title":"Mappings"},{"location":"Document/#linkml-source","text":"","title":"LinkML Source"},{"location":"Document/#direct","text":"name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"Document/#induced","text":"name: Document description: A collection of information intented to be understood together as a whole, and codified in human-readable form. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: document_type: name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false description: name: description description: A free text description or summary of the report. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Document domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false focus: name: focus description: The entity that the report is primarily about from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: focus owner: Document domain_of: - Document - ObservationSet - Observation range: Entity required: false url: name: url description: A URL/web address where the document can be accessed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: url owner: Document domain_of: - ResearchStudy - Questionnaire - Document range: string required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Document domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Document domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Double/","text":"Type: Double A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Double"},{"location":"Double/#type-double","text":"A real number that conforms to the xsd:double specification URI: xsd:double base : float uri : xsd:double","title":"Type: Double"},{"location":"Double/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Double/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposure/","text":"Class: DrugExposure DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. URI: bdchm:DrugExposure classDiagram class DrugExposure Entity <|-- DrugExposure DrugExposure : age_at_exposure_end DrugExposure : age_at_exposure_start DrugExposure : associated_participant DrugExposure --> Participant : associated_participant DrugExposure : associated_visit DrugExposure --> Visit : associated_visit DrugExposure : days_supply DrugExposure : drug_concept DrugExposure --> DrugExposureConceptEnum : drug_concept DrugExposure : exposure_provenance DrugExposure --> DrugExposureProvenanceEnum : exposure_provenance DrugExposure : id DrugExposure : identity DrugExposure : quantity DrugExposure : refills DrugExposure : route_concept DrugExposure --> DrugRouteEnum : route_concept DrugExposure : sig Inheritance Entity DrugExposure Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct drug_concept 0..1 DrugExposureConceptEnum The coded value for a drug direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DrugExposureProvenanceEnum A value representing the provenance of the DrugExposure record direct refills 0..1 Integer Intended refills at time of the prescription direct quantity 0..1 Float To find the dose form of a drug the RELATIONSHIP table can be used where the ... direct days_supply 0..1 Integer The number of days of supply of the medication as recorded in the original pr... direct sig 0..1 String This is the verbatim instruction for the drug as written by the provider direct route_concept 0..1 DrugRouteEnum Route of drug administration direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:DrugExposure native bdchm:DrugExposure LinkML Source Direct name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false Induced name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_start owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_end owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: exposure_provenance owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DrugExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sig owner: DrugExposure domain_of: - DrugExposure range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DrugExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DrugExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DrugExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DrugExposure domain_of: - Entity range: uriorcurie required: true","title":"Class: DrugExposure"},{"location":"DrugExposure/#class-drugexposure","text":"DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. URI: bdchm:DrugExposure classDiagram class DrugExposure Entity <|-- DrugExposure DrugExposure : age_at_exposure_end DrugExposure : age_at_exposure_start DrugExposure : associated_participant DrugExposure --> Participant : associated_participant DrugExposure : associated_visit DrugExposure --> Visit : associated_visit DrugExposure : days_supply DrugExposure : drug_concept DrugExposure --> DrugExposureConceptEnum : drug_concept DrugExposure : exposure_provenance DrugExposure --> DrugExposureProvenanceEnum : exposure_provenance DrugExposure : id DrugExposure : identity DrugExposure : quantity DrugExposure : refills DrugExposure : route_concept DrugExposure --> DrugRouteEnum : route_concept DrugExposure : sig","title":"Class: DrugExposure"},{"location":"DrugExposure/#inheritance","text":"Entity DrugExposure","title":"Inheritance"},{"location":"DrugExposure/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct drug_concept 0..1 DrugExposureConceptEnum The coded value for a drug direct age_at_exposure_start 0..1 Integer The Participant's age (expressed in days) at the exposure start date direct age_at_exposure_end 0..1 Integer The Participant's age (expressed in days) at the exposure end date, if availa... direct exposure_provenance 0..1 DrugExposureProvenanceEnum A value representing the provenance of the DrugExposure record direct refills 0..1 Integer Intended refills at time of the prescription direct quantity 0..1 Float To find the dose form of a drug the RELATIONSHIP table can be used where the ... direct days_supply 0..1 Integer The number of days of supply of the medication as recorded in the original pr... direct sig 0..1 String This is the verbatim instruction for the drug as written by the provider direct route_concept 0..1 DrugRouteEnum Route of drug administration direct associated_participant 0..1 Participant A reference to the Participant to which the exposure is attributed direct associated_visit 0..1 Visit A reference to the Visit the exposure is associated with, if any direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"DrugExposure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugExposure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposure/#mappings","text":"Mapping Type Mapped Value self bdchm:DrugExposure native bdchm:DrugExposure","title":"Mappings"},{"location":"DrugExposure/#linkml-source","text":"","title":"LinkML Source"},{"location":"DrugExposure/#direct","text":"name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit required: false","title":"Direct"},{"location":"DrugExposure/#induced","text":"name: DrugExposure description: DrugExposures are records of a Person suggesting exposure to a medication. The source could be prescription, dispensing, medication administration records (MARs), or patient medication list. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: drug_concept: name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum age_at_exposure_start: name: age_at_exposure_start description: The Participant's age (expressed in days) at the exposure start date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_start owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d age_at_exposure_end: name: age_at_exposure_end description: The Participant's age (expressed in days) at the exposure end date, if available. Otherwise equal to age_at_exposure_start. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_exposure_end owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: integer unit: ucum_code: d exposure_provenance: name: exposure_provenance description: A value representing the provenance of the DrugExposure record. From OMOP Drug Types. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: exposure_provenance owner: DrugExposure domain_of: - DrugExposure - DeviceExposure range: DrugExposureProvenanceEnum refills: name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false quantity: name: quantity description: To find the dose form of a drug the RELATIONSHIP table can be used where the relationship_id is \u2018Has dose form\u2019. If liquid, quantity stands for the total amount dispensed or ordered of ingredient in the units given by the drug_strength table. If the unit from the source data does not align with the unit in the DRUG_STRENGTH table the quantity should be converted to the correct unit given in DRUG_STRENGTH. For clinical drugs with fixed dose forms (tablets etc.) the quantity is the number of units/tablets/capsules prescribed or dispensed (can be partial, but then only 1/2 or 1/3, not 0.01). Clinical drugs with divisible dose forms (injections) the quantity is the amount of ingredient the patient got. For example, if the injection is 2mg/mL but the patient got 80mL then quantity is reported as 160. Quantified clinical drugs with divisible dose forms (prefilled syringes), the quantity is the amount of ingredient similar to clinical drugs. Please see [how to calculate drug dose](https://ohdsi.github.io/CommonDataModel/drug_dose.html) for more information. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: quantity owner: DrugExposure domain_of: - Procedure - DrugExposure - DeviceExposure range: float required: false days_supply: name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false sig: name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sig owner: DrugExposure domain_of: - DrugExposure range: string required: false route_concept: name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum associated_participant: name: associated_participant description: A reference to the Participant to which the exposure is attributed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: DrugExposure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit the exposure is associated with, if any. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: DrugExposure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit required: false identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: DrugExposure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: DrugExposure domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"DrugExposureConceptEnum/","text":"Enum: DrugExposureConceptEnum Drug codes from RxNorm. URI: DrugExposureConceptEnum This is a dynamic enum Slots Name Description drug_concept The coded value for a drug See Also https://bioregistry.io/registry/rxnorm https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html http://www.nlm.nih.gov/research/umls/rxnorm urn:oid:2.16.840.1.113883.6.88 Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DrugExposureConceptEnum description: Drug codes from RxNorm. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/rxnorm - https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html - http://www.nlm.nih.gov/research/umls/rxnorm - urn:oid:2.16.840.1.113883.6.88 rank: 1000 reachable_from: source_ontology: bioregistry:rxnorm","title":"Enum: DrugExposureConceptEnum"},{"location":"DrugExposureConceptEnum/#enum-drugexposureconceptenum","text":"Drug codes from RxNorm. URI: DrugExposureConceptEnum This is a dynamic enum","title":"Enum: DrugExposureConceptEnum"},{"location":"DrugExposureConceptEnum/#slots","text":"Name Description drug_concept The coded value for a drug","title":"Slots"},{"location":"DrugExposureConceptEnum/#see-also","text":"https://bioregistry.io/registry/rxnorm https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html http://www.nlm.nih.gov/research/umls/rxnorm urn:oid:2.16.840.1.113883.6.88","title":"See Also"},{"location":"DrugExposureConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugExposureConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposureConceptEnum/#linkml-source","text":"name: DrugExposureConceptEnum description: Drug codes from RxNorm. from_schema: https://w3id.org/nhlbidatastage/bdchm see_also: - https://bioregistry.io/registry/rxnorm - https://terminology.hl7.org/3.1.0/CodeSystem-v3-rxNorm.html - http://www.nlm.nih.gov/research/umls/rxnorm - urn:oid:2.16.840.1.113883.6.88 rank: 1000 reachable_from: source_ontology: bioregistry:rxnorm","title":"LinkML Source"},{"location":"DrugExposureProvenanceEnum/","text":"Enum: DrugExposureProvenanceEnum Source of drug exposure record URI: DrugExposureProvenanceEnum Permissible Values Value Meaning Description RANDOMIZED DRUG OMOP:44777970 Randomized Drug PATIENT SELF-REPORTED MEDICATION OMOP:44787730 Patient Self-Reported Medication NLP DERIVED OMOP:32426 NLP derived PRESCRIPTION DISPENSED IN PHARMACY OMOP:38000175 Prescription dispensed in pharmacy PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) OMOP:581373 Physician administered drug (identified from EHR order) DISPENSED IN OUTPATIENT OFFICE OMOP:581452 Dispensed in Outpatient office PRESCRIPTION DISPENSED THROUGH MAIL ORDER OMOP:38000176 Prescription dispensed through mail order PRESCRIPTION WRITTEN OMOP:38000177 Prescription written MEDICATION LIST ENTRY OMOP:38000178 Medication list entry PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) OMOP:38000179 Physician administered drug (identified as procedure) INPATIENT ADMINISTRATION OMOP:38000180 Inpatient administration DRUG ERA - 0 DAYS PERSISTENCE WINDOW OMOP:38000181 Drug era - 0 days persistence window DRUG ERA - 30 DAYS PERSISTENCE WINDOW OMOP:38000182 Drug era - 30 days persistence window PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) OMOP:43542356 Physician administered drug (identified from EHR problem list) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) OMOP:43542357 Physician administered drug (identified from referral record) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) OMOP:43542358 Physician administered drug (identified from EHR observation) Slots Name Description exposure_provenance A value representing the provenance of the DrugExposure record Comments Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name? Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DrugExposureProvenanceEnum description: Source of drug exposure record comments: - Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: RANDOMIZED DRUG: text: RANDOMIZED DRUG description: Randomized Drug meaning: OMOP:44777970 PATIENT SELF-REPORTED MEDICATION: text: PATIENT SELF-REPORTED MEDICATION description: Patient Self-Reported Medication meaning: OMOP:44787730 NLP DERIVED: text: NLP DERIVED description: NLP derived meaning: OMOP:32426 PRESCRIPTION DISPENSED IN PHARMACY: text: PRESCRIPTION DISPENSED IN PHARMACY description: Prescription dispensed in pharmacy meaning: OMOP:38000175 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) description: Physician administered drug (identified from EHR order) meaning: OMOP:581373 DISPENSED IN OUTPATIENT OFFICE: text: DISPENSED IN OUTPATIENT OFFICE description: Dispensed in Outpatient office meaning: OMOP:581452 PRESCRIPTION DISPENSED THROUGH MAIL ORDER: text: PRESCRIPTION DISPENSED THROUGH MAIL ORDER description: Prescription dispensed through mail order meaning: OMOP:38000176 PRESCRIPTION WRITTEN: text: PRESCRIPTION WRITTEN description: Prescription written meaning: OMOP:38000177 MEDICATION LIST ENTRY: text: MEDICATION LIST ENTRY description: Medication list entry meaning: OMOP:38000178 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) description: Physician administered drug (identified as procedure) meaning: OMOP:38000179 INPATIENT ADMINISTRATION: text: INPATIENT ADMINISTRATION description: Inpatient administration meaning: OMOP:38000180 DRUG ERA - 0 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 0 DAYS PERSISTENCE WINDOW description: Drug era - 0 days persistence window meaning: OMOP:38000181 DRUG ERA - 30 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 30 DAYS PERSISTENCE WINDOW description: Drug era - 30 days persistence window meaning: OMOP:38000182 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) description: Physician administered drug (identified from EHR problem list) meaning: OMOP:43542356 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) description: Physician administered drug (identified from referral record) meaning: OMOP:43542357 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) description: Physician administered drug (identified from EHR observation) meaning: OMOP:43542358","title":"Enum: DrugExposureProvenanceEnum"},{"location":"DrugExposureProvenanceEnum/#enum-drugexposureprovenanceenum","text":"Source of drug exposure record URI: DrugExposureProvenanceEnum","title":"Enum: DrugExposureProvenanceEnum"},{"location":"DrugExposureProvenanceEnum/#permissible-values","text":"Value Meaning Description RANDOMIZED DRUG OMOP:44777970 Randomized Drug PATIENT SELF-REPORTED MEDICATION OMOP:44787730 Patient Self-Reported Medication NLP DERIVED OMOP:32426 NLP derived PRESCRIPTION DISPENSED IN PHARMACY OMOP:38000175 Prescription dispensed in pharmacy PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) OMOP:581373 Physician administered drug (identified from EHR order) DISPENSED IN OUTPATIENT OFFICE OMOP:581452 Dispensed in Outpatient office PRESCRIPTION DISPENSED THROUGH MAIL ORDER OMOP:38000176 Prescription dispensed through mail order PRESCRIPTION WRITTEN OMOP:38000177 Prescription written MEDICATION LIST ENTRY OMOP:38000178 Medication list entry PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) OMOP:38000179 Physician administered drug (identified as procedure) INPATIENT ADMINISTRATION OMOP:38000180 Inpatient administration DRUG ERA - 0 DAYS PERSISTENCE WINDOW OMOP:38000181 Drug era - 0 days persistence window DRUG ERA - 30 DAYS PERSISTENCE WINDOW OMOP:38000182 Drug era - 30 days persistence window PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) OMOP:43542356 Physician administered drug (identified from EHR problem list) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) OMOP:43542357 Physician administered drug (identified from referral record) PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) OMOP:43542358 Physician administered drug (identified from EHR observation)","title":"Permissible Values"},{"location":"DrugExposureProvenanceEnum/#slots","text":"Name Description exposure_provenance A value representing the provenance of the DrugExposure record","title":"Slots"},{"location":"DrugExposureProvenanceEnum/#comments","text":"Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name?","title":"Comments"},{"location":"DrugExposureProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugExposureProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugExposureProvenanceEnum/#linkml-source","text":"name: DrugExposureProvenanceEnum description: Source of drug exposure record comments: - Taken from OMOP Drug Type values; \"select * from concept where vocabulary_id = 'Drug Type';\" Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: RANDOMIZED DRUG: text: RANDOMIZED DRUG description: Randomized Drug meaning: OMOP:44777970 PATIENT SELF-REPORTED MEDICATION: text: PATIENT SELF-REPORTED MEDICATION description: Patient Self-Reported Medication meaning: OMOP:44787730 NLP DERIVED: text: NLP DERIVED description: NLP derived meaning: OMOP:32426 PRESCRIPTION DISPENSED IN PHARMACY: text: PRESCRIPTION DISPENSED IN PHARMACY description: Prescription dispensed in pharmacy meaning: OMOP:38000175 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR ORDER) description: Physician administered drug (identified from EHR order) meaning: OMOP:581373 DISPENSED IN OUTPATIENT OFFICE: text: DISPENSED IN OUTPATIENT OFFICE description: Dispensed in Outpatient office meaning: OMOP:581452 PRESCRIPTION DISPENSED THROUGH MAIL ORDER: text: PRESCRIPTION DISPENSED THROUGH MAIL ORDER description: Prescription dispensed through mail order meaning: OMOP:38000176 PRESCRIPTION WRITTEN: text: PRESCRIPTION WRITTEN description: Prescription written meaning: OMOP:38000177 MEDICATION LIST ENTRY: text: MEDICATION LIST ENTRY description: Medication list entry meaning: OMOP:38000178 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED AS PROCEDURE) description: Physician administered drug (identified as procedure) meaning: OMOP:38000179 INPATIENT ADMINISTRATION: text: INPATIENT ADMINISTRATION description: Inpatient administration meaning: OMOP:38000180 DRUG ERA - 0 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 0 DAYS PERSISTENCE WINDOW description: Drug era - 0 days persistence window meaning: OMOP:38000181 DRUG ERA - 30 DAYS PERSISTENCE WINDOW: text: DRUG ERA - 30 DAYS PERSISTENCE WINDOW description: Drug era - 30 days persistence window meaning: OMOP:38000182 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR PROBLEM LIST) description: Physician administered drug (identified from EHR problem list) meaning: OMOP:43542356 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM REFERRAL RECORD) description: Physician administered drug (identified from referral record) meaning: OMOP:43542357 PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION): text: PHYSICIAN ADMINISTERED DRUG (IDENTIFIED FROM EHR OBSERVATION) description: Physician administered drug (identified from EHR observation) meaning: OMOP:43542358","title":"LinkML Source"},{"location":"DrugRouteEnum/","text":"Enum: DrugRouteEnum Routes of drug administration. URI: DrugRouteEnum Permissible Values Value Meaning Description ARTERIOVENOUS FISTULA OMOP:44783786 Arteriovenous fistula HAEMODIAFILTRATION OMOP:44801748 Haemodiafiltration SUBLESIONAL OMOP:46270168 Sublesional INTRANEURAL OMOP:46272911 Intraneural INTRAMURAL OMOP:46272926 Intramural INTRACATHETER INSTILLATION OMOP:605428 Intracatheter instillation SUBLABIAL OMOP:600817 Sublabial INTRA-ARTICULAR OMOP:4006860 Intra-articular INTRADIALYTIC OMOP:618805 Intradialytic ARTERIOVENOUS GRAFT OMOP:762840 Arteriovenous graft OTIC OMOP:4023156 Otic ORAL OMOP:4132161 Oral VAGINAL OMOP:4057765 Vaginal ROUTE OF ADMINISTRATION VALUE OMOP:4106215 Route of administration value GASTROSTOMY OMOP:4132254 Gastrostomy NASOGASTRIC OMOP:4132711 Nasogastric JEJUNOSTOMY OMOP:4133177 Jejunostomy SUBCUTANEOUS OMOP:4142048 Subcutaneous GINGIVAL OMOP:4156704 Gingival INTRACARDIAC OMOP:4156705 Intracardiac INTRADERMAL OMOP:4156706 Intradermal INTRAPLEURAL OMOP:4156707 Intrapleural PERIARTICULAR OMOP:4156708 Periarticular ENDOSINUSIAL OMOP:4157756 Endosinusial INTRACAVERNOUS OMOP:4157757 Intracavernous INTRALESIONAL OMOP:4157758 Intralesional INTRALYMPHATIC OMOP:4157759 Intralymphatic INTRAOCULAR OMOP:4157760 Intraocular PERINEURAL OMOP:4157761 Perineural INTRACRANIAL OMOP:4171079 Intracranial DENTAL OMOP:4163765 Dental INTRAAMNIOTIC OMOP:4163767 Intraamniotic INTRABURSAL OMOP:4163768 Intrabursal INTRADISCAL OMOP:4163769 Intradiscal SUBCONJUNCTIVAL OMOP:4163770 Subconjunctival MUCOUS FISTULA OMOP:4171243 Mucous fistula INTRAPROSTATIC OMOP:4171725 Intraprostatic INTRAVENOUS PERIPHERAL OMOP:4171884 Intravenous peripheral PERIOSTEAL OMOP:4171893 Periosteal ESOPHAGOSTOMY OMOP:4172191 Esophagostomy NASODUODENAL OMOP:4172316 Nasoduodenal PERCUTANEOUS OMOP:4177987 Percutaneous SUBORBITAL OMOP:4166865 Suborbital INTRATHORACIC OMOP:4167393 Intrathoracic ENTERAL OMOP:4167540 Enteral INTRAMYOMETRIAL OMOP:4168038 Intramyometrial COLOSTOMY OMOP:4168047 Colostomy INTRATYMPANIC OMOP:4168656 Intratympanic GASTRO-INTESTINAL STOMA OMOP:4168665 Gastro-intestinal stoma INTRAPULMONARY OMOP:4169270 Intrapulmonary INTRASINAL OMOP:4169440 Intrasinal TUMOR CAVITY OMOP:4169472 Tumor cavity SUBMUCOSAL OMOP:4169634 Submucosal INTRADUCTAL OMOP:4170083 Intraductal INTRAVENOUS CENTRAL OMOP:4170113 Intravenous central PARAVERTEBRAL OMOP:4170267 Paravertebral UROSTOMY OMOP:4170435 Urostomy LARYNGEAL OMOP:4170440 Laryngeal SURGICAL CAVITY OMOP:4170771 Surgical cavity INTRAVENOUS OMOP:4171047 Intravenous INTRATESTICULAR OMOP:4171067 Intratesticular ENDOCERVICAL OMOP:4186831 Endocervical ENDOTRACHEOPULMONARY OMOP:4186832 Endotracheopulmonary EXTRA-AMNIOTIC OMOP:4186833 Extra-amniotic GASTROENTERAL OMOP:4186834 Gastroenteral INTRACERVICAL OMOP:4186835 Intracervical INTRACORONARY OMOP:4186836 Intracoronary INTRASTERNAL OMOP:4186837 Intrasternal INTRAVESICAL OMOP:4186838 Intravesical OROMUCOSAL OMOP:4186839 Oromucosal CAUDAL OMOP:4220455 Caudal BUCCAL OMOP:4181897 Buccal OPHTHALMIC OMOP:4184451 Ophthalmic BODY CAVITY OMOP:4222254 Body cavity INTRAOSSEOUS OMOP:4213522 Intraosseous INTRAVENTRICULAR ROUTE - CARDIAC OMOP:4222259 Intraventricular route - cardiac INTRABILIARY OMOP:4223965 Intrabiliary INTRACEREBROVENTRICULAR OMOP:4224886 Intracerebroventricular INTRATHECAL OMOP:4217202 Intrathecal EPIDURAL OMOP:4225555 Epidural INTRATRACHEAL OMOP:4229543 Intratracheal URETHRAL OMOP:4233974 Urethral TRANSMUCOSAL OMOP:4232601 Transmucosal TRANSDERMAL OMOP:4262099 Transdermal INTRA-ARTERIAL OMOP:4240824 Intra-arterial INTRAPERITONEAL OMOP:4243022 Intraperitoneal INTRAMEDULLARY OMOP:4246511 Intramedullary INTRAUTERINE OMOP:4269621 Intrauterine NASAL OMOP:4262914 Nasal TOPICAL OMOP:4263689 Topical RECTAL OMOP:4290759 Rectal SUBLINGUAL OMOP:4292110 Sublingual INTRALUMINAL OMOP:4292410 Intraluminal TRANSCERVICAL OMOP:4304730 Transcervical INTRAABDOMINAL OMOP:4304882 Intraabdominal TRANSURETHRAL OMOP:4305382 Transurethral PERITENDINOUS OMOP:4305564 Peritendinous ILEOSTOMY OMOP:4305679 Ileostomy INTRACORNEAL OMOP:4305690 Intracorneal NASOJEJUNAL OMOP:4305834 Nasojejunal INTRACISTERNAL OMOP:4305993 Intracisternal SUBGINGIVAL OMOP:4306649 Subgingival INTRAOVARIAN OMOP:4306657 Intraovarian INTERSTITIAL OMOP:4327128 Interstitial INTRASYNOVIAL OMOP:4302352 Intrasynovial INTRADUODENAL OMOP:4302354 Intraduodenal SUBTENDINOUS OMOP:4302493 Subtendinous INTRAMUSCULAR OMOP:4302612 Intramuscular INTRAVITREAL OMOP:4302785 Intravitreal INTRASPINAL OMOP:4302788 Intraspinal INTRABRONCHIAL OMOP:4303263 Intrabronchial OROPHARYNGEAL OMOP:4303277 Oropharyngeal INTRACAMERAL OMOP:4303409 Intracameral PARACERVICAL OMOP:4303515 Paracervical PERIURETHRAL OMOP:4303646 Periurethral INTRACORONAL OMOP:4303667 Intracoronal RETROBULBAR OMOP:4303673 Retrobulbar INTRACARTILAGINOUS OMOP:4303676 Intracartilaginous OROGASTRIC OMOP:4303795 Orogastric INTRATENDINOUS OMOP:4303939 Intratendinous PERIBULBAR OMOP:4304274 Peribulbar FISTULA OMOP:4304277 Fistula SURGICAL DRAIN OMOP:4304412 Surgical drain URETERAL OMOP:4304571 Ureteral EPILESIONAL OMOP:35608078 Epilesional EXTRACORPOREAL HEMODIALYSIS OMOP:35624178 Extracorporeal hemodialysis SUPRACHOROIDAL OMOP:37174548 Suprachoroidal EXTRACORPOREAL OMOP:37018288 Extracorporeal INTRACORPORUS CAVERNOSUM OMOP:37174549 Intracorporus cavernosum INTRAGLANDULAR OMOP:37207460 Intraglandular INTRACHOLANGIOPANCREATIC OMOP:37207461 Intracholangiopancreatic INTRAPORTAL OMOP:37207462 Intraportal PERITUMORAL OMOP:37207463 Peritumoral POSTERIOR JUXTASCLERAL OMOP:37207464 Posterior juxtascleral SUBRETINAL OMOP:37207465 Subretinal INFILTRATION OMOP:37397638 Infiltration TRANSENDOCARDIAL OMOP:40487850 Transendocardial TRANSPLACENTAL OMOP:40487858 Transplacental INTRAEPIDERMAL OMOP:40487983 Intraepidermal INTRACEREBRAL OMOP:40488317 Intracerebral INTRAJEJUNAL OMOP:40489989 Intrajejunal INTRACOLONIC OMOP:40489990 Intracolonic CUTANEOUS OMOP:40490507 Cutaneous INTRAILEAL OMOP:40490837 Intraileal PERIODONTAL OMOP:40490866 Periodontal PERIDURAL OMOP:40490896 Peridural LOWER RESPIRATORY TRACT OMOP:40490898 Lower respiratory tract INTRAMAMMARY OMOP:40491321 Intramammary INTRATUMOR OMOP:40491322 Intratumor TRANSTYMPANIC OMOP:40491830 Transtympanic TRANSTRACHEAL OMOP:40491832 Transtracheal INTRAESOPHAGEAL OMOP:40492284 Intraesophageal INTRAGINGIVAL OMOP:40492286 Intragingival INTRAVASCULAR OMOP:40492287 Intravascular INTRADURAL OMOP:40492288 Intradural INTRAMENINGEAL OMOP:40492300 Intrameningeal INTRAGASTRIC OMOP:40492301 Intragastric INTRAPERICARDIAL OMOP:40492305 Intrapericardial INTRALINGUAL OMOP:40493227 Intralingual RESPIRATORY TRACT OMOP:40486069 Respiratory tract INTRAHEPATIC OMOP:40493258 Intrahepatic CONJUNCTIVAL OMOP:40486444 Conjunctival INTRAEPICARDIAL OMOP:40487473 Intraepicardial DIGESTIVE TRACT OMOP:40487501 Digestive tract OCULAR OMOP:40549429 Ocular Slots Name Description route_concept Route of drug administration Comments OMOP contains 165 standard values; select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null; from SNOMED. Do we need descriptions beyond the name? Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: DrugRouteEnum description: Routes of drug administration. comments: - OMOP contains 165 standard values; `select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null;` from SNOMED. Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ARTERIOVENOUS FISTULA: text: ARTERIOVENOUS FISTULA description: Arteriovenous fistula meaning: OMOP:44783786 HAEMODIAFILTRATION: text: HAEMODIAFILTRATION description: Haemodiafiltration meaning: OMOP:44801748 SUBLESIONAL: text: SUBLESIONAL description: Sublesional meaning: OMOP:46270168 INTRANEURAL: text: INTRANEURAL description: Intraneural meaning: OMOP:46272911 INTRAMURAL: text: INTRAMURAL description: Intramural meaning: OMOP:46272926 INTRACATHETER INSTILLATION: text: INTRACATHETER INSTILLATION description: Intracatheter instillation meaning: OMOP:605428 SUBLABIAL: text: SUBLABIAL description: Sublabial meaning: OMOP:600817 INTRA-ARTICULAR: text: INTRA-ARTICULAR description: Intra-articular meaning: OMOP:4006860 INTRADIALYTIC: text: INTRADIALYTIC description: Intradialytic meaning: OMOP:618805 ARTERIOVENOUS GRAFT: text: ARTERIOVENOUS GRAFT description: Arteriovenous graft meaning: OMOP:762840 OTIC: text: OTIC description: Otic meaning: OMOP:4023156 ORAL: text: ORAL description: Oral meaning: OMOP:4132161 VAGINAL: text: VAGINAL description: Vaginal meaning: OMOP:4057765 ROUTE OF ADMINISTRATION VALUE: text: ROUTE OF ADMINISTRATION VALUE description: Route of administration value meaning: OMOP:4106215 GASTROSTOMY: text: GASTROSTOMY description: Gastrostomy meaning: OMOP:4132254 NASOGASTRIC: text: NASOGASTRIC description: Nasogastric meaning: OMOP:4132711 JEJUNOSTOMY: text: JEJUNOSTOMY description: Jejunostomy meaning: OMOP:4133177 SUBCUTANEOUS: text: SUBCUTANEOUS description: Subcutaneous meaning: OMOP:4142048 GINGIVAL: text: GINGIVAL description: Gingival meaning: OMOP:4156704 INTRACARDIAC: text: INTRACARDIAC description: Intracardiac meaning: OMOP:4156705 INTRADERMAL: text: INTRADERMAL description: Intradermal meaning: OMOP:4156706 INTRAPLEURAL: text: INTRAPLEURAL description: Intrapleural meaning: OMOP:4156707 PERIARTICULAR: text: PERIARTICULAR description: Periarticular meaning: OMOP:4156708 ENDOSINUSIAL: text: ENDOSINUSIAL description: Endosinusial meaning: OMOP:4157756 INTRACAVERNOUS: text: INTRACAVERNOUS description: Intracavernous meaning: OMOP:4157757 INTRALESIONAL: text: INTRALESIONAL description: Intralesional meaning: OMOP:4157758 INTRALYMPHATIC: text: INTRALYMPHATIC description: Intralymphatic meaning: OMOP:4157759 INTRAOCULAR: text: INTRAOCULAR description: Intraocular meaning: OMOP:4157760 PERINEURAL: text: PERINEURAL description: Perineural meaning: OMOP:4157761 INTRACRANIAL: text: INTRACRANIAL description: Intracranial meaning: OMOP:4171079 DENTAL: text: DENTAL description: Dental meaning: OMOP:4163765 INTRAAMNIOTIC: text: INTRAAMNIOTIC description: Intraamniotic meaning: OMOP:4163767 INTRABURSAL: text: INTRABURSAL description: Intrabursal meaning: OMOP:4163768 INTRADISCAL: text: INTRADISCAL description: Intradiscal meaning: OMOP:4163769 SUBCONJUNCTIVAL: text: SUBCONJUNCTIVAL description: Subconjunctival meaning: OMOP:4163770 MUCOUS FISTULA: text: MUCOUS FISTULA description: Mucous fistula meaning: OMOP:4171243 INTRAPROSTATIC: text: INTRAPROSTATIC description: Intraprostatic meaning: OMOP:4171725 INTRAVENOUS PERIPHERAL: text: INTRAVENOUS PERIPHERAL description: Intravenous peripheral meaning: OMOP:4171884 PERIOSTEAL: text: PERIOSTEAL description: Periosteal meaning: OMOP:4171893 ESOPHAGOSTOMY: text: ESOPHAGOSTOMY description: Esophagostomy meaning: OMOP:4172191 NASODUODENAL: text: NASODUODENAL description: Nasoduodenal meaning: OMOP:4172316 PERCUTANEOUS: text: PERCUTANEOUS description: Percutaneous meaning: OMOP:4177987 SUBORBITAL: text: SUBORBITAL description: Suborbital meaning: OMOP:4166865 INTRATHORACIC: text: INTRATHORACIC description: Intrathoracic meaning: OMOP:4167393 ENTERAL: text: ENTERAL description: Enteral meaning: OMOP:4167540 INTRAMYOMETRIAL: text: INTRAMYOMETRIAL description: Intramyometrial meaning: OMOP:4168038 COLOSTOMY: text: COLOSTOMY description: Colostomy meaning: OMOP:4168047 INTRATYMPANIC: text: INTRATYMPANIC description: Intratympanic meaning: OMOP:4168656 GASTRO-INTESTINAL STOMA: text: GASTRO-INTESTINAL STOMA description: Gastro-intestinal stoma meaning: OMOP:4168665 INTRAPULMONARY: text: INTRAPULMONARY description: Intrapulmonary meaning: OMOP:4169270 INTRASINAL: text: INTRASINAL description: Intrasinal meaning: OMOP:4169440 TUMOR CAVITY: text: TUMOR CAVITY description: Tumor cavity meaning: OMOP:4169472 SUBMUCOSAL: text: SUBMUCOSAL description: Submucosal meaning: OMOP:4169634 INTRADUCTAL: text: INTRADUCTAL description: Intraductal meaning: OMOP:4170083 INTRAVENOUS CENTRAL: text: INTRAVENOUS CENTRAL description: Intravenous central meaning: OMOP:4170113 PARAVERTEBRAL: text: PARAVERTEBRAL description: Paravertebral meaning: OMOP:4170267 UROSTOMY: text: UROSTOMY description: Urostomy meaning: OMOP:4170435 LARYNGEAL: text: LARYNGEAL description: Laryngeal meaning: OMOP:4170440 SURGICAL CAVITY: text: SURGICAL CAVITY description: Surgical cavity meaning: OMOP:4170771 INTRAVENOUS: text: INTRAVENOUS description: Intravenous meaning: OMOP:4171047 INTRATESTICULAR: text: INTRATESTICULAR description: Intratesticular meaning: OMOP:4171067 ENDOCERVICAL: text: ENDOCERVICAL description: Endocervical meaning: OMOP:4186831 ENDOTRACHEOPULMONARY: text: ENDOTRACHEOPULMONARY description: Endotracheopulmonary meaning: OMOP:4186832 EXTRA-AMNIOTIC: text: EXTRA-AMNIOTIC description: Extra-amniotic meaning: OMOP:4186833 GASTROENTERAL: text: GASTROENTERAL description: Gastroenteral meaning: OMOP:4186834 INTRACERVICAL: text: INTRACERVICAL description: Intracervical meaning: OMOP:4186835 INTRACORONARY: text: INTRACORONARY description: Intracoronary meaning: OMOP:4186836 INTRASTERNAL: text: INTRASTERNAL description: Intrasternal meaning: OMOP:4186837 INTRAVESICAL: text: INTRAVESICAL description: Intravesical meaning: OMOP:4186838 OROMUCOSAL: text: OROMUCOSAL description: Oromucosal meaning: OMOP:4186839 CAUDAL: text: CAUDAL description: Caudal meaning: OMOP:4220455 BUCCAL: text: BUCCAL description: Buccal meaning: OMOP:4181897 OPHTHALMIC: text: OPHTHALMIC description: Ophthalmic meaning: OMOP:4184451 BODY CAVITY: text: BODY CAVITY description: Body cavity meaning: OMOP:4222254 INTRAOSSEOUS: text: INTRAOSSEOUS description: Intraosseous meaning: OMOP:4213522 INTRAVENTRICULAR ROUTE - CARDIAC: text: INTRAVENTRICULAR ROUTE - CARDIAC description: Intraventricular route - cardiac meaning: OMOP:4222259 INTRABILIARY: text: INTRABILIARY description: Intrabiliary meaning: OMOP:4223965 INTRACEREBROVENTRICULAR: text: INTRACEREBROVENTRICULAR description: Intracerebroventricular meaning: OMOP:4224886 INTRATHECAL: text: INTRATHECAL description: Intrathecal meaning: OMOP:4217202 EPIDURAL: text: EPIDURAL description: Epidural meaning: OMOP:4225555 INTRATRACHEAL: text: INTRATRACHEAL description: Intratracheal meaning: OMOP:4229543 URETHRAL: text: URETHRAL description: Urethral meaning: OMOP:4233974 TRANSMUCOSAL: text: TRANSMUCOSAL description: Transmucosal meaning: OMOP:4232601 TRANSDERMAL: text: TRANSDERMAL description: Transdermal meaning: OMOP:4262099 INTRA-ARTERIAL: text: INTRA-ARTERIAL description: Intra-arterial meaning: OMOP:4240824 INTRAPERITONEAL: text: INTRAPERITONEAL description: Intraperitoneal meaning: OMOP:4243022 INTRAMEDULLARY: text: INTRAMEDULLARY description: Intramedullary meaning: OMOP:4246511 INTRAUTERINE: text: INTRAUTERINE description: Intrauterine meaning: OMOP:4269621 NASAL: text: NASAL description: Nasal meaning: OMOP:4262914 TOPICAL: text: TOPICAL description: Topical meaning: OMOP:4263689 RECTAL: text: RECTAL description: Rectal meaning: OMOP:4290759 SUBLINGUAL: text: SUBLINGUAL description: Sublingual meaning: OMOP:4292110 INTRALUMINAL: text: INTRALUMINAL description: Intraluminal meaning: OMOP:4292410 TRANSCERVICAL: text: TRANSCERVICAL description: Transcervical meaning: OMOP:4304730 INTRAABDOMINAL: text: INTRAABDOMINAL description: Intraabdominal meaning: OMOP:4304882 TRANSURETHRAL: text: TRANSURETHRAL description: Transurethral meaning: OMOP:4305382 PERITENDINOUS: text: PERITENDINOUS description: Peritendinous meaning: OMOP:4305564 ILEOSTOMY: text: ILEOSTOMY description: Ileostomy meaning: OMOP:4305679 INTRACORNEAL: text: INTRACORNEAL description: Intracorneal meaning: OMOP:4305690 NASOJEJUNAL: text: NASOJEJUNAL description: Nasojejunal meaning: OMOP:4305834 INTRACISTERNAL: text: INTRACISTERNAL description: Intracisternal meaning: OMOP:4305993 SUBGINGIVAL: text: SUBGINGIVAL description: Subgingival meaning: OMOP:4306649 INTRAOVARIAN: text: INTRAOVARIAN description: Intraovarian meaning: OMOP:4306657 INTERSTITIAL: text: INTERSTITIAL description: Interstitial meaning: OMOP:4327128 INTRASYNOVIAL: text: INTRASYNOVIAL description: Intrasynovial meaning: OMOP:4302352 INTRADUODENAL: text: INTRADUODENAL description: Intraduodenal meaning: OMOP:4302354 SUBTENDINOUS: text: SUBTENDINOUS description: Subtendinous meaning: OMOP:4302493 INTRAMUSCULAR: text: INTRAMUSCULAR description: Intramuscular meaning: OMOP:4302612 INTRAVITREAL: text: INTRAVITREAL description: Intravitreal meaning: OMOP:4302785 INTRASPINAL: text: INTRASPINAL description: Intraspinal meaning: OMOP:4302788 INTRABRONCHIAL: text: INTRABRONCHIAL description: Intrabronchial meaning: OMOP:4303263 OROPHARYNGEAL: text: OROPHARYNGEAL description: Oropharyngeal meaning: OMOP:4303277 INTRACAMERAL: text: INTRACAMERAL description: Intracameral meaning: OMOP:4303409 PARACERVICAL: text: PARACERVICAL description: Paracervical meaning: OMOP:4303515 PERIURETHRAL: text: PERIURETHRAL description: Periurethral meaning: OMOP:4303646 INTRACORONAL: text: INTRACORONAL description: Intracoronal meaning: OMOP:4303667 RETROBULBAR: text: RETROBULBAR description: Retrobulbar meaning: OMOP:4303673 INTRACARTILAGINOUS: text: INTRACARTILAGINOUS description: Intracartilaginous meaning: OMOP:4303676 OROGASTRIC: text: OROGASTRIC description: Orogastric meaning: OMOP:4303795 INTRATENDINOUS: text: INTRATENDINOUS description: Intratendinous meaning: OMOP:4303939 PERIBULBAR: text: PERIBULBAR description: Peribulbar meaning: OMOP:4304274 FISTULA: text: FISTULA description: Fistula meaning: OMOP:4304277 SURGICAL DRAIN: text: SURGICAL DRAIN description: Surgical drain meaning: OMOP:4304412 URETERAL: text: URETERAL description: Ureteral meaning: OMOP:4304571 EPILESIONAL: text: EPILESIONAL description: Epilesional meaning: OMOP:35608078 EXTRACORPOREAL HEMODIALYSIS: text: EXTRACORPOREAL HEMODIALYSIS description: Extracorporeal hemodialysis meaning: OMOP:35624178 SUPRACHOROIDAL: text: SUPRACHOROIDAL description: Suprachoroidal meaning: OMOP:37174548 EXTRACORPOREAL: text: EXTRACORPOREAL description: Extracorporeal meaning: OMOP:37018288 INTRACORPORUS CAVERNOSUM: text: INTRACORPORUS CAVERNOSUM description: Intracorporus cavernosum meaning: OMOP:37174549 INTRAGLANDULAR: text: INTRAGLANDULAR description: Intraglandular meaning: OMOP:37207460 INTRACHOLANGIOPANCREATIC: text: INTRACHOLANGIOPANCREATIC description: Intracholangiopancreatic meaning: OMOP:37207461 INTRAPORTAL: text: INTRAPORTAL description: Intraportal meaning: OMOP:37207462 PERITUMORAL: text: PERITUMORAL description: Peritumoral meaning: OMOP:37207463 POSTERIOR JUXTASCLERAL: text: POSTERIOR JUXTASCLERAL description: Posterior juxtascleral meaning: OMOP:37207464 SUBRETINAL: text: SUBRETINAL description: Subretinal meaning: OMOP:37207465 INFILTRATION: text: INFILTRATION description: Infiltration meaning: OMOP:37397638 TRANSENDOCARDIAL: text: TRANSENDOCARDIAL description: Transendocardial meaning: OMOP:40487850 TRANSPLACENTAL: text: TRANSPLACENTAL description: Transplacental meaning: OMOP:40487858 INTRAEPIDERMAL: text: INTRAEPIDERMAL description: Intraepidermal meaning: OMOP:40487983 INTRACEREBRAL: text: INTRACEREBRAL description: Intracerebral meaning: OMOP:40488317 INTRAJEJUNAL: text: INTRAJEJUNAL description: Intrajejunal meaning: OMOP:40489989 INTRACOLONIC: text: INTRACOLONIC description: Intracolonic meaning: OMOP:40489990 CUTANEOUS: text: CUTANEOUS description: Cutaneous meaning: OMOP:40490507 INTRAILEAL: text: INTRAILEAL description: Intraileal meaning: OMOP:40490837 PERIODONTAL: text: PERIODONTAL description: Periodontal meaning: OMOP:40490866 PERIDURAL: text: PERIDURAL description: Peridural meaning: OMOP:40490896 LOWER RESPIRATORY TRACT: text: LOWER RESPIRATORY TRACT description: Lower respiratory tract meaning: OMOP:40490898 INTRAMAMMARY: text: INTRAMAMMARY description: Intramammary meaning: OMOP:40491321 INTRATUMOR: text: INTRATUMOR description: Intratumor meaning: OMOP:40491322 TRANSTYMPANIC: text: TRANSTYMPANIC description: Transtympanic meaning: OMOP:40491830 TRANSTRACHEAL: text: TRANSTRACHEAL description: Transtracheal meaning: OMOP:40491832 INTRAESOPHAGEAL: text: INTRAESOPHAGEAL description: Intraesophageal meaning: OMOP:40492284 INTRAGINGIVAL: text: INTRAGINGIVAL description: Intragingival meaning: OMOP:40492286 INTRAVASCULAR: text: INTRAVASCULAR description: Intravascular meaning: OMOP:40492287 INTRADURAL: text: INTRADURAL description: Intradural meaning: OMOP:40492288 INTRAMENINGEAL: text: INTRAMENINGEAL description: Intrameningeal meaning: OMOP:40492300 INTRAGASTRIC: text: INTRAGASTRIC description: Intragastric meaning: OMOP:40492301 INTRAPERICARDIAL: text: INTRAPERICARDIAL description: Intrapericardial meaning: OMOP:40492305 INTRALINGUAL: text: INTRALINGUAL description: Intralingual meaning: OMOP:40493227 RESPIRATORY TRACT: text: RESPIRATORY TRACT description: Respiratory tract meaning: OMOP:40486069 INTRAHEPATIC: text: INTRAHEPATIC description: Intrahepatic meaning: OMOP:40493258 CONJUNCTIVAL: text: CONJUNCTIVAL description: Conjunctival meaning: OMOP:40486444 INTRAEPICARDIAL: text: INTRAEPICARDIAL description: Intraepicardial meaning: OMOP:40487473 DIGESTIVE TRACT: text: DIGESTIVE TRACT description: Digestive tract meaning: OMOP:40487501 OCULAR: text: OCULAR description: Ocular meaning: OMOP:40549429","title":"Enum: DrugRouteEnum"},{"location":"DrugRouteEnum/#enum-drugrouteenum","text":"Routes of drug administration. URI: DrugRouteEnum","title":"Enum: DrugRouteEnum"},{"location":"DrugRouteEnum/#permissible-values","text":"Value Meaning Description ARTERIOVENOUS FISTULA OMOP:44783786 Arteriovenous fistula HAEMODIAFILTRATION OMOP:44801748 Haemodiafiltration SUBLESIONAL OMOP:46270168 Sublesional INTRANEURAL OMOP:46272911 Intraneural INTRAMURAL OMOP:46272926 Intramural INTRACATHETER INSTILLATION OMOP:605428 Intracatheter instillation SUBLABIAL OMOP:600817 Sublabial INTRA-ARTICULAR OMOP:4006860 Intra-articular INTRADIALYTIC OMOP:618805 Intradialytic ARTERIOVENOUS GRAFT OMOP:762840 Arteriovenous graft OTIC OMOP:4023156 Otic ORAL OMOP:4132161 Oral VAGINAL OMOP:4057765 Vaginal ROUTE OF ADMINISTRATION VALUE OMOP:4106215 Route of administration value GASTROSTOMY OMOP:4132254 Gastrostomy NASOGASTRIC OMOP:4132711 Nasogastric JEJUNOSTOMY OMOP:4133177 Jejunostomy SUBCUTANEOUS OMOP:4142048 Subcutaneous GINGIVAL OMOP:4156704 Gingival INTRACARDIAC OMOP:4156705 Intracardiac INTRADERMAL OMOP:4156706 Intradermal INTRAPLEURAL OMOP:4156707 Intrapleural PERIARTICULAR OMOP:4156708 Periarticular ENDOSINUSIAL OMOP:4157756 Endosinusial INTRACAVERNOUS OMOP:4157757 Intracavernous INTRALESIONAL OMOP:4157758 Intralesional INTRALYMPHATIC OMOP:4157759 Intralymphatic INTRAOCULAR OMOP:4157760 Intraocular PERINEURAL OMOP:4157761 Perineural INTRACRANIAL OMOP:4171079 Intracranial DENTAL OMOP:4163765 Dental INTRAAMNIOTIC OMOP:4163767 Intraamniotic INTRABURSAL OMOP:4163768 Intrabursal INTRADISCAL OMOP:4163769 Intradiscal SUBCONJUNCTIVAL OMOP:4163770 Subconjunctival MUCOUS FISTULA OMOP:4171243 Mucous fistula INTRAPROSTATIC OMOP:4171725 Intraprostatic INTRAVENOUS PERIPHERAL OMOP:4171884 Intravenous peripheral PERIOSTEAL OMOP:4171893 Periosteal ESOPHAGOSTOMY OMOP:4172191 Esophagostomy NASODUODENAL OMOP:4172316 Nasoduodenal PERCUTANEOUS OMOP:4177987 Percutaneous SUBORBITAL OMOP:4166865 Suborbital INTRATHORACIC OMOP:4167393 Intrathoracic ENTERAL OMOP:4167540 Enteral INTRAMYOMETRIAL OMOP:4168038 Intramyometrial COLOSTOMY OMOP:4168047 Colostomy INTRATYMPANIC OMOP:4168656 Intratympanic GASTRO-INTESTINAL STOMA OMOP:4168665 Gastro-intestinal stoma INTRAPULMONARY OMOP:4169270 Intrapulmonary INTRASINAL OMOP:4169440 Intrasinal TUMOR CAVITY OMOP:4169472 Tumor cavity SUBMUCOSAL OMOP:4169634 Submucosal INTRADUCTAL OMOP:4170083 Intraductal INTRAVENOUS CENTRAL OMOP:4170113 Intravenous central PARAVERTEBRAL OMOP:4170267 Paravertebral UROSTOMY OMOP:4170435 Urostomy LARYNGEAL OMOP:4170440 Laryngeal SURGICAL CAVITY OMOP:4170771 Surgical cavity INTRAVENOUS OMOP:4171047 Intravenous INTRATESTICULAR OMOP:4171067 Intratesticular ENDOCERVICAL OMOP:4186831 Endocervical ENDOTRACHEOPULMONARY OMOP:4186832 Endotracheopulmonary EXTRA-AMNIOTIC OMOP:4186833 Extra-amniotic GASTROENTERAL OMOP:4186834 Gastroenteral INTRACERVICAL OMOP:4186835 Intracervical INTRACORONARY OMOP:4186836 Intracoronary INTRASTERNAL OMOP:4186837 Intrasternal INTRAVESICAL OMOP:4186838 Intravesical OROMUCOSAL OMOP:4186839 Oromucosal CAUDAL OMOP:4220455 Caudal BUCCAL OMOP:4181897 Buccal OPHTHALMIC OMOP:4184451 Ophthalmic BODY CAVITY OMOP:4222254 Body cavity INTRAOSSEOUS OMOP:4213522 Intraosseous INTRAVENTRICULAR ROUTE - CARDIAC OMOP:4222259 Intraventricular route - cardiac INTRABILIARY OMOP:4223965 Intrabiliary INTRACEREBROVENTRICULAR OMOP:4224886 Intracerebroventricular INTRATHECAL OMOP:4217202 Intrathecal EPIDURAL OMOP:4225555 Epidural INTRATRACHEAL OMOP:4229543 Intratracheal URETHRAL OMOP:4233974 Urethral TRANSMUCOSAL OMOP:4232601 Transmucosal TRANSDERMAL OMOP:4262099 Transdermal INTRA-ARTERIAL OMOP:4240824 Intra-arterial INTRAPERITONEAL OMOP:4243022 Intraperitoneal INTRAMEDULLARY OMOP:4246511 Intramedullary INTRAUTERINE OMOP:4269621 Intrauterine NASAL OMOP:4262914 Nasal TOPICAL OMOP:4263689 Topical RECTAL OMOP:4290759 Rectal SUBLINGUAL OMOP:4292110 Sublingual INTRALUMINAL OMOP:4292410 Intraluminal TRANSCERVICAL OMOP:4304730 Transcervical INTRAABDOMINAL OMOP:4304882 Intraabdominal TRANSURETHRAL OMOP:4305382 Transurethral PERITENDINOUS OMOP:4305564 Peritendinous ILEOSTOMY OMOP:4305679 Ileostomy INTRACORNEAL OMOP:4305690 Intracorneal NASOJEJUNAL OMOP:4305834 Nasojejunal INTRACISTERNAL OMOP:4305993 Intracisternal SUBGINGIVAL OMOP:4306649 Subgingival INTRAOVARIAN OMOP:4306657 Intraovarian INTERSTITIAL OMOP:4327128 Interstitial INTRASYNOVIAL OMOP:4302352 Intrasynovial INTRADUODENAL OMOP:4302354 Intraduodenal SUBTENDINOUS OMOP:4302493 Subtendinous INTRAMUSCULAR OMOP:4302612 Intramuscular INTRAVITREAL OMOP:4302785 Intravitreal INTRASPINAL OMOP:4302788 Intraspinal INTRABRONCHIAL OMOP:4303263 Intrabronchial OROPHARYNGEAL OMOP:4303277 Oropharyngeal INTRACAMERAL OMOP:4303409 Intracameral PARACERVICAL OMOP:4303515 Paracervical PERIURETHRAL OMOP:4303646 Periurethral INTRACORONAL OMOP:4303667 Intracoronal RETROBULBAR OMOP:4303673 Retrobulbar INTRACARTILAGINOUS OMOP:4303676 Intracartilaginous OROGASTRIC OMOP:4303795 Orogastric INTRATENDINOUS OMOP:4303939 Intratendinous PERIBULBAR OMOP:4304274 Peribulbar FISTULA OMOP:4304277 Fistula SURGICAL DRAIN OMOP:4304412 Surgical drain URETERAL OMOP:4304571 Ureteral EPILESIONAL OMOP:35608078 Epilesional EXTRACORPOREAL HEMODIALYSIS OMOP:35624178 Extracorporeal hemodialysis SUPRACHOROIDAL OMOP:37174548 Suprachoroidal EXTRACORPOREAL OMOP:37018288 Extracorporeal INTRACORPORUS CAVERNOSUM OMOP:37174549 Intracorporus cavernosum INTRAGLANDULAR OMOP:37207460 Intraglandular INTRACHOLANGIOPANCREATIC OMOP:37207461 Intracholangiopancreatic INTRAPORTAL OMOP:37207462 Intraportal PERITUMORAL OMOP:37207463 Peritumoral POSTERIOR JUXTASCLERAL OMOP:37207464 Posterior juxtascleral SUBRETINAL OMOP:37207465 Subretinal INFILTRATION OMOP:37397638 Infiltration TRANSENDOCARDIAL OMOP:40487850 Transendocardial TRANSPLACENTAL OMOP:40487858 Transplacental INTRAEPIDERMAL OMOP:40487983 Intraepidermal INTRACEREBRAL OMOP:40488317 Intracerebral INTRAJEJUNAL OMOP:40489989 Intrajejunal INTRACOLONIC OMOP:40489990 Intracolonic CUTANEOUS OMOP:40490507 Cutaneous INTRAILEAL OMOP:40490837 Intraileal PERIODONTAL OMOP:40490866 Periodontal PERIDURAL OMOP:40490896 Peridural LOWER RESPIRATORY TRACT OMOP:40490898 Lower respiratory tract INTRAMAMMARY OMOP:40491321 Intramammary INTRATUMOR OMOP:40491322 Intratumor TRANSTYMPANIC OMOP:40491830 Transtympanic TRANSTRACHEAL OMOP:40491832 Transtracheal INTRAESOPHAGEAL OMOP:40492284 Intraesophageal INTRAGINGIVAL OMOP:40492286 Intragingival INTRAVASCULAR OMOP:40492287 Intravascular INTRADURAL OMOP:40492288 Intradural INTRAMENINGEAL OMOP:40492300 Intrameningeal INTRAGASTRIC OMOP:40492301 Intragastric INTRAPERICARDIAL OMOP:40492305 Intrapericardial INTRALINGUAL OMOP:40493227 Intralingual RESPIRATORY TRACT OMOP:40486069 Respiratory tract INTRAHEPATIC OMOP:40493258 Intrahepatic CONJUNCTIVAL OMOP:40486444 Conjunctival INTRAEPICARDIAL OMOP:40487473 Intraepicardial DIGESTIVE TRACT OMOP:40487501 Digestive tract OCULAR OMOP:40549429 Ocular","title":"Permissible Values"},{"location":"DrugRouteEnum/#slots","text":"Name Description route_concept Route of drug administration","title":"Slots"},{"location":"DrugRouteEnum/#comments","text":"OMOP contains 165 standard values; select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null; from SNOMED. Do we need descriptions beyond the name?","title":"Comments"},{"location":"DrugRouteEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"DrugRouteEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"DrugRouteEnum/#linkml-source","text":"name: DrugRouteEnum description: Routes of drug administration. comments: - OMOP contains 165 standard values; `select * from concept where domain_id = 'Route' and invalid_reason is null and standard_concept is not null;` from SNOMED. Do we need descriptions beyond the name? from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ARTERIOVENOUS FISTULA: text: ARTERIOVENOUS FISTULA description: Arteriovenous fistula meaning: OMOP:44783786 HAEMODIAFILTRATION: text: HAEMODIAFILTRATION description: Haemodiafiltration meaning: OMOP:44801748 SUBLESIONAL: text: SUBLESIONAL description: Sublesional meaning: OMOP:46270168 INTRANEURAL: text: INTRANEURAL description: Intraneural meaning: OMOP:46272911 INTRAMURAL: text: INTRAMURAL description: Intramural meaning: OMOP:46272926 INTRACATHETER INSTILLATION: text: INTRACATHETER INSTILLATION description: Intracatheter instillation meaning: OMOP:605428 SUBLABIAL: text: SUBLABIAL description: Sublabial meaning: OMOP:600817 INTRA-ARTICULAR: text: INTRA-ARTICULAR description: Intra-articular meaning: OMOP:4006860 INTRADIALYTIC: text: INTRADIALYTIC description: Intradialytic meaning: OMOP:618805 ARTERIOVENOUS GRAFT: text: ARTERIOVENOUS GRAFT description: Arteriovenous graft meaning: OMOP:762840 OTIC: text: OTIC description: Otic meaning: OMOP:4023156 ORAL: text: ORAL description: Oral meaning: OMOP:4132161 VAGINAL: text: VAGINAL description: Vaginal meaning: OMOP:4057765 ROUTE OF ADMINISTRATION VALUE: text: ROUTE OF ADMINISTRATION VALUE description: Route of administration value meaning: OMOP:4106215 GASTROSTOMY: text: GASTROSTOMY description: Gastrostomy meaning: OMOP:4132254 NASOGASTRIC: text: NASOGASTRIC description: Nasogastric meaning: OMOP:4132711 JEJUNOSTOMY: text: JEJUNOSTOMY description: Jejunostomy meaning: OMOP:4133177 SUBCUTANEOUS: text: SUBCUTANEOUS description: Subcutaneous meaning: OMOP:4142048 GINGIVAL: text: GINGIVAL description: Gingival meaning: OMOP:4156704 INTRACARDIAC: text: INTRACARDIAC description: Intracardiac meaning: OMOP:4156705 INTRADERMAL: text: INTRADERMAL description: Intradermal meaning: OMOP:4156706 INTRAPLEURAL: text: INTRAPLEURAL description: Intrapleural meaning: OMOP:4156707 PERIARTICULAR: text: PERIARTICULAR description: Periarticular meaning: OMOP:4156708 ENDOSINUSIAL: text: ENDOSINUSIAL description: Endosinusial meaning: OMOP:4157756 INTRACAVERNOUS: text: INTRACAVERNOUS description: Intracavernous meaning: OMOP:4157757 INTRALESIONAL: text: INTRALESIONAL description: Intralesional meaning: OMOP:4157758 INTRALYMPHATIC: text: INTRALYMPHATIC description: Intralymphatic meaning: OMOP:4157759 INTRAOCULAR: text: INTRAOCULAR description: Intraocular meaning: OMOP:4157760 PERINEURAL: text: PERINEURAL description: Perineural meaning: OMOP:4157761 INTRACRANIAL: text: INTRACRANIAL description: Intracranial meaning: OMOP:4171079 DENTAL: text: DENTAL description: Dental meaning: OMOP:4163765 INTRAAMNIOTIC: text: INTRAAMNIOTIC description: Intraamniotic meaning: OMOP:4163767 INTRABURSAL: text: INTRABURSAL description: Intrabursal meaning: OMOP:4163768 INTRADISCAL: text: INTRADISCAL description: Intradiscal meaning: OMOP:4163769 SUBCONJUNCTIVAL: text: SUBCONJUNCTIVAL description: Subconjunctival meaning: OMOP:4163770 MUCOUS FISTULA: text: MUCOUS FISTULA description: Mucous fistula meaning: OMOP:4171243 INTRAPROSTATIC: text: INTRAPROSTATIC description: Intraprostatic meaning: OMOP:4171725 INTRAVENOUS PERIPHERAL: text: INTRAVENOUS PERIPHERAL description: Intravenous peripheral meaning: OMOP:4171884 PERIOSTEAL: text: PERIOSTEAL description: Periosteal meaning: OMOP:4171893 ESOPHAGOSTOMY: text: ESOPHAGOSTOMY description: Esophagostomy meaning: OMOP:4172191 NASODUODENAL: text: NASODUODENAL description: Nasoduodenal meaning: OMOP:4172316 PERCUTANEOUS: text: PERCUTANEOUS description: Percutaneous meaning: OMOP:4177987 SUBORBITAL: text: SUBORBITAL description: Suborbital meaning: OMOP:4166865 INTRATHORACIC: text: INTRATHORACIC description: Intrathoracic meaning: OMOP:4167393 ENTERAL: text: ENTERAL description: Enteral meaning: OMOP:4167540 INTRAMYOMETRIAL: text: INTRAMYOMETRIAL description: Intramyometrial meaning: OMOP:4168038 COLOSTOMY: text: COLOSTOMY description: Colostomy meaning: OMOP:4168047 INTRATYMPANIC: text: INTRATYMPANIC description: Intratympanic meaning: OMOP:4168656 GASTRO-INTESTINAL STOMA: text: GASTRO-INTESTINAL STOMA description: Gastro-intestinal stoma meaning: OMOP:4168665 INTRAPULMONARY: text: INTRAPULMONARY description: Intrapulmonary meaning: OMOP:4169270 INTRASINAL: text: INTRASINAL description: Intrasinal meaning: OMOP:4169440 TUMOR CAVITY: text: TUMOR CAVITY description: Tumor cavity meaning: OMOP:4169472 SUBMUCOSAL: text: SUBMUCOSAL description: Submucosal meaning: OMOP:4169634 INTRADUCTAL: text: INTRADUCTAL description: Intraductal meaning: OMOP:4170083 INTRAVENOUS CENTRAL: text: INTRAVENOUS CENTRAL description: Intravenous central meaning: OMOP:4170113 PARAVERTEBRAL: text: PARAVERTEBRAL description: Paravertebral meaning: OMOP:4170267 UROSTOMY: text: UROSTOMY description: Urostomy meaning: OMOP:4170435 LARYNGEAL: text: LARYNGEAL description: Laryngeal meaning: OMOP:4170440 SURGICAL CAVITY: text: SURGICAL CAVITY description: Surgical cavity meaning: OMOP:4170771 INTRAVENOUS: text: INTRAVENOUS description: Intravenous meaning: OMOP:4171047 INTRATESTICULAR: text: INTRATESTICULAR description: Intratesticular meaning: OMOP:4171067 ENDOCERVICAL: text: ENDOCERVICAL description: Endocervical meaning: OMOP:4186831 ENDOTRACHEOPULMONARY: text: ENDOTRACHEOPULMONARY description: Endotracheopulmonary meaning: OMOP:4186832 EXTRA-AMNIOTIC: text: EXTRA-AMNIOTIC description: Extra-amniotic meaning: OMOP:4186833 GASTROENTERAL: text: GASTROENTERAL description: Gastroenteral meaning: OMOP:4186834 INTRACERVICAL: text: INTRACERVICAL description: Intracervical meaning: OMOP:4186835 INTRACORONARY: text: INTRACORONARY description: Intracoronary meaning: OMOP:4186836 INTRASTERNAL: text: INTRASTERNAL description: Intrasternal meaning: OMOP:4186837 INTRAVESICAL: text: INTRAVESICAL description: Intravesical meaning: OMOP:4186838 OROMUCOSAL: text: OROMUCOSAL description: Oromucosal meaning: OMOP:4186839 CAUDAL: text: CAUDAL description: Caudal meaning: OMOP:4220455 BUCCAL: text: BUCCAL description: Buccal meaning: OMOP:4181897 OPHTHALMIC: text: OPHTHALMIC description: Ophthalmic meaning: OMOP:4184451 BODY CAVITY: text: BODY CAVITY description: Body cavity meaning: OMOP:4222254 INTRAOSSEOUS: text: INTRAOSSEOUS description: Intraosseous meaning: OMOP:4213522 INTRAVENTRICULAR ROUTE - CARDIAC: text: INTRAVENTRICULAR ROUTE - CARDIAC description: Intraventricular route - cardiac meaning: OMOP:4222259 INTRABILIARY: text: INTRABILIARY description: Intrabiliary meaning: OMOP:4223965 INTRACEREBROVENTRICULAR: text: INTRACEREBROVENTRICULAR description: Intracerebroventricular meaning: OMOP:4224886 INTRATHECAL: text: INTRATHECAL description: Intrathecal meaning: OMOP:4217202 EPIDURAL: text: EPIDURAL description: Epidural meaning: OMOP:4225555 INTRATRACHEAL: text: INTRATRACHEAL description: Intratracheal meaning: OMOP:4229543 URETHRAL: text: URETHRAL description: Urethral meaning: OMOP:4233974 TRANSMUCOSAL: text: TRANSMUCOSAL description: Transmucosal meaning: OMOP:4232601 TRANSDERMAL: text: TRANSDERMAL description: Transdermal meaning: OMOP:4262099 INTRA-ARTERIAL: text: INTRA-ARTERIAL description: Intra-arterial meaning: OMOP:4240824 INTRAPERITONEAL: text: INTRAPERITONEAL description: Intraperitoneal meaning: OMOP:4243022 INTRAMEDULLARY: text: INTRAMEDULLARY description: Intramedullary meaning: OMOP:4246511 INTRAUTERINE: text: INTRAUTERINE description: Intrauterine meaning: OMOP:4269621 NASAL: text: NASAL description: Nasal meaning: OMOP:4262914 TOPICAL: text: TOPICAL description: Topical meaning: OMOP:4263689 RECTAL: text: RECTAL description: Rectal meaning: OMOP:4290759 SUBLINGUAL: text: SUBLINGUAL description: Sublingual meaning: OMOP:4292110 INTRALUMINAL: text: INTRALUMINAL description: Intraluminal meaning: OMOP:4292410 TRANSCERVICAL: text: TRANSCERVICAL description: Transcervical meaning: OMOP:4304730 INTRAABDOMINAL: text: INTRAABDOMINAL description: Intraabdominal meaning: OMOP:4304882 TRANSURETHRAL: text: TRANSURETHRAL description: Transurethral meaning: OMOP:4305382 PERITENDINOUS: text: PERITENDINOUS description: Peritendinous meaning: OMOP:4305564 ILEOSTOMY: text: ILEOSTOMY description: Ileostomy meaning: OMOP:4305679 INTRACORNEAL: text: INTRACORNEAL description: Intracorneal meaning: OMOP:4305690 NASOJEJUNAL: text: NASOJEJUNAL description: Nasojejunal meaning: OMOP:4305834 INTRACISTERNAL: text: INTRACISTERNAL description: Intracisternal meaning: OMOP:4305993 SUBGINGIVAL: text: SUBGINGIVAL description: Subgingival meaning: OMOP:4306649 INTRAOVARIAN: text: INTRAOVARIAN description: Intraovarian meaning: OMOP:4306657 INTERSTITIAL: text: INTERSTITIAL description: Interstitial meaning: OMOP:4327128 INTRASYNOVIAL: text: INTRASYNOVIAL description: Intrasynovial meaning: OMOP:4302352 INTRADUODENAL: text: INTRADUODENAL description: Intraduodenal meaning: OMOP:4302354 SUBTENDINOUS: text: SUBTENDINOUS description: Subtendinous meaning: OMOP:4302493 INTRAMUSCULAR: text: INTRAMUSCULAR description: Intramuscular meaning: OMOP:4302612 INTRAVITREAL: text: INTRAVITREAL description: Intravitreal meaning: OMOP:4302785 INTRASPINAL: text: INTRASPINAL description: Intraspinal meaning: OMOP:4302788 INTRABRONCHIAL: text: INTRABRONCHIAL description: Intrabronchial meaning: OMOP:4303263 OROPHARYNGEAL: text: OROPHARYNGEAL description: Oropharyngeal meaning: OMOP:4303277 INTRACAMERAL: text: INTRACAMERAL description: Intracameral meaning: OMOP:4303409 PARACERVICAL: text: PARACERVICAL description: Paracervical meaning: OMOP:4303515 PERIURETHRAL: text: PERIURETHRAL description: Periurethral meaning: OMOP:4303646 INTRACORONAL: text: INTRACORONAL description: Intracoronal meaning: OMOP:4303667 RETROBULBAR: text: RETROBULBAR description: Retrobulbar meaning: OMOP:4303673 INTRACARTILAGINOUS: text: INTRACARTILAGINOUS description: Intracartilaginous meaning: OMOP:4303676 OROGASTRIC: text: OROGASTRIC description: Orogastric meaning: OMOP:4303795 INTRATENDINOUS: text: INTRATENDINOUS description: Intratendinous meaning: OMOP:4303939 PERIBULBAR: text: PERIBULBAR description: Peribulbar meaning: OMOP:4304274 FISTULA: text: FISTULA description: Fistula meaning: OMOP:4304277 SURGICAL DRAIN: text: SURGICAL DRAIN description: Surgical drain meaning: OMOP:4304412 URETERAL: text: URETERAL description: Ureteral meaning: OMOP:4304571 EPILESIONAL: text: EPILESIONAL description: Epilesional meaning: OMOP:35608078 EXTRACORPOREAL HEMODIALYSIS: text: EXTRACORPOREAL HEMODIALYSIS description: Extracorporeal hemodialysis meaning: OMOP:35624178 SUPRACHOROIDAL: text: SUPRACHOROIDAL description: Suprachoroidal meaning: OMOP:37174548 EXTRACORPOREAL: text: EXTRACORPOREAL description: Extracorporeal meaning: OMOP:37018288 INTRACORPORUS CAVERNOSUM: text: INTRACORPORUS CAVERNOSUM description: Intracorporus cavernosum meaning: OMOP:37174549 INTRAGLANDULAR: text: INTRAGLANDULAR description: Intraglandular meaning: OMOP:37207460 INTRACHOLANGIOPANCREATIC: text: INTRACHOLANGIOPANCREATIC description: Intracholangiopancreatic meaning: OMOP:37207461 INTRAPORTAL: text: INTRAPORTAL description: Intraportal meaning: OMOP:37207462 PERITUMORAL: text: PERITUMORAL description: Peritumoral meaning: OMOP:37207463 POSTERIOR JUXTASCLERAL: text: POSTERIOR JUXTASCLERAL description: Posterior juxtascleral meaning: OMOP:37207464 SUBRETINAL: text: SUBRETINAL description: Subretinal meaning: OMOP:37207465 INFILTRATION: text: INFILTRATION description: Infiltration meaning: OMOP:37397638 TRANSENDOCARDIAL: text: TRANSENDOCARDIAL description: Transendocardial meaning: OMOP:40487850 TRANSPLACENTAL: text: TRANSPLACENTAL description: Transplacental meaning: OMOP:40487858 INTRAEPIDERMAL: text: INTRAEPIDERMAL description: Intraepidermal meaning: OMOP:40487983 INTRACEREBRAL: text: INTRACEREBRAL description: Intracerebral meaning: OMOP:40488317 INTRAJEJUNAL: text: INTRAJEJUNAL description: Intrajejunal meaning: OMOP:40489989 INTRACOLONIC: text: INTRACOLONIC description: Intracolonic meaning: OMOP:40489990 CUTANEOUS: text: CUTANEOUS description: Cutaneous meaning: OMOP:40490507 INTRAILEAL: text: INTRAILEAL description: Intraileal meaning: OMOP:40490837 PERIODONTAL: text: PERIODONTAL description: Periodontal meaning: OMOP:40490866 PERIDURAL: text: PERIDURAL description: Peridural meaning: OMOP:40490896 LOWER RESPIRATORY TRACT: text: LOWER RESPIRATORY TRACT description: Lower respiratory tract meaning: OMOP:40490898 INTRAMAMMARY: text: INTRAMAMMARY description: Intramammary meaning: OMOP:40491321 INTRATUMOR: text: INTRATUMOR description: Intratumor meaning: OMOP:40491322 TRANSTYMPANIC: text: TRANSTYMPANIC description: Transtympanic meaning: OMOP:40491830 TRANSTRACHEAL: text: TRANSTRACHEAL description: Transtracheal meaning: OMOP:40491832 INTRAESOPHAGEAL: text: INTRAESOPHAGEAL description: Intraesophageal meaning: OMOP:40492284 INTRAGINGIVAL: text: INTRAGINGIVAL description: Intragingival meaning: OMOP:40492286 INTRAVASCULAR: text: INTRAVASCULAR description: Intravascular meaning: OMOP:40492287 INTRADURAL: text: INTRADURAL description: Intradural meaning: OMOP:40492288 INTRAMENINGEAL: text: INTRAMENINGEAL description: Intrameningeal meaning: OMOP:40492300 INTRAGASTRIC: text: INTRAGASTRIC description: Intragastric meaning: OMOP:40492301 INTRAPERICARDIAL: text: INTRAPERICARDIAL description: Intrapericardial meaning: OMOP:40492305 INTRALINGUAL: text: INTRALINGUAL description: Intralingual meaning: OMOP:40493227 RESPIRATORY TRACT: text: RESPIRATORY TRACT description: Respiratory tract meaning: OMOP:40486069 INTRAHEPATIC: text: INTRAHEPATIC description: Intrahepatic meaning: OMOP:40493258 CONJUNCTIVAL: text: CONJUNCTIVAL description: Conjunctival meaning: OMOP:40486444 INTRAEPICARDIAL: text: INTRAEPICARDIAL description: Intraepicardial meaning: OMOP:40487473 DIGESTIVE TRACT: text: DIGESTIVE TRACT description: Digestive tract meaning: OMOP:40487501 OCULAR: text: OCULAR description: Ocular meaning: OMOP:40549429","title":"LinkML Source"},{"location":"Entity/","text":"Class: Entity Any resource that has its own identifier NOTE : this is an abstract class and should not be instantiated directly URI: schema:Thing classDiagram class Entity Entity <|-- Person Entity <|-- Demography Entity <|-- Participant Entity <|-- ResearchStudy Entity <|-- Consent Entity <|-- Visit Entity <|-- Organization Entity <|-- TimePoint Entity <|-- Questionnaire Entity <|-- QuestionnaireItem Entity <|-- QuestionnaireResponse Entity <|-- Condition Entity <|-- Procedure Entity <|-- DrugExposure Entity <|-- DeviceExposure Entity <|-- File Entity <|-- Document Entity <|-- Specimen Entity <|-- SpecimenContainer Entity <|-- SpecimenCreationActivity Entity <|-- SpecimenProcessingActivity Entity <|-- SpecimenStorageActivity Entity <|-- SpecimenTransportActivity Entity <|-- BiologicProduct Entity <|-- Substance Entity <|-- Quantity Entity <|-- BodySite Entity <|-- ObservationSet Entity <|-- Observation Entity : id 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The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Entity domain_of: - Entity range: uriorcurie class_uri: schema:Thing","title":"Class: Entity"},{"location":"Entity/#class-entity","text":"Any resource that has its own identifier NOTE : this is an abstract class and should not be instantiated directly URI: schema:Thing classDiagram class Entity Entity <|-- Person Entity <|-- Demography Entity <|-- Participant Entity <|-- ResearchStudy Entity <|-- Consent Entity <|-- Visit Entity <|-- Organization Entity <|-- TimePoint Entity <|-- Questionnaire Entity <|-- QuestionnaireItem Entity <|-- QuestionnaireResponse Entity <|-- Condition Entity <|-- Procedure Entity <|-- DrugExposure Entity <|-- DeviceExposure Entity <|-- File Entity <|-- Document Entity <|-- Specimen Entity <|-- SpecimenContainer Entity <|-- SpecimenCreationActivity Entity <|-- SpecimenProcessingActivity Entity <|-- SpecimenStorageActivity Entity <|-- SpecimenTransportActivity Entity <|-- BiologicProduct Entity <|-- Substance Entity <|-- Quantity Entity <|-- BodySite Entity <|-- ObservationSet Entity <|-- Observation Entity : id","title":"Class: Entity"},{"location":"Entity/#inheritance","text":"Entity Person Demography Participant ResearchStudy Consent Visit Organization TimePoint Questionnaire QuestionnaireItem QuestionnaireResponse Condition Procedure DrugExposure DeviceExposure File Document Specimen SpecimenContainer SpecimenCreationActivity SpecimenProcessingActivity SpecimenStorageActivity SpecimenTransportActivity BiologicProduct Substance Quantity BodySite ObservationSet Observation","title":"Inheritance"},{"location":"Entity/#slots","text":"Name Cardinality and Range Description Inheritance id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record direct","title":"Slots"},{"location":"Entity/#usages","text":"used by used in type used DimensionalObservation focus range Entity DimensionalObservationSet focus range Entity Document focus range Entity SpecimenQualityObservation focus range Entity SpecimenQuantityObservation focus range Entity ObservationSet focus range Entity Observation focus range Entity","title":"Usages"},{"location":"Entity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Entity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Entity/#mappings","text":"Mapping Type Mapped Value self schema:Thing native bdchm:Entity","title":"Mappings"},{"location":"Entity/#linkml-source","text":"","title":"LinkML Source"},{"location":"Entity/#direct","text":"name: Entity description: Any resource that has its own identifier from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - id class_uri: schema:Thing","title":"Direct"},{"location":"Entity/#induced","text":"name: Entity description: Any resource that has its own identifier from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Entity domain_of: - Entity range: uriorcurie class_uri: schema:Thing","title":"Induced"},{"location":"EthnicityEnum/","text":"Enum: EthnicityEnum A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for ethnicity. URI: EthnicityEnum Permissible Values Value Meaning Description HISPANIC_OR_LATINO OMOP:38003563 A person of Cuban, Mexican, Puerto Rican, South or Central American, or other... NOT_HISPANIC_OR_LATINO OMOP:38003564 A person not of Cuban, Mexican, Puerto Rican, South or Central American, or o... Slots Name Description ethnicity An individual's self-described social and cultural grouping, specifically whe... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: EthnicityEnum description: A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for ethnicity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: HISPANIC_OR_LATINO: text: HISPANIC_OR_LATINO description: A person of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. The term, \"Spanish origin\" can be used in addition to \"Hispanic or Latino\". (OMB) meaning: OMOP:38003563 NOT_HISPANIC_OR_LATINO: text: NOT_HISPANIC_OR_LATINO description: A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. meaning: OMOP:38003564","title":"Enum: EthnicityEnum"},{"location":"EthnicityEnum/#enum-ethnicityenum","text":"A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for ethnicity. URI: EthnicityEnum","title":"Enum: EthnicityEnum"},{"location":"EthnicityEnum/#permissible-values","text":"Value Meaning Description HISPANIC_OR_LATINO OMOP:38003563 A person of Cuban, Mexican, Puerto Rican, South or Central American, or other... 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The term, \"Spanish origin\" can be used in addition to \"Hispanic or Latino\". (OMB) meaning: OMOP:38003563 NOT_HISPANIC_OR_LATINO: text: NOT_HISPANIC_OR_LATINO description: A person not of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. meaning: OMOP:38003564","title":"LinkML Source"},{"location":"File/","text":"Class: File Abstract class for various kinds of files. Subclasses may be defined for specific file types. URI: bdchm:File classDiagram class File Entity <|-- File File : associated_participant File --> Participant : associated_participant File : data_category File : data_type File : derived_from File --> File : derived_from File : description File : file_location File : file_name File : file_size File : format File : id File : identity File : md5sum Inheritance Entity File Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct file_name 0..1 String The name (or part of a name) of a file (of any type) direct file_size 0..1 Integer The size of the data file (object) in bytes direct file_location 0..* Uriorcurie A unique identifier or url for identifying or locating the file direct md5sum 0..1 String The 128-bit hash value expressed as a 32 digit hexadecimal number used as a f... direct data_type 0..1 String The nature or genre of the resource direct data_category 0..1 String A broad categorization of the contents of the data file direct format 0..1 String The file format, physical medium, or dimensions of the resource direct description 0..1 String An account of the resource direct associated_participant 0..1 Participant A reference to the Participant to which this file relates direct derived_from 0..1 File A File from which this File is derived direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used File derived_from range File Comments This is taken largely from the Gen3 Core Metadata Collection definition. Gen3 apparently took most of the attributes listed here from the Dublin Core /elements/1.1/ namespace . Attributes different from those in Dublin Core are noted as such in the comments. The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? Tentatively including three attribute for addressing this -- identifier, file_path, and uri. There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:File native bdchm:File LinkML Source Direct name: File description: Abstract class for various kinds of files. Subclasses may be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer file_location: name: file_location description: A unique identifier or url for identifying or locating the file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: uriorcurie md5sum: name: md5sum description: The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant derived_from: name: derived_from description: A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: File Induced name: File description: Abstract class for various kinds of files. Subclasses may be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer file_location: name: file_location description: A unique identifier or url for identifying or locating the file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: file_location owner: File domain_of: - File range: uriorcurie md5sum: name: md5sum description: The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: md5sum owner: File domain_of: - File range: string data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: File domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: File domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant derived_from: name: derived_from description: A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: derived_from owner: File domain_of: - File range: File identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: File domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: File domain_of: - Entity range: uriorcurie required: true","title":"Class: File"},{"location":"File/#class-file","text":"Abstract class for various kinds of files. Subclasses may be defined for specific file types. URI: bdchm:File classDiagram class File Entity <|-- File File : associated_participant File --> Participant : associated_participant File : data_category File : data_type File : derived_from File --> File : derived_from File : description File : file_location File : file_name File : file_size File : format File : id File : identity File : md5sum","title":"Class: File"},{"location":"File/#inheritance","text":"Entity File","title":"Inheritance"},{"location":"File/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct file_name 0..1 String The name (or part of a name) of a file (of any type) direct file_size 0..1 Integer The size of the data file (object) in bytes direct file_location 0..* Uriorcurie A unique identifier or url for identifying or locating the file direct md5sum 0..1 String The 128-bit hash value expressed as a 32 digit hexadecimal number used as a f... direct data_type 0..1 String The nature or genre of the resource direct data_category 0..1 String A broad categorization of the contents of the data file direct format 0..1 String The file format, physical medium, or dimensions of the resource direct description 0..1 String An account of the resource direct associated_participant 0..1 Participant A reference to the Participant to which this file relates direct derived_from 0..1 File A File from which this File is derived direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"File/#usages","text":"used by used in type used File derived_from range File","title":"Usages"},{"location":"File/#comments","text":"This is taken largely from the Gen3 Core Metadata Collection definition. Gen3 apparently took most of the attributes listed here from the Dublin Core /elements/1.1/ namespace . Attributes different from those in Dublin Core are noted as such in the comments. The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? Tentatively including three attribute for addressing this -- identifier, file_path, and uri. There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files.","title":"Comments"},{"location":"File/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"File/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"File/#mappings","text":"Mapping Type Mapped Value self bdchm:File native bdchm:File","title":"Mappings"},{"location":"File/#linkml-source","text":"","title":"LinkML Source"},{"location":"File/#direct","text":"name: File description: Abstract class for various kinds of files. Subclasses may be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer file_location: name: file_location description: A unique identifier or url for identifying or locating the file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: uriorcurie md5sum: name: md5sum description: The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant derived_from: name: derived_from description: A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: File","title":"Direct"},{"location":"File/#induced","text":"name: File description: Abstract class for various kinds of files. Subclasses may be defined for specific file types. comments: - This is taken largely from the [Gen3 Core Metadata Collection](https://gen3.biodatacatalyst.nhlbi.nih.gov/DD) definition. - Gen3 apparently took most of the attributes listed here from the [Dublin Core /elements/1.1/ namespace](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-3). - Attributes different from those in Dublin Core are noted as such in the comments. - The Document entity was defined in this model prior to defining this File entity. Should it be modified to be a subclass of this? - Unlike Document, which has a url property, the Gen3 Core Metadata definition doesn't have a file location or unique identifier. Should that be left to specific File subclasses or defined here? - Tentatively including three attribute for addressing this -- identifier, file_path, and uri. - There appear to be 11 specific file types defined in Gen3, 8 types classified as Data Files and 3 classified as Index Files. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: file_name: name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string file_size: name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer file_location: name: file_location description: A unique identifier or url for identifying or locating the file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: file_location owner: File domain_of: - File range: uriorcurie md5sum: name: md5sum description: The 128-bit hash value expressed as a 32 digit hexadecimal number used as a file's digital fingerprint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: md5sum owner: File domain_of: - File range: string data_type: name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string data_category: name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string format: name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string description: name: description description: 'An account of the resource. Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.' from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: File domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string associated_participant: name: associated_participant description: A reference to the Participant to which this file relates. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: File domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant derived_from: name: derived_from description: A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: derived_from owner: File domain_of: - File range: File identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: File domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: File domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Float/","text":"Type: Float A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Float"},{"location":"Float/#type-float","text":"A real number that conforms to the xsd:float specification URI: xsd:float base : float uri : xsd:float","title":"Type: Float"},{"location":"Float/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Float/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"HpoPhenotypicAbnormalityEnum/","text":"Enum: HpoPhenotypicAbnormalityEnum A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. URI: HpoPhenotypicAbnormalityEnum This is a dynamic enum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: HpoPhenotypicAbnormalityEnum description: A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:hp source_nodes: - HP:0000118 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: HpoPhenotypicAbnormalityEnum"},{"location":"HpoPhenotypicAbnormalityEnum/#enum-hpophenotypicabnormalityenum","text":"A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. URI: HpoPhenotypicAbnormalityEnum This is a dynamic enum","title":"Enum: HpoPhenotypicAbnormalityEnum"},{"location":"HpoPhenotypicAbnormalityEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"HpoPhenotypicAbnormalityEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"HpoPhenotypicAbnormalityEnum/#linkml-source","text":"name: HpoPhenotypicAbnormalityEnum description: A constrained set of enumerative values containing the HPO values for phenotypic abnormalities. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:hp source_nodes: - HP:0000118 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Integer/","text":"Type: Integer An integer URI: xsd:integer base : int uri : xsd:integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Integer"},{"location":"Integer/#type-integer","text":"An integer URI: xsd:integer base : int uri : xsd:integer","title":"Type: Integer"},{"location":"Integer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Integer/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Jsonpath/","text":"Type: Jsonpath A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Jsonpath"},{"location":"Jsonpath/#type-jsonpath","text":"A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Jsonpath"},{"location":"Jsonpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpath/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Jsonpointer/","text":"Type: Jsonpointer A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#type-jsonpointer","text":"A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Jsonpointer"},{"location":"Jsonpointer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Jsonpointer/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"MondoHumanDiseaseEnum/","text":"Enum: MondoHumanDiseaseEnum A constrained set of enumerative values containing the MONDO values for human diseases. URI: MondoHumanDiseaseEnum This is a dynamic enum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: MondoHumanDiseaseEnum description: A constrained set of enumerative values containing the MONDO values for human diseases. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:mondo source_nodes: - MONDO:0700096 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: MondoHumanDiseaseEnum"},{"location":"MondoHumanDiseaseEnum/#enum-mondohumandiseaseenum","text":"A constrained set of enumerative values containing the MONDO values for human diseases. URI: MondoHumanDiseaseEnum This is a dynamic enum","title":"Enum: MondoHumanDiseaseEnum"},{"location":"MondoHumanDiseaseEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"MondoHumanDiseaseEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"MondoHumanDiseaseEnum/#linkml-source","text":"name: MondoHumanDiseaseEnum description: A constrained set of enumerative values containing the MONDO values for human diseases. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:mondo source_nodes: - MONDO:0700096 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Ncname/","text":"Type: Ncname Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Ncname"},{"location":"Ncname/#type-ncname","text":"Prefix part of CURIE URI: xsd:string base : NCName uri : xsd:string repr : str","title":"Type: Ncname"},{"location":"Ncname/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Ncname/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Nodeidentifier/","text":"Type: Nodeidentifier A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#type-nodeidentifier","text":"A URI, CURIE or BNODE that represents a node in a model. URI: shex:nonLiteral base : NodeIdentifier uri : shex:nonLiteral repr : str","title":"Type: Nodeidentifier"},{"location":"Nodeidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Nodeidentifier/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Objectidentifier/","text":"Type: Objectidentifier A URI or CURIE that represents an object in the model. URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str Comments Used for inheritance and type checking Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#type-objectidentifier","text":"A URI or CURIE that represents an object in the model. URI: shex:iri base : ElementIdentifier uri : shex:iri repr : str","title":"Type: Objectidentifier"},{"location":"Objectidentifier/#comments","text":"Used for inheritance and type checking","title":"Comments"},{"location":"Objectidentifier/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Objectidentifier/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Observation/","text":"Class: Observation A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. URI: bdchm:Observation classDiagram class Observation Entity <|-- Observation Observation <|-- DimensionalObservation Observation <|-- SpecimenQualityObservation Observation <|-- SpecimenQuantityObservation Observation : age_at_observation Observation : associated_participant Observation --> Participant : associated_participant Observation : associated_visit Observation --> Visit : associated_visit Observation : category Observation : focus Observation --> Entity : focus Observation : id Observation : method_type Observation : observation_type Observation : performed_by Observation --> Organization : performed_by Observation : value Observation --> ObservationValue : value Inheritance Entity Observation DimensionalObservation SpecimenQualityObservation SpecimenQuantityObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made direct category 0..1 String The general category of observation described direct observation_type 1..1 String The type of Observation being represented (e direct method_type 0..1 String A type of method used in generating the Observation result direct focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) direct associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded direct performed_by 0..1 Organization The organization or group that performed the observation activity direct value 1..1 ObservationValue The value for an Observation direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used ObservationSet observations range Observation Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Observation native bdchm:Observation LinkML Source Direct name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: ObservationValue required: true Induced name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: Observation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: Observation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: Observation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: Observation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: Observation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: Observation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Observation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: Observation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: Observation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValue required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Observation domain_of: - Entity range: uriorcurie required: true","title":"Class: Observation"},{"location":"Observation/#class-observation","text":"A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. URI: bdchm:Observation classDiagram class Observation Entity <|-- Observation Observation <|-- DimensionalObservation Observation <|-- SpecimenQualityObservation Observation <|-- SpecimenQuantityObservation Observation : age_at_observation Observation : associated_participant Observation --> Participant : associated_participant Observation : associated_visit Observation --> Visit : associated_visit Observation : category Observation : focus Observation --> Entity : focus Observation : id Observation : method_type Observation : observation_type Observation : performed_by Observation --> Organization : performed_by Observation : value Observation --> ObservationValue : value","title":"Class: Observation"},{"location":"Observation/#inheritance","text":"Entity Observation DimensionalObservation SpecimenQualityObservation SpecimenQuantityObservation","title":"Inheritance"},{"location":"Observation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made direct category 0..1 String The general category of observation described direct observation_type 1..1 String The type of Observation being represented (e direct method_type 0..1 String A type of method used in generating the Observation result direct focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) direct associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded direct performed_by 0..1 Organization The organization or group that performed the observation activity direct value 1..1 ObservationValue The value for an Observation direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Observation/#usages","text":"used by used in type used ObservationSet observations range Observation","title":"Usages"},{"location":"Observation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Observation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Observation/#mappings","text":"Mapping Type Mapped Value self bdchm:Observation native bdchm:Observation","title":"Mappings"},{"location":"Observation/#linkml-source","text":"","title":"LinkML Source"},{"location":"Observation/#direct","text":"name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: ObservationValue required: true","title":"Direct"},{"location":"Observation/#induced","text":"name: Observation description: A data structure with key (observation_type) and value (value) attributes that represents a single observation, such as the hematocrit component of a complete blood count panel. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: Observation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: Observation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: Observation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: Observation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: Observation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: Observation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Observation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: Observation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The value for an Observation. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: Observation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValue required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Observation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ObservationSet/","text":"Class: ObservationSet A structured object to hold related Observations in a set. URI: bdchm:ObservationSet classDiagram class ObservationSet Entity <|-- ObservationSet ObservationSet <|-- DimensionalObservationSet ObservationSet : associated_participant ObservationSet --> Participant : associated_participant ObservationSet : category ObservationSet : focus ObservationSet --> Entity : focus ObservationSet : id ObservationSet : method_type ObservationSet : observations ObservationSet --> Observation : observations ObservationSet : performed_by ObservationSet --> Organization : performed_by Inheritance Entity ObservationSet DimensionalObservationSet Slots Name Cardinality and Range Description Inheritance observations 0..* Observation A set of one or more observations direct category 0..1 String The general category of observation set described direct focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) direct method_type 0..* String The type of method used in generating the ObservationSet direct performed_by 0..1 Organization The organization or group that performed the observation activity direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationSet native bdchm:ObservationSet LinkML Source Direct name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - observations attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false Induced name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: ObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: ObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: ObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: ObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: ObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: ObservationSet domain_of: - ObservationSet range: Observation id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Class: ObservationSet"},{"location":"ObservationSet/#class-observationset","text":"A structured object to hold related Observations in a set. URI: bdchm:ObservationSet classDiagram class ObservationSet Entity <|-- ObservationSet ObservationSet <|-- DimensionalObservationSet ObservationSet : associated_participant ObservationSet --> Participant : associated_participant ObservationSet : category ObservationSet : focus ObservationSet --> Entity : focus ObservationSet : id ObservationSet : method_type ObservationSet : observations ObservationSet --> Observation : observations ObservationSet : performed_by ObservationSet --> Organization : performed_by","title":"Class: ObservationSet"},{"location":"ObservationSet/#inheritance","text":"Entity ObservationSet DimensionalObservationSet","title":"Inheritance"},{"location":"ObservationSet/#slots","text":"Name Cardinality and Range Description Inheritance observations 0..* Observation A set of one or more observations direct category 0..1 String The general category of observation set described direct focus 0..* Entity The entity or entities directly observed/measured in generating an observatio... direct associated_participant 0..1 Participant The Participant that the observation is about (if not the direct focus) direct method_type 0..* String The type of method used in generating the ObservationSet direct performed_by 0..1 Organization The organization or group that performed the observation activity direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"ObservationSet/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationSet/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationSet/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationSet native bdchm:ObservationSet","title":"Mappings"},{"location":"ObservationSet/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationSet/#direct","text":"name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - observations attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Organization required: false","title":"Direct"},{"location":"ObservationSet/#induced","text":"name: ObservationSet description: A structured object to hold related Observations in a set. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: category: name: category description: The general category of observation set described from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_ObservationSet_category multivalued: false alias: category owner: ObservationSet domain_of: - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", and \"associated_participant\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in an entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: focus owner: ObservationSet domain_of: - Document - ObservationSet - Observation range: Entity required: false inlined: true inlined_as_list: true associated_participant: name: associated_participant description: The Participant that the observation is about (if not the direct focus). Observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: ObservationSet domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false method_type: name: method_type description: The type of method used in generating the ObservationSet comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\"). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_ObservationSet_method_type multivalued: true alias: method_type owner: ObservationSet domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: ObservationSet domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false observations: name: observations description: A set of one or more observations. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: observations owner: ObservationSet domain_of: - ObservationSet range: Observation id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ObservationSet domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ObservationValue/","text":"Class: ObservationValue Single-valued observation valueholiding slot NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:ObservationValue classDiagram class ObservationValue ObservationValue <|-- ObservationValueDecimal ObservationValue <|-- ObservationValueInteger ObservationValue <|-- ObservationValueBoolean ObservationValue <|-- ObservationValueString ObservationValue <|-- ObservationValueQuantity ObservationValue : name ObservationValue : type ObservationValue : value Inheritance ObservationValue ObservationValueDecimal ObservationValueInteger ObservationValueBoolean ObservationValueString ObservationValueQuantity Slots Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct Usages used by used in type used Observation value range ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValue native bdchm:ObservationValue LinkML Source Direct name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string Induced name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Class: ObservationValue"},{"location":"ObservationValue/#class-observationvalue","text":"Single-valued observation valueholiding slot NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:ObservationValue classDiagram class ObservationValue ObservationValue <|-- ObservationValueDecimal ObservationValue <|-- ObservationValueInteger ObservationValue <|-- ObservationValueBoolean ObservationValue <|-- ObservationValueString ObservationValue <|-- ObservationValueQuantity ObservationValue : name ObservationValue : type ObservationValue : value","title":"Class: ObservationValue"},{"location":"ObservationValue/#inheritance","text":"ObservationValue ObservationValueDecimal ObservationValueInteger ObservationValueBoolean ObservationValueString ObservationValueQuantity","title":"Inheritance"},{"location":"ObservationValue/#slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct","title":"Slots"},{"location":"ObservationValue/#usages","text":"used by used in type used Observation value range ObservationValue","title":"Usages"},{"location":"ObservationValue/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValue/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValue/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValue native bdchm:ObservationValue","title":"Mappings"},{"location":"ObservationValue/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValue/#direct","text":"name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string","title":"Direct"},{"location":"ObservationValue/#induced","text":"name: ObservationValue description: Single-valued observation valueholiding slot from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueBoolean/","text":"Class: ObservationValueBoolean Single-valued boolean observation URI: bdchm:ObservationValueBoolean classDiagram class ObservationValueBoolean ObservationValue <|-- ObservationValueBoolean ObservationValueBoolean : name ObservationValueBoolean : type ObservationValueBoolean : value Inheritance ObservationValue ObservationValueBoolean Slots Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueBoolean native bdchm:ObservationValueBoolean LinkML Source Direct name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true Induced name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueBoolean"},{"location":"ObservationValueBoolean/#class-observationvalueboolean","text":"Single-valued boolean observation URI: bdchm:ObservationValueBoolean classDiagram class ObservationValueBoolean ObservationValue <|-- ObservationValueBoolean ObservationValueBoolean : name ObservationValueBoolean : type ObservationValueBoolean : value","title":"Class: ObservationValueBoolean"},{"location":"ObservationValueBoolean/#inheritance","text":"ObservationValue ObservationValueBoolean","title":"Inheritance"},{"location":"ObservationValueBoolean/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueBoolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueBoolean/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueBoolean/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueBoolean native bdchm:ObservationValueBoolean","title":"Mappings"},{"location":"ObservationValueBoolean/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueBoolean/#direct","text":"name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true","title":"Direct"},{"location":"ObservationValueBoolean/#induced","text":"name: ObservationValueBoolean description: Single-valued boolean observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueDecimal/","text":"Class: ObservationValueDecimal Single-valued decimal observation URI: bdchm:ObservationValueDecimal classDiagram class ObservationValueDecimal ObservationValue <|-- ObservationValueDecimal ObservationValueDecimal : name ObservationValueDecimal : type ObservationValueDecimal : value Inheritance ObservationValue ObservationValueDecimal Slots Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueDecimal native bdchm:ObservationValueDecimal LinkML Source Direct name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true Induced name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueDecimal"},{"location":"ObservationValueDecimal/#class-observationvaluedecimal","text":"Single-valued decimal observation URI: bdchm:ObservationValueDecimal classDiagram class ObservationValueDecimal ObservationValue <|-- ObservationValueDecimal ObservationValueDecimal : name ObservationValueDecimal : type ObservationValueDecimal : value","title":"Class: ObservationValueDecimal"},{"location":"ObservationValueDecimal/#inheritance","text":"ObservationValue ObservationValueDecimal","title":"Inheritance"},{"location":"ObservationValueDecimal/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueDecimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueDecimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueDecimal/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueDecimal native bdchm:ObservationValueDecimal","title":"Mappings"},{"location":"ObservationValueDecimal/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueDecimal/#direct","text":"name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true","title":"Direct"},{"location":"ObservationValueDecimal/#induced","text":"name: ObservationValueDecimal description: Single-valued decimal observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueInteger/","text":"Class: ObservationValueInteger Single-valued integer observation URI: bdchm:ObservationValueInteger classDiagram class ObservationValueInteger ObservationValue <|-- ObservationValueInteger ObservationValueInteger : name ObservationValueInteger : type ObservationValueInteger : value Inheritance ObservationValue ObservationValueInteger Slots Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueInteger native bdchm:ObservationValueInteger LinkML Source Direct name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true Induced name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueInteger"},{"location":"ObservationValueInteger/#class-observationvalueinteger","text":"Single-valued integer observation URI: bdchm:ObservationValueInteger classDiagram class ObservationValueInteger ObservationValue <|-- ObservationValueInteger ObservationValueInteger : name ObservationValueInteger : type ObservationValueInteger : value","title":"Class: ObservationValueInteger"},{"location":"ObservationValueInteger/#inheritance","text":"ObservationValue ObservationValueInteger","title":"Inheritance"},{"location":"ObservationValueInteger/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueInteger/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueInteger/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueInteger/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueInteger native bdchm:ObservationValueInteger","title":"Mappings"},{"location":"ObservationValueInteger/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueInteger/#direct","text":"name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true","title":"Direct"},{"location":"ObservationValueInteger/#induced","text":"name: ObservationValueInteger description: Single-valued integer observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueQuantity/","text":"Class: ObservationValueQuantity Single-valued Quantity observation URI: bdchm:ObservationValueQuantity classDiagram class ObservationValueQuantity ObservationValue <|-- ObservationValueQuantity ObservationValueQuantity : name ObservationValueQuantity : type ObservationValueQuantity : value ObservationValueQuantity --> Quantity : value Inheritance ObservationValue ObservationValueQuantity Slots Name Cardinality and Range Description Inheritance value 1..1 Quantity A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Usages used by used in type used DimensionalObservation value range ObservationValueQuantity SpecimenQuantityObservation value range ObservationValueQuantity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueQuantity native bdchm:ObservationValueQuantity LinkML Source Direct name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true Induced name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueQuantity domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueQuantity"},{"location":"ObservationValueQuantity/#class-observationvaluequantity","text":"Single-valued Quantity observation URI: bdchm:ObservationValueQuantity classDiagram class ObservationValueQuantity ObservationValue <|-- ObservationValueQuantity ObservationValueQuantity : name ObservationValueQuantity : type ObservationValueQuantity : value ObservationValueQuantity --> Quantity : value","title":"Class: ObservationValueQuantity"},{"location":"ObservationValueQuantity/#inheritance","text":"ObservationValue ObservationValueQuantity","title":"Inheritance"},{"location":"ObservationValueQuantity/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Quantity A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueQuantity/#usages","text":"used by used in type used DimensionalObservation value range ObservationValueQuantity SpecimenQuantityObservation value range ObservationValueQuantity","title":"Usages"},{"location":"ObservationValueQuantity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueQuantity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueQuantity/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueQuantity native bdchm:ObservationValueQuantity","title":"Mappings"},{"location":"ObservationValueQuantity/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueQuantity/#direct","text":"name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true","title":"Direct"},{"location":"ObservationValueQuantity/#induced","text":"name: ObservationValueQuantity description: Single-valued Quantity observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: Quantity required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueQuantity domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueQuantity domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"ObservationValueString/","text":"Class: ObservationValueString Single-valued string observation URI: bdchm:ObservationValueString classDiagram class ObservationValueString ObservationValue <|-- ObservationValueString ObservationValueString : name ObservationValueString : type ObservationValueString : value Inheritance ObservationValue ObservationValueString Slots Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue Usages used by used in type used SpecimenQualityObservation value range ObservationValueString Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ObservationValueString native bdchm:ObservationValueString LinkML Source Direct name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true Induced name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: ObservationValueString"},{"location":"ObservationValueString/#class-observationvaluestring","text":"Single-valued string observation URI: bdchm:ObservationValueString classDiagram class ObservationValueString ObservationValue <|-- ObservationValueString ObservationValueString : name ObservationValueString : type ObservationValueString : value","title":"Class: ObservationValueString"},{"location":"ObservationValueString/#inheritance","text":"ObservationValue ObservationValueString","title":"Inheritance"},{"location":"ObservationValueString/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value ObservationValue type 0..1 String ObservationValue name 0..1 String ObservationValue","title":"Slots"},{"location":"ObservationValueString/#usages","text":"used by used in type used SpecimenQualityObservation value range ObservationValueString","title":"Usages"},{"location":"ObservationValueString/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ObservationValueString/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ObservationValueString/#mappings","text":"Mapping Type Mapped Value self bdchm:ObservationValueString native bdchm:ObservationValueString","title":"Mappings"},{"location":"ObservationValueString/#linkml-source","text":"","title":"LinkML Source"},{"location":"ObservationValueString/#direct","text":"name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true","title":"Direct"},{"location":"ObservationValueString/#induced","text":"name: ObservationValueString description: Single-valued string observation from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: ObservationValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: ObservationValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm designates_type: true alias: type owner: ObservationValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: ObservationValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"Organization/","text":"Class: Organization A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. URI: bdchm:Organization classDiagram class Organization Entity <|-- Organization Organization : alias Organization : id Organization : identity Organization : name Organization : organization_type Inheritance Entity Organization Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String The full legal name by which the organization is known (e direct alias 0..1 String A secondary name for the organization such as a short name or abbreviation (e direct organization_type 0..1 String The type of the organization (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant originating_site range Organization DimensionalObservation performed_by range Organization DimensionalObservationSet performed_by range Organization SpecimenCreationActivity performed_by range Organization SpecimenQualityObservation performed_by range Organization SpecimenQuantityObservation performed_by range Organization SpecimenTransportActivity transport_origin range Organization SpecimenTransportActivity transport_destination range Organization ObservationSet performed_by range Organization Observation performed_by range Organization Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Organization native bdchm:Organization LinkML Source Direct name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string Induced name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Organization domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: alias owner: Organization domain_of: - Organization range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: organization_type owner: Organization domain_of: - Organization range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Organization domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Organization domain_of: - Entity range: uriorcurie required: true","title":"Class: Organization"},{"location":"Organization/#class-organization","text":"A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. URI: bdchm:Organization classDiagram class Organization Entity <|-- Organization Organization : alias Organization : id Organization : identity Organization : name Organization : organization_type","title":"Class: Organization"},{"location":"Organization/#inheritance","text":"Entity Organization","title":"Inheritance"},{"location":"Organization/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String The full legal name by which the organization is known (e direct alias 0..1 String A secondary name for the organization such as a short name or abbreviation (e direct organization_type 0..1 String The type of the organization (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Organization/#usages","text":"used by used in type used Participant originating_site range Organization DimensionalObservation performed_by range Organization DimensionalObservationSet performed_by range Organization SpecimenCreationActivity performed_by range Organization SpecimenQualityObservation performed_by range Organization SpecimenQuantityObservation performed_by range Organization SpecimenTransportActivity transport_origin range Organization SpecimenTransportActivity transport_destination range Organization ObservationSet performed_by range Organization Observation performed_by range Organization","title":"Usages"},{"location":"Organization/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Organization/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Organization/#mappings","text":"Mapping Type Mapped Value self bdchm:Organization native bdchm:Organization","title":"Mappings"},{"location":"Organization/#linkml-source","text":"","title":"LinkML Source"},{"location":"Organization/#direct","text":"name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string","title":"Direct"},{"location":"Organization/#induced","text":"name: Organization description: A grouping of people or organizations with a common purpose such as a data coordinating center, an university, or an institute within a university. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: The full legal name by which the organization is known (e.g. 'National Cancer Institute') from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Organization domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string alias: name: alias description: A secondary name for the organization such as a short name or abbreviation (e.g. 'NCI') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: alias owner: Organization domain_of: - Organization range: string organization_type: name: organization_type description: The type of the organization (e.g. 'Cancer Genome Characterization Center') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: organization_type owner: Organization domain_of: - Organization range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Organization domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Organization domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Participant/","text":"Class: Participant A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. URI: bdchm:Participant classDiagram class Participant Entity <|-- Participant Participant : age_at_enrollment Participant : associated_person Participant --> Person : associated_person Participant : consents Participant --> Consent : consents Participant : description Participant : id Participant : identity Participant : index_timepoint Participant : member_of_research_study Participant --> ResearchStudy : member_of_research_study Participant : originating_site Participant --> Organization : originating_site Participant : study_arm Inheritance Entity Participant Slots Name Cardinality and Range Description Inheritance associated_person 0..1 Person A reference to the Person that is associated with this record direct identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the research s... direct member_of_research_study 0..1 ResearchStudy A reference to the Study(s) of which this Participant is a member direct age_at_enrollment 0..1 Integer The age in days when the Participant enrolled on the ResearchStudy direct index_timepoint 0..1 String The text term used to describe the reference or anchor date used for date obf... direct originating_site 0..1 Organization The Organization through which a subject was enrolled on a ResearchStudy direct study_arm 0..* String The arm(s) of the study on which the Participant is enrolled direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Demography associated_participant range Participant Visit associated_participant range Participant Condition associated_participant range Participant Procedure associated_participant range Participant DrugExposure associated_participant range Participant DeviceExposure associated_participant range Participant DimensionalObservation associated_participant range Participant DimensionalObservationSet associated_participant range Participant File associated_participant range Participant Specimen source_participant range Participant SpecimenQualityObservation associated_participant range Participant SpecimenQuantityObservation associated_participant range Participant ObservationSet associated_participant range Participant Observation associated_participant range Participant Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Participant native bdchm:Participant LinkML Source Direct name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - associated_person - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Consent Induced name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description owner: Participant domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: member_of_research_study owner: Participant domain_of: - Participant range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_enrollment owner: Participant domain_of: - Participant range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_timepoint owner: Participant domain_of: - Participant range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: originating_site owner: Participant domain_of: - Participant range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: consents owner: Participant domain_of: - Participant - ResearchStudy range: Consent associated_person: name: associated_person description: A reference to the Person that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_person owner: Participant domain_of: - Participant range: Person identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Participant domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Participant domain_of: - Entity range: uriorcurie required: true","title":"Class: Participant"},{"location":"Participant/#class-participant","text":"A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. URI: bdchm:Participant classDiagram class Participant Entity <|-- Participant Participant : age_at_enrollment Participant : associated_person Participant --> Person : associated_person Participant : consents Participant --> Consent : consents Participant : description Participant : id Participant : identity Participant : index_timepoint Participant : member_of_research_study Participant --> ResearchStudy : member_of_research_study Participant : originating_site Participant --> Organization : originating_site Participant : study_arm","title":"Class: Participant"},{"location":"Participant/#inheritance","text":"Entity Participant","title":"Inheritance"},{"location":"Participant/#slots","text":"Name Cardinality and Range Description Inheritance associated_person 0..1 Person A reference to the Person that is associated with this record direct identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional info/explanation about the research s... direct member_of_research_study 0..1 ResearchStudy A reference to the Study(s) of which this Participant is a member direct age_at_enrollment 0..1 Integer The age in days when the Participant enrolled on the ResearchStudy direct index_timepoint 0..1 String The text term used to describe the reference or anchor date used for date obf... direct originating_site 0..1 Organization The Organization through which a subject was enrolled on a ResearchStudy direct study_arm 0..* String The arm(s) of the study on which the Participant is enrolled direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Participant/#usages","text":"used by used in type used Demography associated_participant range Participant Visit associated_participant range Participant Condition associated_participant range Participant Procedure associated_participant range Participant DrugExposure associated_participant range Participant DeviceExposure associated_participant range Participant DimensionalObservation associated_participant range Participant DimensionalObservationSet associated_participant range Participant File associated_participant range Participant Specimen source_participant range Participant SpecimenQualityObservation associated_participant range Participant SpecimenQuantityObservation associated_participant range Participant ObservationSet associated_participant range Participant Observation associated_participant range Participant","title":"Usages"},{"location":"Participant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Participant/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Participant/#mappings","text":"Mapping Type Mapped Value self bdchm:Participant native bdchm:Participant","title":"Mappings"},{"location":"Participant/#linkml-source","text":"","title":"LinkML Source"},{"location":"Participant/#direct","text":"name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - associated_person - identity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Consent","title":"Direct"},{"location":"Participant/#induced","text":"name: Participant description: A Participant is the entity of interest in a research study, typically a human being or an animal, but can also be a device, group of humans or animals, or a tissue sample. Human research subjects are usually not traceable to a particular person to protect the subject\u2019s privacy. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional info/explanation about the research subject. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description owner: Participant domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string member_of_research_study: name: member_of_research_study description: A reference to the Study(s) of which this Participant is a member from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: member_of_research_study owner: Participant domain_of: - Participant range: ResearchStudy age_at_enrollment: name: age_at_enrollment description: The age in days when the Participant enrolled on the ResearchStudy from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_enrollment owner: Participant domain_of: - Participant range: integer unit: ucum_code: d index_timepoint: name: index_timepoint description: The text term used to describe the reference or anchor date used for date obfuscation, where a single date is obscured by creating one or more date ranges in relation to this date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_timepoint owner: Participant domain_of: - Participant range: string originating_site: name: originating_site description: The Organization through which a subject was enrolled on a ResearchStudy. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: originating_site owner: Participant domain_of: - Participant range: Organization study_arm: name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: consents owner: Participant domain_of: - Participant - ResearchStudy range: Consent associated_person: name: associated_person description: A reference to the Person that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_person owner: Participant domain_of: - Participant range: Person identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Participant domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Participant domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Person/","text":"Class: Person Administrative information about an individual or animal receiving care or other health-related services. URI: bdchm:Person classDiagram class Person Entity <|-- Person Person : age_at_death Person : breed Person --> VertebrateBreedEnum : breed Person : cause_of_death Person : id Person : identity Person : species Person --> CellularOrganismSpeciesEnum : species Person : vital_status Person --> VitalStatusEnum : vital_status Person : year_of_birth Person : year_of_death Inheritance Entity Person Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct species 0..1 CellularOrganismSpeciesEnum The scientific binomial name for the species of the Person (e direct breed 0..1 VertebrateBreedEnum A label given to a group of animals homogeneous in appearance and other chara... direct year_of_birth 0..1 Integer Numeric value to represent the calendar year in which an individual was born direct vital_status 0..1 VitalStatusEnum Coded value indicating the state or condition of being living or deceased; al... direct age_at_death 0..1 Integer The age of an individual at the time of death, expressed in days since birth direct year_of_death 0..1 Integer Numeric value to represent the calendar year in which an individual died direct cause_of_death 0..1 String Coded value indicating the circumstance or condition that results in the deat... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant associated_person range Person Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Person native bdchm:Person LinkML Source Direct name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string Induced name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: species owner: Person domain_of: - Person range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_birth owner: Person domain_of: - Person range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_death owner: Person domain_of: - Person range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_death owner: Person domain_of: - Person range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Person domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Person domain_of: - Entity range: uriorcurie required: true","title":"Class: Person"},{"location":"Person/#class-person","text":"Administrative information about an individual or animal receiving care or other health-related services. URI: bdchm:Person classDiagram class Person Entity <|-- Person Person : age_at_death Person : breed Person --> VertebrateBreedEnum : breed Person : cause_of_death Person : id Person : identity Person : species Person --> CellularOrganismSpeciesEnum : species Person : vital_status Person --> VitalStatusEnum : vital_status Person : year_of_birth Person : year_of_death","title":"Class: Person"},{"location":"Person/#inheritance","text":"Entity Person","title":"Inheritance"},{"location":"Person/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct species 0..1 CellularOrganismSpeciesEnum The scientific binomial name for the species of the Person (e direct breed 0..1 VertebrateBreedEnum A label given to a group of animals homogeneous in appearance and other chara... direct year_of_birth 0..1 Integer Numeric value to represent the calendar year in which an individual was born direct vital_status 0..1 VitalStatusEnum Coded value indicating the state or condition of being living or deceased; al... direct age_at_death 0..1 Integer The age of an individual at the time of death, expressed in days since birth direct year_of_death 0..1 Integer Numeric value to represent the calendar year in which an individual died direct cause_of_death 0..1 String Coded value indicating the circumstance or condition that results in the deat... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Person/#usages","text":"used by used in type used Participant associated_person range Person","title":"Usages"},{"location":"Person/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Person/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Person/#mappings","text":"Mapping Type Mapped Value self bdchm:Person native bdchm:Person","title":"Mappings"},{"location":"Person/#linkml-source","text":"","title":"LinkML Source"},{"location":"Person/#direct","text":"name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string","title":"Direct"},{"location":"Person/#induced","text":"name: Person description: Administrative information about an individual or animal receiving care or other health-related services. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: species: name: species description: The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). Values should be derived from the NCBI organismal taxonomy (http://purl.obolibrary.org/obo/ncbitaxon.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: species owner: Person domain_of: - Person range: CellularOrganismSpeciesEnum breed: name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum year_of_birth: name: year_of_birth description: Numeric value to represent the calendar year in which an individual was born. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_birth owner: Person domain_of: - Person range: integer vital_status: name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum age_at_death: name: age_at_death description: The age of an individual at the time of death, expressed in days since birth from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_death owner: Person domain_of: - Person range: integer unit: ucum_code: d year_of_death: name: year_of_death description: Numeric value to represent the calendar year in which an individual died. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: year_of_death owner: Person domain_of: - Person range: integer cause_of_death: name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Person domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Person domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Procedure/","text":"Class: Procedure Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] URI: bdchm:Procedure classDiagram class Procedure Entity <|-- Procedure Procedure : age_at_procedure Procedure : associated_participant Procedure --> Participant : associated_participant Procedure : associated_visit Procedure --> Visit : associated_visit Procedure : id Procedure : identity Procedure : procedure_concept Procedure --> ProcedureConceptEnum : procedure_concept Procedure : procedure_provenance Procedure --> ProvenanceEnum : procedure_provenance Procedure : quantity Procedure --> Quantity : quantity Inheritance Entity Procedure Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct procedure_concept 0..1 ProcedureConceptEnum The coded value that describes the procedure, derived from OMOP codes direct age_at_procedure 0..1 Integer The Participant's age (expressed in days) when the procedure was performed direct procedure_provenance 0..1 ProvenanceEnum A value representing the provenance of the Procedure record direct quantity 0..1 Quantity The quantity of procedures ordered or administered direct associated_participant 0..1 Participant A reference to the Participant on which the Procedure was performed direct associated_visit 0..1 Visit A reference to the Visit during which this Procedure was performed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Procedure native bdchm:Procedure LinkML Source Direct name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit Induced name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_concept owner: Procedure domain_of: - Procedure range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_procedure owner: Procedure domain_of: - Procedure range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_provenance owner: Procedure domain_of: - Procedure range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: quantity owner: Procedure domain_of: - Procedure - DrugExposure - DeviceExposure range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Procedure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Procedure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Procedure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Procedure domain_of: - Entity range: uriorcurie required: true","title":"Class: Procedure"},{"location":"Procedure/#class-procedure","text":"Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] URI: bdchm:Procedure classDiagram class Procedure Entity <|-- Procedure Procedure : age_at_procedure Procedure : associated_participant Procedure --> Participant : associated_participant Procedure : associated_visit Procedure --> Visit : associated_visit Procedure : id Procedure : identity Procedure : procedure_concept Procedure --> ProcedureConceptEnum : procedure_concept Procedure : procedure_provenance Procedure --> ProvenanceEnum : procedure_provenance Procedure : quantity Procedure --> Quantity : quantity","title":"Class: Procedure"},{"location":"Procedure/#inheritance","text":"Entity Procedure","title":"Inheritance"},{"location":"Procedure/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct procedure_concept 0..1 ProcedureConceptEnum The coded value that describes the procedure, derived from OMOP codes direct age_at_procedure 0..1 Integer The Participant's age (expressed in days) when the procedure was performed direct procedure_provenance 0..1 ProvenanceEnum A value representing the provenance of the Procedure record direct quantity 0..1 Quantity The quantity of procedures ordered or administered direct associated_participant 0..1 Participant A reference to the Participant on which the Procedure was performed direct associated_visit 0..1 Visit A reference to the Visit during which this Procedure was performed direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Procedure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Procedure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Procedure/#mappings","text":"Mapping Type Mapped Value self bdchm:Procedure native bdchm:Procedure","title":"Mappings"},{"location":"Procedure/#linkml-source","text":"","title":"LinkML Source"},{"location":"Procedure/#direct","text":"name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Visit","title":"Direct"},{"location":"Procedure/#induced","text":"name: Procedure description: Procedure contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patient to have a diagnostic or therapeutic purpose. Procedures are present in various data sources in different forms with varying levels of standardization. [Derived from OMOP] from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: procedure_concept: name: procedure_concept description: The coded value that describes the procedure, derived from OMOP codes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_concept owner: Procedure domain_of: - Procedure range: ProcedureConceptEnum age_at_procedure: name: age_at_procedure description: The Participant's age (expressed in days) when the procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_procedure owner: Procedure domain_of: - Procedure range: integer unit: ucum_code: d procedure_provenance: name: procedure_provenance description: A value representing the provenance of the Procedure record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: procedure_provenance owner: Procedure domain_of: - Procedure range: ProvenanceEnum quantity: name: quantity description: The quantity of procedures ordered or administered. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: quantity owner: Procedure domain_of: - Procedure - DrugExposure - DeviceExposure range: Quantity associated_participant: name: associated_participant description: A reference to the Participant on which the Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Procedure domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant associated_visit: name: associated_visit description: A reference to the Visit during which this Procedure was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: Procedure domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Procedure domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Procedure domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ProcedureConceptEnum/","text":"Enum: ProcedureConceptEnum Procedure codes from OMOP. URI: ProcedureConceptEnum This is a dynamic enum Slots Name Description procedure_concept The coded value that describes the procedure, derived from OMOP codes Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ProcedureConceptEnum description: Procedure codes from OMOP. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: OMOP","title":"Enum: ProcedureConceptEnum"},{"location":"ProcedureConceptEnum/#enum-procedureconceptenum","text":"Procedure codes from OMOP. URI: ProcedureConceptEnum This is a dynamic enum","title":"Enum: ProcedureConceptEnum"},{"location":"ProcedureConceptEnum/#slots","text":"Name Description procedure_concept The coded value that describes the procedure, derived from OMOP codes","title":"Slots"},{"location":"ProcedureConceptEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ProcedureConceptEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ProcedureConceptEnum/#linkml-source","text":"name: ProcedureConceptEnum description: Procedure codes from OMOP. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: OMOP","title":"LinkML Source"},{"location":"ProvenanceEnum/","text":"Enum: ProvenanceEnum A constrained set of enumerative values containing the OMOP values for provenance. URI: ProvenanceEnum Permissible Values Value Meaning Description EHR_BILLING_DIAGNOSIS OMOP:4822159 EHR_CHIEF_COMPLAINT OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS OMOP:4822160 EHR_EPISODE_ENTRY OMOP:4822135 EHR_PROBLEM_LIST_ENTRY OMOP:4822121 FIRST_POSITION_CONDITION OMOP:4822128 NLP_DERIVED OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION OMOP:4822157 PRIMARY_CONDITION OMOP:4822127 REFERRAL_RECORD OMOP:4822125 SECONDARY_CONDITION OMOP:4822129 TUMOR_REGISTRY OMOP:4822266 Slots Name Description condition_provenance A value representing the provenance of the Condition record procedure_provenance A value representing the provenance of the Procedure record Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: EHR_BILLING_DIAGNOSIS: text: EHR_BILLING_DIAGNOSIS meaning: OMOP:4822159 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT meaning: OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS: text: EHR_ENCOUNTER_DIAGNOSIS meaning: OMOP:4822160 EHR_EPISODE_ENTRY: text: EHR_EPISODE_ENTRY meaning: OMOP:4822135 EHR_PROBLEM_LIST_ENTRY: text: EHR_PROBLEM_LIST_ENTRY meaning: OMOP:4822121 FIRST_POSITION_CONDITION: text: FIRST_POSITION_CONDITION meaning: OMOP:4822128 NLP_DERIVED: text: NLP_DERIVED meaning: OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR: text: OBSERVATION_RECORDED_FROM_EHR meaning: OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION: text: PATIENT_SELF-REPORTED_CONDITION meaning: OMOP:4822157 PRIMARY_CONDITION: text: PRIMARY_CONDITION meaning: OMOP:4822127 REFERRAL_RECORD: text: REFERRAL_RECORD meaning: OMOP:4822125 SECONDARY_CONDITION: text: SECONDARY_CONDITION meaning: OMOP:4822129 TUMOR_REGISTRY: text: TUMOR_REGISTRY meaning: OMOP:4822266","title":"Enum: ProvenanceEnum"},{"location":"ProvenanceEnum/#enum-provenanceenum","text":"A constrained set of enumerative values containing the OMOP values for provenance. URI: ProvenanceEnum","title":"Enum: ProvenanceEnum"},{"location":"ProvenanceEnum/#permissible-values","text":"Value Meaning Description EHR_BILLING_DIAGNOSIS OMOP:4822159 EHR_CHIEF_COMPLAINT OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS OMOP:4822160 EHR_EPISODE_ENTRY OMOP:4822135 EHR_PROBLEM_LIST_ENTRY OMOP:4822121 FIRST_POSITION_CONDITION OMOP:4822128 NLP_DERIVED OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION OMOP:4822157 PRIMARY_CONDITION OMOP:4822127 REFERRAL_RECORD OMOP:4822125 SECONDARY_CONDITION OMOP:4822129 TUMOR_REGISTRY OMOP:4822266","title":"Permissible Values"},{"location":"ProvenanceEnum/#slots","text":"Name Description condition_provenance A value representing the provenance of the Condition record procedure_provenance A value representing the provenance of the Procedure record","title":"Slots"},{"location":"ProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ProvenanceEnum/#linkml-source","text":"name: ProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: EHR_BILLING_DIAGNOSIS: text: EHR_BILLING_DIAGNOSIS meaning: OMOP:4822159 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT meaning: OMOP:4822124 EHR_ENCOUNTER_DIAGNOSIS: text: EHR_ENCOUNTER_DIAGNOSIS meaning: OMOP:4822160 EHR_EPISODE_ENTRY: text: EHR_EPISODE_ENTRY meaning: OMOP:4822135 EHR_PROBLEM_LIST_ENTRY: text: EHR_PROBLEM_LIST_ENTRY meaning: OMOP:4822121 FIRST_POSITION_CONDITION: text: FIRST_POSITION_CONDITION meaning: OMOP:4822128 NLP_DERIVED: text: NLP_DERIVED meaning: OMOP:4822058 OBSERVATION_RECORDED_FROM_EHR: text: OBSERVATION_RECORDED_FROM_EHR meaning: OMOP:4822126 PATIENT_SELF-REPORTED_CONDITION: text: PATIENT_SELF-REPORTED_CONDITION meaning: OMOP:4822157 PRIMARY_CONDITION: text: PRIMARY_CONDITION meaning: OMOP:4822127 REFERRAL_RECORD: text: REFERRAL_RECORD meaning: OMOP:4822125 SECONDARY_CONDITION: text: SECONDARY_CONDITION meaning: OMOP:4822129 TUMOR_REGISTRY: text: TUMOR_REGISTRY meaning: OMOP:4822266","title":"LinkML Source"},{"location":"Quantity/","text":"Class: Quantity A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. URI: bdchm:Quantity classDiagram class Quantity Entity <|-- Quantity Quantity : id Quantity : unit Quantity --> UnitOfMeasurementEnum : unit Quantity : value_concept Quantity : value_decimal Inheritance Entity Quantity Slots Name Cardinality and Range Description Inheritance value_decimal 0..1 Decimal An amount, in the given units (if specified) direct value_concept 0..1 String A coded value representing a quantity (e direct unit 0..1 UnitOfMeasurementEnum A coded or free text (in the direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Procedure quantity range Quantity SpecimenCreationActivity quantity_collected range Quantity SpecimenProcessingActivity duration range Quantity SpecimenStorageActivity duration range Quantity Substance substance_quantity range Quantity ObservationValueQuantity value range Quantity Comments QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Quantity native bdchm:Quantity LinkML Source Direct name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: UnitOfMeasurementEnum required: false Induced name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Quantity domain_of: - Entity range: uriorcurie required: true","title":"Class: Quantity"},{"location":"Quantity/#class-quantity","text":"A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. URI: bdchm:Quantity classDiagram class Quantity Entity <|-- Quantity Quantity : id Quantity : unit Quantity --> UnitOfMeasurementEnum : unit Quantity : value_concept Quantity : value_decimal","title":"Class: Quantity"},{"location":"Quantity/#inheritance","text":"Entity Quantity","title":"Inheritance"},{"location":"Quantity/#slots","text":"Name Cardinality and Range Description Inheritance value_decimal 0..1 Decimal An amount, in the given units (if specified) direct value_concept 0..1 String A coded value representing a quantity (e direct unit 0..1 UnitOfMeasurementEnum A coded or free text (in the direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Quantity/#usages","text":"used by used in type used Procedure quantity range Quantity SpecimenCreationActivity quantity_collected range Quantity SpecimenProcessingActivity duration range Quantity SpecimenStorageActivity duration range Quantity Substance substance_quantity range Quantity ObservationValueQuantity value range Quantity","title":"Usages"},{"location":"Quantity/#comments","text":"QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate.","title":"Comments"},{"location":"Quantity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Quantity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Quantity/#mappings","text":"Mapping Type Mapped Value self bdchm:Quantity native bdchm:Quantity","title":"Mappings"},{"location":"Quantity/#linkml-source","text":"","title":"LinkML Source"},{"location":"Quantity/#direct","text":"name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: UnitOfMeasurementEnum required: false","title":"Direct"},{"location":"Quantity/#induced","text":"name: Quantity description: A structured object to represent an amount of something (e.g., weight, mass, length, duration of time) - including a value and unit. comments: - QuantityMeasure may be implemented as an Observation-like object that will let us capture any type of measure of the amount of some substance (e.g. \"weight\", \"volume\"), with distinct timestamps and methods associated. It could be implemented as a \"simple\" observation (one measurement per instance, where the \"code\" fields is bound to a value set describing the different types of quantity measures allowed - e.g. \"weight\", \"volume\", \"concentration\"), or as \"composite\" observation (multiple measurements possible in a single instance, each captured as a component defined to hold a specific type of quantity measure - e.g. \"weight\", \"volume\", \"concentration\"). The number of different quantity measures we anticipate needed to support, and the potential for data sparseness, are factors that determine whether a simple or composite Observation would be most appropriate. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: value_decimal: name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false value_concept: name: value_concept description: A coded value representing a quantity (e.g. \"Adjacent (< or = 2cm)\") from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false unit: name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Quantity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Questionnaire/","text":"Class: Questionnaire A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) URI: bdchm:Questionnaire classDiagram class Questionnaire Entity <|-- Questionnaire Questionnaire : copyright Questionnaire : copyright_label Questionnaire : description Questionnaire : id Questionnaire : identity Questionnaire : items Questionnaire --> QuestionnaireItem : items Questionnaire : language Questionnaire : name Questionnaire : publisher Questionnaire : title Questionnaire : url Questionnaire : version Inheritance Entity Questionnaire Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String Name for this Questionnaire (computer friendly) direct title 0..1 String Name for this Questionnaire (human friendly) direct description 0..1 String Natural language description of the Questionnaire direct url 0..1 Uriorcurie Canonical identifier for this Questionnaire, represented as an absolute URI (... direct version 0..1 String The identifier that is used to identify this version of the questionnaire whe... direct publisher 0..1 String Name of the publisher/steward (organization or individual) of this Questionna... direct copyright 0..1 String Textual description of any use and/or publishing restrictions direct copyright_label 0..1 String Copyright holder and year(s) direct language 0..* String The language(s) in which questions are presented direct items 1..* QuestionnaireItem A collection of QuestionnaireItem objects which encapsulate the question bein... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Questionnaire native bdchm:Questionnaire LinkML Source Direct name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: QuestionnaireItem required: true Induced name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Questionnaire domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: Questionnaire domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: url owner: Questionnaire domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: publisher owner: Questionnaire domain_of: - Questionnaire range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: language owner: Questionnaire domain_of: - Questionnaire range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: items owner: Questionnaire domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireItem required: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Questionnaire domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Questionnaire domain_of: - Entity range: uriorcurie required: true","title":"Class: Questionnaire"},{"location":"Questionnaire/#class-questionnaire","text":"A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) URI: bdchm:Questionnaire classDiagram class Questionnaire Entity <|-- Questionnaire Questionnaire : copyright Questionnaire : copyright_label Questionnaire : description Questionnaire : id Questionnaire : identity Questionnaire : items Questionnaire --> QuestionnaireItem : items Questionnaire : language Questionnaire : name Questionnaire : publisher Questionnaire : title Questionnaire : url Questionnaire : version","title":"Class: Questionnaire"},{"location":"Questionnaire/#inheritance","text":"Entity Questionnaire","title":"Inheritance"},{"location":"Questionnaire/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String Name for this Questionnaire (computer friendly) direct title 0..1 String Name for this Questionnaire (human friendly) direct description 0..1 String Natural language description of the Questionnaire direct url 0..1 Uriorcurie Canonical identifier for this Questionnaire, represented as an absolute URI (... direct version 0..1 String The identifier that is used to identify this version of the questionnaire whe... direct publisher 0..1 String Name of the publisher/steward (organization or individual) of this Questionna... direct copyright 0..1 String Textual description of any use and/or publishing restrictions direct copyright_label 0..1 String Copyright holder and year(s) direct language 0..* String The language(s) in which questions are presented direct items 1..* QuestionnaireItem A collection of QuestionnaireItem objects which encapsulate the question bein... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Questionnaire/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Questionnaire/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Questionnaire/#mappings","text":"Mapping Type Mapped Value self bdchm:Questionnaire native bdchm:Questionnaire","title":"Mappings"},{"location":"Questionnaire/#linkml-source","text":"","title":"LinkML Source"},{"location":"Questionnaire/#direct","text":"name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: QuestionnaireItem required: true","title":"Direct"},{"location":"Questionnaire/#induced","text":"name: Questionnaire description: A Questionnaire is an organized collection of questions intended to solicit information from patients, providers or other individuals involved in the healthcare domain. They may be simple flat lists of questions or can be hierarchically organized in groups and sub-groups, each containing questions. The Questionnaire defines the questions to be asked, how they are ordered and grouped, any intervening instructional text and what the constraints are on the allowed answers. The results of a Questionnaire can be communicated using the QuestionnaireResponse. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: Name for this Questionnaire (computer friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: Questionnaire domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string title: name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string description: name: description description: Natural language description of the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: Questionnaire domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string url: name: url description: Canonical identifier for this Questionnaire, represented as an absolute URI (globally unique) from_schema: https://w3id.org/nhlbidatastage/bdchm alias: url owner: Questionnaire domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie version: name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string publisher: name: publisher description: Name of the publisher/steward (organization or individual) of this Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: publisher owner: Questionnaire domain_of: - Questionnaire range: string copyright: name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string copyright_label: name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string language: name: language description: The language(s) in which questions are presented. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: language owner: Questionnaire domain_of: - Questionnaire range: string items: name: items description: A collection of QuestionnaireItem objects which encapsulate the question being asked. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: items owner: Questionnaire domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireItem required: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Questionnaire domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Questionnaire domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"QuestionnaireItem/","text":"Class: QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire URI: bdchm:QuestionnaireItem classDiagram class QuestionnaireItem Entity <|-- QuestionnaireItem QuestionnaireItem : code QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : part_of QuestionnaireItem --> QuestionnaireItem : part_of QuestionnaireItem : text Inheritance Entity QuestionnaireItem Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct text 0..1 String Name for group or question text direct code 0..1 String Corresponding concept for this item in a terminology direct part_of 0..1 QuestionnaireItem A reference to a parent QuestionnaireItem direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Questionnaire items range QuestionnaireItem QuestionnaireItem part_of range QuestionnaireItem QuestionnaireResponseItem has_questionnaire_item range QuestionnaireItem Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireItem native bdchm:QuestionnaireItem LinkML Source Direct name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm range: QuestionnaireItem Induced name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: text owner: QuestionnaireItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: part_of owner: QuestionnaireItem domain_of: - ResearchStudy - QuestionnaireItem range: QuestionnaireItem identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: QuestionnaireItem domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireItem domain_of: - Entity range: uriorcurie required: true","title":"Class: QuestionnaireItem"},{"location":"QuestionnaireItem/#class-questionnaireitem","text":"QuestionnaireItem defines a question or section within the Questionnaire URI: bdchm:QuestionnaireItem classDiagram class QuestionnaireItem Entity <|-- QuestionnaireItem QuestionnaireItem : code QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : part_of QuestionnaireItem --> QuestionnaireItem : part_of QuestionnaireItem : text","title":"Class: QuestionnaireItem"},{"location":"QuestionnaireItem/#inheritance","text":"Entity QuestionnaireItem","title":"Inheritance"},{"location":"QuestionnaireItem/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct text 0..1 String Name for group or question text direct code 0..1 String Corresponding concept for this item in a terminology direct part_of 0..1 QuestionnaireItem A reference to a parent QuestionnaireItem direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"QuestionnaireItem/#usages","text":"used by used in type used Questionnaire items range QuestionnaireItem QuestionnaireItem part_of range QuestionnaireItem QuestionnaireResponseItem has_questionnaire_item range QuestionnaireItem","title":"Usages"},{"location":"QuestionnaireItem/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireItem/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireItem/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireItem native bdchm:QuestionnaireItem","title":"Mappings"},{"location":"QuestionnaireItem/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireItem/#direct","text":"name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm range: QuestionnaireItem","title":"Direct"},{"location":"QuestionnaireItem/#induced","text":"name: QuestionnaireItem description: QuestionnaireItem defines a question or section within the Questionnaire from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: text owner: QuestionnaireItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string code: name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string part_of: name: part_of description: A reference to a parent QuestionnaireItem. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: part_of owner: QuestionnaireItem domain_of: - ResearchStudy - QuestionnaireItem range: QuestionnaireItem identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: QuestionnaireItem domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireItem domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"QuestionnaireResponse/","text":"Class: QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponse classDiagram class QuestionnaireResponse Entity <|-- QuestionnaireResponse QuestionnaireResponse : age_at_response QuestionnaireResponse : associated_visit QuestionnaireResponse --> Visit : associated_visit QuestionnaireResponse : id QuestionnaireResponse : items QuestionnaireResponse --> QuestionnaireResponseItem : items Inheritance Entity QuestionnaireResponse Slots Name Cardinality and Range Description Inheritance age_at_response 0..1 Integer The age (in days) of the Participant when the QuestionnaireResponse was captu... direct items 1..* QuestionnaireResponseItem A collection of QuestionnaireResponseItem objects which encapsulate the quest... direct associated_visit 0..1 Visit A reference to the Visit during which this QuestionnaireResponse was captured direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponse native bdchm:QuestionnaireResponse LinkML Source Direct name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Visit Induced name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_response owner: QuestionnaireResponse domain_of: - QuestionnaireResponse range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: items owner: QuestionnaireResponse domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_visit owner: QuestionnaireResponse domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireResponse domain_of: - Entity range: uriorcurie required: true","title":"Class: QuestionnaireResponse"},{"location":"QuestionnaireResponse/#class-questionnaireresponse","text":"QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponse classDiagram class QuestionnaireResponse Entity <|-- QuestionnaireResponse QuestionnaireResponse : age_at_response QuestionnaireResponse : associated_visit QuestionnaireResponse --> Visit : associated_visit QuestionnaireResponse : id QuestionnaireResponse : items QuestionnaireResponse --> QuestionnaireResponseItem : items","title":"Class: QuestionnaireResponse"},{"location":"QuestionnaireResponse/#inheritance","text":"Entity QuestionnaireResponse","title":"Inheritance"},{"location":"QuestionnaireResponse/#slots","text":"Name Cardinality and Range Description Inheritance age_at_response 0..1 Integer The age (in days) of the Participant when the QuestionnaireResponse was captu... direct items 1..* QuestionnaireResponseItem A collection of QuestionnaireResponseItem objects which encapsulate the quest... direct associated_visit 0..1 Visit A reference to the Visit during which this QuestionnaireResponse was captured direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"QuestionnaireResponse/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponse/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponse/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponse native bdchm:QuestionnaireResponse","title":"Mappings"},{"location":"QuestionnaireResponse/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponse/#direct","text":"name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: Visit","title":"Direct"},{"location":"QuestionnaireResponse/#induced","text":"name: QuestionnaireResponse description: QuestionnaireResponse provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: age_at_response: name: age_at_response description: The age (in days) of the Participant when the QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_response owner: QuestionnaireResponse domain_of: - QuestionnaireResponse range: integer unit: ucum_code: d items: name: items description: A collection of QuestionnaireResponseItem objects which encapsulate the question being asked and the response. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: items owner: QuestionnaireResponse domain_of: - Questionnaire - QuestionnaireResponse range: QuestionnaireResponseItem required: true associated_visit: name: associated_visit description: A reference to the Visit during which this QuestionnaireResponse was captured. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_visit owner: QuestionnaireResponse domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: QuestionnaireResponse domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"QuestionnaireResponseItem/","text":"Class: QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponseItem classDiagram class QuestionnaireResponseItem QuestionnaireResponseItem : has_questionnaire_item QuestionnaireResponseItem --> QuestionnaireItem : has_questionnaire_item QuestionnaireResponseItem : response_value QuestionnaireResponseItem --> QuestionnaireResponseValue : response_value QuestionnaireResponseItem : text Slots Name Cardinality and Range Description Inheritance has_questionnaire_item 0..1 QuestionnaireItem A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... direct text 0..1 String Name for group or question text direct response_value 1..1 QuestionnaireResponseValue direct Usages used by used in type used QuestionnaireResponse items range QuestionnaireResponseItem Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseItem native bdchm:QuestionnaireResponseItem LinkML Source Direct name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireResponseValue required: true Induced name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm alias: text owner: QuestionnaireResponseItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: response_value owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"Class: QuestionnaireResponseItem"},{"location":"QuestionnaireResponseItem/#class-questionnaireresponseitem","text":"QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) URI: bdchm:QuestionnaireResponseItem classDiagram class QuestionnaireResponseItem QuestionnaireResponseItem : has_questionnaire_item QuestionnaireResponseItem --> QuestionnaireItem : has_questionnaire_item QuestionnaireResponseItem : response_value QuestionnaireResponseItem --> QuestionnaireResponseValue : response_value QuestionnaireResponseItem : text","title":"Class: QuestionnaireResponseItem"},{"location":"QuestionnaireResponseItem/#slots","text":"Name Cardinality and Range Description Inheritance has_questionnaire_item 0..1 QuestionnaireItem A reference to the QuestionnaireItem that this QuestionnaireResponseItem resp... direct text 0..1 String Name for group or question text direct response_value 1..1 QuestionnaireResponseValue direct","title":"Slots"},{"location":"QuestionnaireResponseItem/#usages","text":"used by used in type used QuestionnaireResponse items range QuestionnaireResponseItem","title":"Usages"},{"location":"QuestionnaireResponseItem/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseItem/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseItem/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseItem native bdchm:QuestionnaireResponseItem","title":"Mappings"},{"location":"QuestionnaireResponseItem/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseItem/#direct","text":"name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: QuestionnaireResponseValue required: true","title":"Direct"},{"location":"QuestionnaireResponseItem/#induced","text":"name: QuestionnaireResponseItem description: QuestionnaireResponseItem provides a complete or partial list of answers to a set of questions filled when responding to a questionnaire. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: has_questionnaire_item: name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem text: name: text description: Name for group or question text from_schema: https://w3id.org/nhlbidatastage/bdchm alias: text owner: QuestionnaireResponseItem domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string response_value: name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: response_value owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"Induced"},{"location":"QuestionnaireResponseValue/","text":"Class: QuestionnaireResponseValue Single-valued answer to the question. (FHIR) NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:QuestionnaireResponseValue classDiagram class QuestionnaireResponseValue QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValue : name QuestionnaireResponseValue : type QuestionnaireResponseValue : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueDecimal QuestionnaireResponseValueBoolean QuestionnaireResponseValueInteger QuestionnaireResponseValueTimePoint QuestionnaireResponseValueString Slots Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct Usages used by used in type used QuestionnaireResponseItem response_value range QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValue native bdchm:QuestionnaireResponseValue LinkML Source Direct name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string Induced name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Class: QuestionnaireResponseValue"},{"location":"QuestionnaireResponseValue/#class-questionnaireresponsevalue","text":"Single-valued answer to the question. (FHIR) NOTE : this is an abstract class and should not be instantiated directly URI: bdchm:QuestionnaireResponseValue classDiagram class QuestionnaireResponseValue QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValue : name QuestionnaireResponseValue : type QuestionnaireResponseValue : value","title":"Class: QuestionnaireResponseValue"},{"location":"QuestionnaireResponseValue/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueDecimal QuestionnaireResponseValueBoolean QuestionnaireResponseValueInteger QuestionnaireResponseValueTimePoint QuestionnaireResponseValueString","title":"Inheritance"},{"location":"QuestionnaireResponseValue/#slots","text":"Name Cardinality and Range Description Inheritance value 0..1 String A general slot to hold a value direct type 0..1 String direct name 0..1 String direct","title":"Slots"},{"location":"QuestionnaireResponseValue/#usages","text":"used by used in type used QuestionnaireResponseItem response_value range QuestionnaireResponseValue","title":"Usages"},{"location":"QuestionnaireResponseValue/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValue/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValue/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValue native bdchm:QuestionnaireResponseValue","title":"Mappings"},{"location":"QuestionnaireResponseValue/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValue/#direct","text":"name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true slots: - value attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm range: string","title":"Direct"},{"location":"QuestionnaireResponseValue/#induced","text":"name: QuestionnaireResponseValue description: Single-valued answer to the question. (FHIR) from_schema: https://w3id.org/nhlbidatastage/bdchm abstract: true attributes: type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValue domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValue domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueBoolean/","text":"Class: QuestionnaireResponseValueBoolean Single-valued boolean answer to the question URI: bdchm:QuestionnaireResponseValueBoolean classDiagram class QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValueBoolean : name QuestionnaireResponseValueBoolean : type QuestionnaireResponseValueBoolean : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueBoolean Slots Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueBoolean native bdchm:QuestionnaireResponseValueBoolean LinkML Source Direct name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true Induced name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueBoolean"},{"location":"QuestionnaireResponseValueBoolean/#class-questionnaireresponsevalueboolean","text":"Single-valued boolean answer to the question URI: bdchm:QuestionnaireResponseValueBoolean classDiagram class QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValueBoolean : name QuestionnaireResponseValueBoolean : type QuestionnaireResponseValueBoolean : value","title":"Class: QuestionnaireResponseValueBoolean"},{"location":"QuestionnaireResponseValueBoolean/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueBoolean","title":"Inheritance"},{"location":"QuestionnaireResponseValueBoolean/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Boolean A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueBoolean/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueBoolean/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueBoolean/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueBoolean native bdchm:QuestionnaireResponseValueBoolean","title":"Mappings"},{"location":"QuestionnaireResponseValueBoolean/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueBoolean/#direct","text":"name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true","title":"Direct"},{"location":"QuestionnaireResponseValueBoolean/#induced","text":"name: QuestionnaireResponseValueBoolean description: Single-valued boolean answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: boolean required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueBoolean domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueBoolean domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueDecimal/","text":"Class: QuestionnaireResponseValueDecimal Single-valued decimal answer to the question URI: bdchm:QuestionnaireResponseValueDecimal classDiagram class QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValueDecimal : name QuestionnaireResponseValueDecimal : type QuestionnaireResponseValueDecimal : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueDecimal Slots Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueDecimal native bdchm:QuestionnaireResponseValueDecimal LinkML Source Direct name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true Induced name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueDecimal"},{"location":"QuestionnaireResponseValueDecimal/#class-questionnaireresponsevaluedecimal","text":"Single-valued decimal answer to the question URI: bdchm:QuestionnaireResponseValueDecimal classDiagram class QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValueDecimal : name QuestionnaireResponseValueDecimal : type QuestionnaireResponseValueDecimal : value","title":"Class: QuestionnaireResponseValueDecimal"},{"location":"QuestionnaireResponseValueDecimal/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueDecimal","title":"Inheritance"},{"location":"QuestionnaireResponseValueDecimal/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Decimal A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueDecimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueDecimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueDecimal/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueDecimal native bdchm:QuestionnaireResponseValueDecimal","title":"Mappings"},{"location":"QuestionnaireResponseValueDecimal/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueDecimal/#direct","text":"name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true","title":"Direct"},{"location":"QuestionnaireResponseValueDecimal/#induced","text":"name: QuestionnaireResponseValueDecimal description: Single-valued decimal answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: decimal required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueDecimal domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueDecimal domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueInteger/","text":"Class: QuestionnaireResponseValueInteger Single-valued integer answer to the question URI: bdchm:QuestionnaireResponseValueInteger classDiagram class QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValueInteger : name QuestionnaireResponseValueInteger : type QuestionnaireResponseValueInteger : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueInteger Slots Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueInteger native bdchm:QuestionnaireResponseValueInteger LinkML Source Direct name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true Induced name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueInteger"},{"location":"QuestionnaireResponseValueInteger/#class-questionnaireresponsevalueinteger","text":"Single-valued integer answer to the question URI: bdchm:QuestionnaireResponseValueInteger classDiagram class QuestionnaireResponseValueInteger QuestionnaireResponseValue <|-- QuestionnaireResponseValueInteger QuestionnaireResponseValueInteger : name QuestionnaireResponseValueInteger : type QuestionnaireResponseValueInteger : value","title":"Class: QuestionnaireResponseValueInteger"},{"location":"QuestionnaireResponseValueInteger/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueInteger","title":"Inheritance"},{"location":"QuestionnaireResponseValueInteger/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 Integer A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueInteger/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueInteger/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueInteger/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueInteger native bdchm:QuestionnaireResponseValueInteger","title":"Mappings"},{"location":"QuestionnaireResponseValueInteger/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueInteger/#direct","text":"name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true","title":"Direct"},{"location":"QuestionnaireResponseValueInteger/#induced","text":"name: QuestionnaireResponseValueInteger description: Single-valued integer answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: integer required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueInteger domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueInteger domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueString/","text":"Class: QuestionnaireResponseValueString Single-valued string answer to the question URI: bdchm:QuestionnaireResponseValueString classDiagram class QuestionnaireResponseValueString QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValueString : name QuestionnaireResponseValueString : type QuestionnaireResponseValueString : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueString Slots Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueString native bdchm:QuestionnaireResponseValueString LinkML Source Direct name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true Induced name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueString"},{"location":"QuestionnaireResponseValueString/#class-questionnaireresponsevaluestring","text":"Single-valued string answer to the question URI: bdchm:QuestionnaireResponseValueString classDiagram class QuestionnaireResponseValueString QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireResponseValueString : name QuestionnaireResponseValueString : type QuestionnaireResponseValueString : value","title":"Class: QuestionnaireResponseValueString"},{"location":"QuestionnaireResponseValueString/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueString","title":"Inheritance"},{"location":"QuestionnaireResponseValueString/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 String A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueString/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueString/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueString/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueString native bdchm:QuestionnaireResponseValueString","title":"Mappings"},{"location":"QuestionnaireResponseValueString/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueString/#direct","text":"name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true","title":"Direct"},{"location":"QuestionnaireResponseValueString/#induced","text":"name: QuestionnaireResponseValueString description: Single-valued string answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueString domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueString domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"QuestionnaireResponseValueTimePoint/","text":"Class: QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question URI: bdchm:QuestionnaireResponseValueTimePoint classDiagram class QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValueTimePoint : name QuestionnaireResponseValueTimePoint : type QuestionnaireResponseValueTimePoint : value QuestionnaireResponseValueTimePoint --> TimePoint : value Inheritance QuestionnaireResponseValue QuestionnaireResponseValueTimePoint Slots Name Cardinality and Range Description Inheritance value 1..1 TimePoint A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueTimePoint native bdchm:QuestionnaireResponseValueTimePoint LinkML Source Direct name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true Induced name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueTimePoint domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Class: QuestionnaireResponseValueTimePoint"},{"location":"QuestionnaireResponseValueTimePoint/#class-questionnaireresponsevaluetimepoint","text":"Single-valued TimePoint answer to the question URI: bdchm:QuestionnaireResponseValueTimePoint classDiagram class QuestionnaireResponseValueTimePoint QuestionnaireResponseValue <|-- QuestionnaireResponseValueTimePoint QuestionnaireResponseValueTimePoint : name QuestionnaireResponseValueTimePoint : type QuestionnaireResponseValueTimePoint : value QuestionnaireResponseValueTimePoint --> TimePoint : value","title":"Class: QuestionnaireResponseValueTimePoint"},{"location":"QuestionnaireResponseValueTimePoint/#inheritance","text":"QuestionnaireResponseValue QuestionnaireResponseValueTimePoint","title":"Inheritance"},{"location":"QuestionnaireResponseValueTimePoint/#slots","text":"Name Cardinality and Range Description Inheritance value 1..1 TimePoint A general slot to hold a value QuestionnaireResponseValue type 0..1 String QuestionnaireResponseValue name 0..1 String QuestionnaireResponseValue","title":"Slots"},{"location":"QuestionnaireResponseValueTimePoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"QuestionnaireResponseValueTimePoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"QuestionnaireResponseValueTimePoint/#mappings","text":"Mapping Type Mapped Value self bdchm:QuestionnaireResponseValueTimePoint native bdchm:QuestionnaireResponseValueTimePoint","title":"Mappings"},{"location":"QuestionnaireResponseValueTimePoint/#linkml-source","text":"","title":"LinkML Source"},{"location":"QuestionnaireResponseValueTimePoint/#direct","text":"name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true","title":"Direct"},{"location":"QuestionnaireResponseValueTimePoint/#induced","text":"name: QuestionnaireResponseValueTimePoint description: Single-valued TimePoint answer to the question from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: QuestionnaireResponseValue slot_usage: value: name: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true attributes: value: name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: TimePoint required: true type: name: type from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 designates_type: true alias: type owner: QuestionnaireResponseValueTimePoint domain_of: - QuestionnaireResponseValue - ObservationValue range: string name: name: name from_schema: https://w3id.org/nhlbidatastage/bdchm alias: name owner: QuestionnaireResponseValueTimePoint domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string","title":"Induced"},{"location":"RaceEnum/","text":"Enum: RaceEnum A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. URI: RaceEnum Permissible Values Value Meaning Description AMERICAN_INDIAN_OR_ALASKA_NATIVE OMOP:8657 A person having origins in any of the original peoples of North and South Ame... ASIAN OMOP:8515 A person having origins in any of the original peoples of the Far East, South... BLACK_OR_AFRICAN_AMERICAN OMOP:8516 A person having origins in any of the Black racial groups of Africa NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER OMOP:8557 Denotes a person having origins in any of the original peoples of Hawaii, Gua... UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused WHITE OMOP:8527 Denotes person with European, Middle Eastern, or North African ancestral orig... Slots Name Description race An arbitrary classification of a taxonomic group that is a division of a spec... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: RaceEnum description: A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: text: AMERICAN_INDIAN_OR_ALASKA_NATIVE description: A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB) meaning: OMOP:8657 ASIAN: text: ASIAN description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) meaning: OMOP:8515 BLACK_OR_AFRICAN_AMERICAN: text: BLACK_OR_AFRICAN_AMERICAN description: A person having origins in any of the Black racial groups of Africa. Terms such as \"Haitian\" or \"Negro\" can be used in addition to \"Black or African American\". (OMB) meaning: OMOP:8516 NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: text: NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER description: Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuukese (Trukese), Fijian, Kosraean, Melanesian, Micronesian, Northern Mariana Islander, Palauan, Papua New Guinean, Pohnpeian, Polynesian, Solomon Islander, Tahitian, Tokelauan, Tongan, Yapese, or Pacific Islander, not specified. meaning: OMOP:8557 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552 WHITE: text: WHITE description: Denotes person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. meaning: OMOP:8527","title":"Enum: RaceEnum"},{"location":"RaceEnum/#enum-raceenum","text":"A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. URI: RaceEnum","title":"Enum: RaceEnum"},{"location":"RaceEnum/#permissible-values","text":"Value Meaning Description AMERICAN_INDIAN_OR_ALASKA_NATIVE OMOP:8657 A person having origins in any of the original peoples of North and South Ame... ASIAN OMOP:8515 A person having origins in any of the original peoples of the Far East, South... BLACK_OR_AFRICAN_AMERICAN OMOP:8516 A person having origins in any of the Black racial groups of Africa NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER OMOP:8557 Denotes a person having origins in any of the original peoples of Hawaii, Gua... UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused WHITE OMOP:8527 Denotes person with European, Middle Eastern, or North African ancestral orig...","title":"Permissible Values"},{"location":"RaceEnum/#slots","text":"Name Description race An arbitrary classification of a taxonomic group that is a division of a spec...","title":"Slots"},{"location":"RaceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"RaceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"RaceEnum/#linkml-source","text":"name: RaceEnum description: A constrained set of enumerative values containing the United States Office of Management and Budget (OMB) values for race. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: AMERICAN_INDIAN_OR_ALASKA_NATIVE: text: AMERICAN_INDIAN_OR_ALASKA_NATIVE description: A person having origins in any of the original peoples of North and South America (including Central America) and who maintains tribal affiliation or community attachment. (OMB) meaning: OMOP:8657 ASIAN: text: ASIAN description: A person having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent, including for example, Cambodia, China, India, Japan, Korea, Malaysia, Pakistan, the Philippine Islands, Thailand, and Vietnam. (OMB) meaning: OMOP:8515 BLACK_OR_AFRICAN_AMERICAN: text: BLACK_OR_AFRICAN_AMERICAN description: A person having origins in any of the Black racial groups of Africa. Terms such as \"Haitian\" or \"Negro\" can be used in addition to \"Black or African American\". (OMB) meaning: OMOP:8516 NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER: text: NATIVE_HAWAIIAN_OR_OTHER_PACIFIC_ISLANDER description: Denotes a person having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. The term covers particularly people who identify themselves as part-Hawaiian, Native Hawaiian, Guamanian or Chamorro, Carolinian, Samoan, Chuukese (Trukese), Fijian, Kosraean, Melanesian, Micronesian, Northern Mariana Islander, Palauan, Papua New Guinean, Pohnpeian, Polynesian, Solomon Islander, Tahitian, Tokelauan, Tongan, Yapese, or Pacific Islander, not specified. meaning: OMOP:8557 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552 WHITE: text: WHITE description: Denotes person with European, Middle Eastern, or North African ancestral origin who identifies, or is identified, as White. meaning: OMOP:8527","title":"LinkML Source"},{"location":"ResearchStudy/","text":"Class: ResearchStudy A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. URI: bdchm:ResearchStudy classDiagram class ResearchStudy Entity <|-- ResearchStudy ResearchStudy : associated_timepoint ResearchStudy --> TimePoint : associated_timepoint ResearchStudy : consents ResearchStudy --> Consent : consents ResearchStudy : date_ended ResearchStudy --> TimePoint : date_ended ResearchStudy : date_started ResearchStudy --> TimePoint : date_started ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : part_of ResearchStudy --> ResearchStudy : part_of ResearchStudy : principal_investigator ResearchStudy : research_project_type ResearchStudy : sponsor ResearchStudy : url Inheritance Entity ResearchStudy Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String An unabridged name of a research program, project, or study direct name_shortened 0..1 String An abbreviated name of a research program, project, or study direct description 0..1 String An unabridged description of a research program, project, or study direct description_shortened 0..1 String An abbreviated description of a research program, project, or study direct sponsor 0..1 String An entity that is responsible for the initiation, management, and/or financin... direct date_started 0..1 TimePoint The date when the research project began direct date_ended 0..1 TimePoint The date when the research project ended direct url 0..1 Uriorcurie A URL address for a resource that provides information about a research progr... direct part_of 0..1 ResearchStudy A reference to a parent ResearchStudy (e direct research_project_type 0..1 String The 'type' of ResearchStudy represented (e direct associated_timepoint 0..* TimePoint A collection of timepoint observations that are relevant to research projects... direct principal_investigator 0..* String The investigator or investigators leading a project direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Participant member_of_research_study range ResearchStudy ResearchStudy part_of range ResearchStudy ResearchStudyCollection entries range ResearchStudy Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ResearchStudy native bdchm:ResearchStudy LinkML Source Direct name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Consent Induced name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name owner: ResearchStudy domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: ResearchStudy domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_started owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_ended owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: url owner: ResearchStudy domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: part_of owner: ResearchStudy domain_of: - ResearchStudy - QuestionnaireItem range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: principal_investigator owner: ResearchStudy domain_of: - ResearchStudy range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: consents owner: ResearchStudy domain_of: - Participant - ResearchStudy range: Consent identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: ResearchStudy domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ResearchStudy domain_of: - Entity range: uriorcurie required: true","title":"Class: ResearchStudy"},{"location":"ResearchStudy/#class-researchstudy","text":"A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. URI: bdchm:ResearchStudy classDiagram class ResearchStudy Entity <|-- ResearchStudy ResearchStudy : associated_timepoint ResearchStudy --> TimePoint : associated_timepoint ResearchStudy : consents ResearchStudy --> Consent : consents ResearchStudy : date_ended ResearchStudy --> TimePoint : date_ended ResearchStudy : date_started ResearchStudy --> TimePoint : date_started ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : part_of ResearchStudy --> ResearchStudy : part_of ResearchStudy : principal_investigator ResearchStudy : research_project_type ResearchStudy : sponsor ResearchStudy : url","title":"Class: ResearchStudy"},{"location":"ResearchStudy/#inheritance","text":"Entity ResearchStudy","title":"Inheritance"},{"location":"ResearchStudy/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct name 0..1 String An unabridged name of a research program, project, or study direct name_shortened 0..1 String An abbreviated name of a research program, project, or study direct description 0..1 String An unabridged description of a research program, project, or study direct description_shortened 0..1 String An abbreviated description of a research program, project, or study direct sponsor 0..1 String An entity that is responsible for the initiation, management, and/or financin... direct date_started 0..1 TimePoint The date when the research project began direct date_ended 0..1 TimePoint The date when the research project ended direct url 0..1 Uriorcurie A URL address for a resource that provides information about a research progr... direct part_of 0..1 ResearchStudy A reference to a parent ResearchStudy (e direct research_project_type 0..1 String The 'type' of ResearchStudy represented (e direct associated_timepoint 0..* TimePoint A collection of timepoint observations that are relevant to research projects... direct principal_investigator 0..* String The investigator or investigators leading a project direct consents 0..* Consent Data Use Restrictions that are used to indicate permissions/restrictions for ... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"ResearchStudy/#usages","text":"used by used in type used Participant member_of_research_study range ResearchStudy ResearchStudy part_of range ResearchStudy ResearchStudyCollection entries range ResearchStudy","title":"Usages"},{"location":"ResearchStudy/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ResearchStudy/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ResearchStudy/#mappings","text":"Mapping Type Mapped Value self bdchm:ResearchStudy native bdchm:ResearchStudy","title":"Mappings"},{"location":"ResearchStudy/#linkml-source","text":"","title":"LinkML Source"},{"location":"ResearchStudy/#direct","text":"name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Consent","title":"Direct"},{"location":"ResearchStudy/#induced","text":"name: ResearchStudy description: A process where a researcher or organization plans and then executes a series of steps intended to increase the field of healthcare-related knowledge. This includes studies of safety, efficacy, comparative effectiveness and other information about medications, devices, therapies and other interventional and investigative techniques. A ResearchStudy involves the gathering of information about human or animal subjects. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: name: name: name description: An unabridged name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name owner: ResearchStudy domain_of: - ResearchStudy - Organization - Questionnaire - QuestionnaireResponseValue - ObservationValue range: string name_shortened: name: name_shortened description: An abbreviated name of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: name_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string description: name: description description: An unabridged description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: description owner: ResearchStudy domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string description_shortened: name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string sponsor: name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string date_started: name: date_started description: The date when the research project began. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_started owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint date_ended: name: date_ended description: The date when the research project ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_ended owner: ResearchStudy domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint url: name: url description: A URL address for a resource that provides information about a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: url owner: ResearchStudy domain_of: - ResearchStudy - Questionnaire - Document range: uriorcurie part_of: name: part_of description: A reference to a parent ResearchStudy (e.g. a link to the overarching CPTAC ResearchStudy from a substudy of CPTAC) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: part_of owner: ResearchStudy domain_of: - ResearchStudy - QuestionnaireItem range: ResearchStudy research_project_type: name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string associated_timepoint: name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint principal_investigator: name: principal_investigator description: The investigator or investigators leading a project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: principal_investigator owner: ResearchStudy domain_of: - ResearchStudy range: string consents: name: consents description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: consents owner: ResearchStudy domain_of: - Participant - ResearchStudy range: Consent identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: ResearchStudy domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: ResearchStudy domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"ResearchStudyCollection/","text":"Class: ResearchStudyCollection A holder for ResearchStudy objects URI: bdchm:ResearchStudyCollection classDiagram class ResearchStudyCollection ResearchStudyCollection : entries ResearchStudyCollection --> ResearchStudy : entries Slots Name Cardinality and Range Description Inheritance entries 0..* ResearchStudy direct Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:ResearchStudyCollection native bdchm:ResearchStudyCollection LinkML Source Direct name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: ResearchStudy inlined: true tree_root: true Induced name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true tree_root: true","title":"Class: ResearchStudyCollection"},{"location":"ResearchStudyCollection/#class-researchstudycollection","text":"A holder for ResearchStudy objects URI: bdchm:ResearchStudyCollection classDiagram class ResearchStudyCollection ResearchStudyCollection : entries ResearchStudyCollection --> ResearchStudy : entries","title":"Class: ResearchStudyCollection"},{"location":"ResearchStudyCollection/#slots","text":"Name Cardinality and Range Description Inheritance entries 0..* ResearchStudy direct","title":"Slots"},{"location":"ResearchStudyCollection/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ResearchStudyCollection/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ResearchStudyCollection/#mappings","text":"Mapping Type Mapped Value self bdchm:ResearchStudyCollection native bdchm:ResearchStudyCollection","title":"Mappings"},{"location":"ResearchStudyCollection/#linkml-source","text":"","title":"LinkML Source"},{"location":"ResearchStudyCollection/#direct","text":"name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: ResearchStudy inlined: true tree_root: true","title":"Direct"},{"location":"ResearchStudyCollection/#induced","text":"name: ResearchStudyCollection description: A holder for ResearchStudy objects from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: entries: name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true tree_root: true","title":"Induced"},{"location":"SectionLocationEnum/","text":"Enum: SectionLocationEnum The location in a parent specimen from which a section/portion was excised. URI: SectionLocationEnum Permissible Values Value Meaning Description BOTTOM None The part of a specimen designated as its 'bottom' based on specified orientat... TOP None The part of a specimen designated as its 'top' based on specified orientation... UNKNOWN None An unknown location on a specimen Slots Name Description section_location The location in a parent specimen from which a section/portion was excised (e Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SectionLocationEnum description: The location in a parent specimen from which a section/portion was excised. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: BOTTOM: text: BOTTOM description: The part of a specimen designated as its 'bottom' based on specified orientation criteria. TOP: text: TOP description: The part of a specimen designated as its 'top' based on specified orientation criteria. UNKNOWN: text: UNKNOWN description: An unknown location on a specimen.","title":"Enum: SectionLocationEnum"},{"location":"SectionLocationEnum/#enum-sectionlocationenum","text":"The location in a parent specimen from which a section/portion was excised. URI: SectionLocationEnum","title":"Enum: SectionLocationEnum"},{"location":"SectionLocationEnum/#permissible-values","text":"Value Meaning Description BOTTOM None The part of a specimen designated as its 'bottom' based on specified orientat... TOP None The part of a specimen designated as its 'top' based on specified orientation... UNKNOWN None An unknown location on a specimen","title":"Permissible Values"},{"location":"SectionLocationEnum/#slots","text":"Name Description section_location The location in a parent specimen from which a section/portion was excised (e","title":"Slots"},{"location":"SectionLocationEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SectionLocationEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SectionLocationEnum/#linkml-source","text":"name: SectionLocationEnum description: The location in a parent specimen from which a section/portion was excised. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: BOTTOM: text: BOTTOM description: The part of a specimen designated as its 'bottom' based on specified orientation criteria. TOP: text: TOP description: The part of a specimen designated as its 'top' based on specified orientation criteria. UNKNOWN: text: UNKNOWN description: An unknown location on a specimen.","title":"LinkML Source"},{"location":"SexEnum/","text":"Enum: SexEnum A constrained set of enumerative values containing the OMOP values for sex. URI: SexEnum Permissible Values Value Meaning Description MALE OMOP:8507 A person who belongs to the sex that normally produces sperm FEMALE OMOP:8532 A person who belongs to the sex that normally produces ova UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused Slots Name Description sex The biologic character or quality that distinguishes male and female from one... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SexEnum description: A constrained set of enumerative values containing the OMOP values for sex. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: MALE: text: MALE description: A person who belongs to the sex that normally produces sperm. meaning: OMOP:8507 FEMALE: text: FEMALE description: A person who belongs to the sex that normally produces ova. meaning: OMOP:8532 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552","title":"Enum: SexEnum"},{"location":"SexEnum/#enum-sexenum","text":"A constrained set of enumerative values containing the OMOP values for sex. URI: SexEnum","title":"Enum: SexEnum"},{"location":"SexEnum/#permissible-values","text":"Value Meaning Description MALE OMOP:8507 A person who belongs to the sex that normally produces sperm FEMALE OMOP:8532 A person who belongs to the sex that normally produces ova UNKNOWN OMOP:8552 Not known, not observed, not recorded, or refused","title":"Permissible Values"},{"location":"SexEnum/#slots","text":"Name Description sex The biologic character or quality that distinguishes male and female from one...","title":"Slots"},{"location":"SexEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SexEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SexEnum/#linkml-source","text":"name: SexEnum description: A constrained set of enumerative values containing the OMOP values for sex. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: MALE: text: MALE description: A person who belongs to the sex that normally produces sperm. meaning: OMOP:8507 FEMALE: text: FEMALE description: A person who belongs to the sex that normally produces ova. meaning: OMOP:8532 UNKNOWN: text: UNKNOWN description: Not known, not observed, not recorded, or refused. meaning: OMOP:8552","title":"LinkML Source"},{"location":"SourceMaterialTypeEnum/","text":"Enum: SourceMaterialTypeEnum URI: SourceMaterialTypeEnum Permissible Values Value Meaning Description ADDITIONAL_METASTATIC None ADDITIONAL_NEW_PRIMARY None BENIGN_NEOPLASMS None BLOOD_DERIVED_CANCER_BONE_MARROW None BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT None BLOOD_DERIVED_LIQUID_BIOPSY None BLOOD_DERIVED_NORMAL None BONE_MARROW_NORMAL None BUCCAL_CELL_NORMAL None CELL_LINE_DERIVED_XENOGRAFT_TISSUE None CELL_LINES None CONTROL_ANALYTE None DNA None EBV_IMMORTALIZED_NORMAL None EXPANDED_NEXT_GENERATION_CANCER_MODEL None FFPE_RECURRENT None FFPE_SCROLLS None FIBROBLASTS_FROM_BONE_MARROW_NORMAL None GRANULOCYTES None HUMAN_TUMOR_ORIGINAL_CELLS None IN_SITU_NEOPLASMS None LYMPHOID_NORMAL None METASTATIC None MIXED_ADHERENT_SUSPENSION None MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL None NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR None NEXT_GENERATION_CANCER_MODEL None NORMAL_ADJACENT_TISSUE None PLEURAL_EFFUSION None POST_NEOADJUVANT_THERAPY None PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW None PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None PRIMARY_TUMOR None PRIMARY_XENOGRAFT_TISSUE None RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW None RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None RECURRENT_TUMOR None RNA None SALIVA None SLIDES None SOLID_TISSUE_NORMAL None TOTAL_RNA None TUMOR None TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY None XENOGRAFT_TISSUE None NOT_ALLOWED_TO_COLLECT None NOT_REPORTED None UNKNOWN None Slots Name Description source_material_type The general kind of material from which the specimen was derived Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SourceMaterialTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ADDITIONAL_METASTATIC: text: ADDITIONAL_METASTATIC ADDITIONAL_NEW_PRIMARY: text: ADDITIONAL_NEW_PRIMARY BENIGN_NEOPLASMS: text: BENIGN_NEOPLASMS BLOOD_DERIVED_CANCER_BONE_MARROW: text: BLOOD_DERIVED_CANCER_BONE_MARROW BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT BLOOD_DERIVED_LIQUID_BIOPSY: text: BLOOD_DERIVED_LIQUID_BIOPSY BLOOD_DERIVED_NORMAL: text: BLOOD_DERIVED_NORMAL BONE_MARROW_NORMAL: text: BONE_MARROW_NORMAL BUCCAL_CELL_NORMAL: text: BUCCAL_CELL_NORMAL CELL_LINE_DERIVED_XENOGRAFT_TISSUE: text: CELL_LINE_DERIVED_XENOGRAFT_TISSUE CELL_LINES: text: CELL_LINES CONTROL_ANALYTE: text: CONTROL_ANALYTE DNA: text: DNA EBV_IMMORTALIZED_NORMAL: text: EBV_IMMORTALIZED_NORMAL EXPANDED_NEXT_GENERATION_CANCER_MODEL: text: EXPANDED_NEXT_GENERATION_CANCER_MODEL FFPE_RECURRENT: text: FFPE_RECURRENT FFPE_SCROLLS: text: FFPE_SCROLLS FIBROBLASTS_FROM_BONE_MARROW_NORMAL: text: FIBROBLASTS_FROM_BONE_MARROW_NORMAL GRANULOCYTES: text: GRANULOCYTES HUMAN_TUMOR_ORIGINAL_CELLS: text: HUMAN_TUMOR_ORIGINAL_CELLS IN_SITU_NEOPLASMS: text: IN_SITU_NEOPLASMS LYMPHOID_NORMAL: text: LYMPHOID_NORMAL METASTATIC: text: METASTATIC MIXED_ADHERENT_SUSPENSION: text: MIXED_ADHERENT_SUSPENSION MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL: text: MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR: text: NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR NEXT_GENERATION_CANCER_MODEL: text: NEXT_GENERATION_CANCER_MODEL NORMAL_ADJACENT_TISSUE: text: NORMAL_ADJACENT_TISSUE PLEURAL_EFFUSION: text: PLEURAL_EFFUSION POST_NEOADJUVANT_THERAPY: text: POST_NEOADJUVANT_THERAPY PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW: text: PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD PRIMARY_TUMOR: text: PRIMARY_TUMOR PRIMARY_XENOGRAFT_TISSUE: text: PRIMARY_XENOGRAFT_TISSUE RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW: text: RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD RECURRENT_TUMOR: text: RECURRENT_TUMOR RNA: text: RNA SALIVA: text: SALIVA SLIDES: text: SLIDES SOLID_TISSUE_NORMAL: text: SOLID_TISSUE_NORMAL TOTAL_RNA: text: TOTAL_RNA TUMOR: text: TUMOR TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY: text: TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY XENOGRAFT_TISSUE: text: XENOGRAFT_TISSUE NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT NOT_REPORTED: text: NOT_REPORTED UNKNOWN: text: UNKNOWN","title":"Enum: SourceMaterialTypeEnum"},{"location":"SourceMaterialTypeEnum/#enum-sourcematerialtypeenum","text":"URI: SourceMaterialTypeEnum","title":"Enum: SourceMaterialTypeEnum"},{"location":"SourceMaterialTypeEnum/#permissible-values","text":"Value Meaning Description ADDITIONAL_METASTATIC None ADDITIONAL_NEW_PRIMARY None BENIGN_NEOPLASMS None BLOOD_DERIVED_CANCER_BONE_MARROW None BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT None BLOOD_DERIVED_LIQUID_BIOPSY None BLOOD_DERIVED_NORMAL None BONE_MARROW_NORMAL None BUCCAL_CELL_NORMAL None CELL_LINE_DERIVED_XENOGRAFT_TISSUE None CELL_LINES None CONTROL_ANALYTE None DNA None EBV_IMMORTALIZED_NORMAL None EXPANDED_NEXT_GENERATION_CANCER_MODEL None FFPE_RECURRENT None FFPE_SCROLLS None FIBROBLASTS_FROM_BONE_MARROW_NORMAL None GRANULOCYTES None HUMAN_TUMOR_ORIGINAL_CELLS None IN_SITU_NEOPLASMS None LYMPHOID_NORMAL None METASTATIC None MIXED_ADHERENT_SUSPENSION None MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL None NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR None NEXT_GENERATION_CANCER_MODEL None NORMAL_ADJACENT_TISSUE None PLEURAL_EFFUSION None POST_NEOADJUVANT_THERAPY None PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW None PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None PRIMARY_TUMOR None PRIMARY_XENOGRAFT_TISSUE None RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW None RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD None RECURRENT_TUMOR None RNA None SALIVA None SLIDES None SOLID_TISSUE_NORMAL None TOTAL_RNA None TUMOR None TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY None XENOGRAFT_TISSUE None NOT_ALLOWED_TO_COLLECT None NOT_REPORTED None UNKNOWN None","title":"Permissible Values"},{"location":"SourceMaterialTypeEnum/#slots","text":"Name Description source_material_type The general kind of material from which the specimen was derived","title":"Slots"},{"location":"SourceMaterialTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SourceMaterialTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SourceMaterialTypeEnum/#linkml-source","text":"name: SourceMaterialTypeEnum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ADDITIONAL_METASTATIC: text: ADDITIONAL_METASTATIC ADDITIONAL_NEW_PRIMARY: text: ADDITIONAL_NEW_PRIMARY BENIGN_NEOPLASMS: text: BENIGN_NEOPLASMS BLOOD_DERIVED_CANCER_BONE_MARROW: text: BLOOD_DERIVED_CANCER_BONE_MARROW BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT: text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT BLOOD_DERIVED_LIQUID_BIOPSY: text: BLOOD_DERIVED_LIQUID_BIOPSY BLOOD_DERIVED_NORMAL: text: BLOOD_DERIVED_NORMAL BONE_MARROW_NORMAL: text: BONE_MARROW_NORMAL BUCCAL_CELL_NORMAL: text: BUCCAL_CELL_NORMAL CELL_LINE_DERIVED_XENOGRAFT_TISSUE: text: CELL_LINE_DERIVED_XENOGRAFT_TISSUE CELL_LINES: text: CELL_LINES CONTROL_ANALYTE: text: CONTROL_ANALYTE DNA: text: DNA EBV_IMMORTALIZED_NORMAL: text: EBV_IMMORTALIZED_NORMAL EXPANDED_NEXT_GENERATION_CANCER_MODEL: text: EXPANDED_NEXT_GENERATION_CANCER_MODEL FFPE_RECURRENT: text: FFPE_RECURRENT FFPE_SCROLLS: text: FFPE_SCROLLS FIBROBLASTS_FROM_BONE_MARROW_NORMAL: text: FIBROBLASTS_FROM_BONE_MARROW_NORMAL GRANULOCYTES: text: GRANULOCYTES HUMAN_TUMOR_ORIGINAL_CELLS: text: HUMAN_TUMOR_ORIGINAL_CELLS IN_SITU_NEOPLASMS: text: IN_SITU_NEOPLASMS LYMPHOID_NORMAL: text: LYMPHOID_NORMAL METASTATIC: text: METASTATIC MIXED_ADHERENT_SUSPENSION: text: MIXED_ADHERENT_SUSPENSION MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL: text: MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR: text: NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR NEXT_GENERATION_CANCER_MODEL: text: NEXT_GENERATION_CANCER_MODEL NORMAL_ADJACENT_TISSUE: text: NORMAL_ADJACENT_TISSUE PLEURAL_EFFUSION: text: PLEURAL_EFFUSION POST_NEOADJUVANT_THERAPY: text: POST_NEOADJUVANT_THERAPY PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW: text: PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD PRIMARY_TUMOR: text: PRIMARY_TUMOR PRIMARY_XENOGRAFT_TISSUE: text: PRIMARY_XENOGRAFT_TISSUE RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW: text: RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: text: RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD RECURRENT_TUMOR: text: RECURRENT_TUMOR RNA: text: RNA SALIVA: text: SALIVA SLIDES: text: SLIDES SOLID_TISSUE_NORMAL: text: SOLID_TISSUE_NORMAL TOTAL_RNA: text: TOTAL_RNA TUMOR: text: TUMOR TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY: text: TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY XENOGRAFT_TISSUE: text: XENOGRAFT_TISSUE NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT NOT_REPORTED: text: NOT_REPORTED UNKNOWN: text: UNKNOWN","title":"LinkML Source"},{"location":"Sparqlpath/","text":"Type: Sparqlpath A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. URI: xsd:string base : str uri : xsd:string repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#type-sparqlpath","text":"A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF. URI: xsd:string base : str uri : xsd:string repr : str","title":"Type: Sparqlpath"},{"location":"Sparqlpath/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Sparqlpath/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Specimen/","text":"Class: Specimen Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. URI: bdchm:Specimen classDiagram class Specimen Entity <|-- Specimen Specimen : analyte_type Specimen --> AnalyteTypeEnum : analyte_type Specimen : cellular_composition_type Specimen : contained_in Specimen --> SpecimenContainer : contained_in Specimen : creation_activity Specimen --> SpecimenCreationActivity : creation_activity Specimen : derived_product Specimen --> BiologicProduct : derived_product Specimen : description Specimen : dimensional_measures Specimen --> DimensionalObservationSet : dimensional_measures Specimen : id Specimen : identity Specimen : parent_specimen Specimen --> Specimen : parent_specimen Specimen : processing_activity Specimen --> SpecimenProcessingActivity : processing_activity Specimen : quality_measure Specimen --> SpecimenQualityObservation : quality_measure Specimen : quantity_measure Specimen --> SpecimenQuantityObservation : quantity_measure Specimen : related_document Specimen --> Document : related_document Specimen : section_location Specimen --> SectionLocationEnum : section_location Specimen : source_material_type Specimen --> SourceMaterialTypeEnum : source_material_type Specimen : source_participant Specimen --> Participant : source_participant Specimen : specimen_type Specimen --> SpecimenTypeEnum : specimen_type Specimen : storage_activity Specimen --> SpecimenStorageActivity : storage_activity Specimen : transport_activity Specimen --> SpecimenTransportActivity : transport_activity Inheritance Entity Specimen Slots Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional information or explanation about the ... direct specimen_type 0..1 SpecimenTypeEnum The high-level type of the specimen, based on its derivation provenance (i direct analyte_type 0..1 AnalyteTypeEnum For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... direct source_material_type 0..1 SourceMaterialTypeEnum The general kind of material from which the specimen was derived direct parent_specimen 0..* Specimen An existing specimen from which the specimen of interest was directly derived... direct source_participant 0..1 Participant A specific Subject from which the specimen was directly or indirectly derived direct creation_activity 0..1 SpecimenCreationActivity The activity through which a specimen was created, by removing material from ... direct processing_activity 0..* SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... direct storage_activity 0..* SpecimenStorageActivity An activity that results in the storage or maintenance of a specimen in a par... direct transport_activity 0..* SpecimenTransportActivity An activity through which the specimen is transported between locations direct contained_in 0..1 SpecimenContainer A physical container in which a specimen is presently held or attached - as ... direct dimensional_measures 0..1 DimensionalObservationSet Observations about the current physical dimensions of an object (e direct quantity_measure 0..* SpecimenQuantityObservation An observation related to the present quantity of a specimen - e direct quality_measure 0..* SpecimenQualityObservation An observation about characteristics of a specimen that are indicative of its... direct cellular_composition_type 0..1 String A term describing the type of cell or cellular material comprising a specimen direct related_document 0..* Document A reference to an external document that is about or related to the specimen ... direct section_location 0..1 SectionLocationEnum The location in a parent specimen from which a section/portion was excised (e direct derived_product 0..* BiologicProduct A 'living' biologically active product that was derived from the specimen (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen parent_specimen range Specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Specimen native bdchm:Specimen LinkML Source Direct name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: BiologicProduct required: false inlined: true inlined_as_list: true Induced name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Specimen domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false alias: analyte_type owner: Specimen domain_of: - Specimen range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_material_type owner: Specimen domain_of: - Specimen range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: parent_specimen owner: Specimen domain_of: - Specimen range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: processing_activity owner: Specimen domain_of: - Specimen range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quantity_measure owner: Specimen domain_of: - Specimen range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quality_measure owner: Specimen domain_of: - Specimen range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false alias: section_location owner: Specimen domain_of: - Specimen range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Specimen domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Specimen domain_of: - Entity range: uriorcurie required: true","title":"Class: Specimen"},{"location":"Specimen/#class-specimen","text":"Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. URI: bdchm:Specimen classDiagram class Specimen Entity <|-- Specimen Specimen : analyte_type Specimen --> AnalyteTypeEnum : analyte_type Specimen : cellular_composition_type Specimen : contained_in Specimen --> SpecimenContainer : contained_in Specimen : creation_activity Specimen --> SpecimenCreationActivity : creation_activity Specimen : derived_product Specimen --> BiologicProduct : derived_product Specimen : description Specimen : dimensional_measures Specimen --> DimensionalObservationSet : dimensional_measures Specimen : id Specimen : identity Specimen : parent_specimen Specimen --> Specimen : parent_specimen Specimen : processing_activity Specimen --> SpecimenProcessingActivity : processing_activity Specimen : quality_measure Specimen --> SpecimenQualityObservation : quality_measure Specimen : quantity_measure Specimen --> SpecimenQuantityObservation : quantity_measure Specimen : related_document Specimen --> Document : related_document Specimen : section_location Specimen --> SectionLocationEnum : section_location Specimen : source_material_type Specimen --> SourceMaterialTypeEnum : source_material_type Specimen : source_participant Specimen --> Participant : source_participant Specimen : specimen_type Specimen --> SpecimenTypeEnum : specimen_type Specimen : storage_activity Specimen --> SpecimenStorageActivity : storage_activity Specimen : transport_activity Specimen --> SpecimenTransportActivity : transport_activity","title":"Class: Specimen"},{"location":"Specimen/#inheritance","text":"Entity Specimen","title":"Inheritance"},{"location":"Specimen/#slots","text":"Name Cardinality and Range Description Inheritance identity 0..* Uriorcurie A 'business' identifier or accession number for the entity, typically as prov... direct description 0..1 String A free text field to capture additional information or explanation about the ... direct specimen_type 0..1 SpecimenTypeEnum The high-level type of the specimen, based on its derivation provenance (i direct analyte_type 0..1 AnalyteTypeEnum For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), th... direct source_material_type 0..1 SourceMaterialTypeEnum The general kind of material from which the specimen was derived direct parent_specimen 0..* Specimen An existing specimen from which the specimen of interest was directly derived... direct source_participant 0..1 Participant A specific Subject from which the specimen was directly or indirectly derived direct creation_activity 0..1 SpecimenCreationActivity The activity through which a specimen was created, by removing material from ... direct processing_activity 0..* SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... direct storage_activity 0..* SpecimenStorageActivity An activity that results in the storage or maintenance of a specimen in a par... direct transport_activity 0..* SpecimenTransportActivity An activity through which the specimen is transported between locations direct contained_in 0..1 SpecimenContainer A physical container in which a specimen is presently held or attached - as ... direct dimensional_measures 0..1 DimensionalObservationSet Observations about the current physical dimensions of an object (e direct quantity_measure 0..* SpecimenQuantityObservation An observation related to the present quantity of a specimen - e direct quality_measure 0..* SpecimenQualityObservation An observation about characteristics of a specimen that are indicative of its... direct cellular_composition_type 0..1 String A term describing the type of cell or cellular material comprising a specimen direct related_document 0..* Document A reference to an external document that is about or related to the specimen ... direct section_location 0..1 SectionLocationEnum The location in a parent specimen from which a section/portion was excised (e direct derived_product 0..* BiologicProduct A 'living' biologically active product that was derived from the specimen (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Specimen/#usages","text":"used by used in type used Specimen parent_specimen range Specimen","title":"Usages"},{"location":"Specimen/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Specimen/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Specimen/#mappings","text":"Mapping Type Mapped Value self bdchm:Specimen native bdchm:Specimen","title":"Mappings"},{"location":"Specimen/#linkml-source","text":"","title":"LinkML Source"},{"location":"Specimen/#direct","text":"name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity slots: - identity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: BiologicProduct required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"Specimen/#induced","text":"name: Specimen description: Any material taken as a sample from a biological entity (living or dead), or from a physical object or the environment. Specimens are usually collected as an example of their kind, often for use in some investigation. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: description: name: description description: A free text field to capture additional information or explanation about the specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: description owner: Specimen domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string required: false specimen_type: name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false analyte_type: name: analyte_type description: For specimens of type 'analyte' (or an 'aliquot' derived from an analyte), this is the category of chemcial the analyte of interest represents (e.g. DNA, RNA) examples: - value: DNA - value: FFPE DNA - value: GenomePlex (Rubicon) Amplified DNA - value: Repli-G (Qiagen) DNA - value: RNA - value: FFPE RNA from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_analyte_type multivalued: false alias: analyte_type owner: Specimen domain_of: - Specimen range: AnalyteTypeEnum required: false source_material_type: name: source_material_type description: The general kind of material from which the specimen was derived. comments: - Values captured here may describe the type of molecular mixture, cell, tissue, organ, body fluid, embryo, excretory substance, or experimental system from which a specimen was derived. examples: - value: Tissue - value: Blood - value: Tumor Aspirate - value: Cell Line - value: Expanded Next Generation Cancer Model - value: Pleural Effusion - value: Xenograft Tissue from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_material_type owner: Specimen domain_of: - Specimen range: SourceMaterialTypeEnum required: false parent_specimen: name: parent_specimen description: An existing specimen from which the specimen of interest was directly derived (i.e its immediate parent specimen). comments: - This property indicates only the direct parent specimen(s). Cardinality is 0..m to account for specimens derived from pooling of multiple specimens. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: parent_specimen owner: Specimen domain_of: - Specimen range: Specimen required: false inlined: true inlined_as_list: true source_participant: name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false creation_activity: name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false processing_activity: name: processing_activity description: An activity that modifies the physical structure, composition, or state of a specimen. comments: - Note that a given specimen may undergo more than one distinct processing activity, through application of different methodologies that modify its physical state. However, if an activity generates a new specimen (e.g. via portioning, slicing) it is considered a SpeciemnCreationActivity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: processing_activity owner: Specimen domain_of: - Specimen range: SpecimenProcessingActivity required: false storage_activity: name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false transport_activity: name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false contained_in: name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false dimensional_measures: name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false quantity_measure: name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quantity_measure owner: Specimen domain_of: - Specimen range: SpecimenQuantityObservation required: false quality_measure: name: quality_measure description: An observation about characteristics of a specimen that are indicative of its quality or suitability for use. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quality_measure owner: Specimen domain_of: - Specimen range: SpecimenQualityObservation required: false cellular_composition_type: name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false related_document: name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false section_location: name: section_location description: The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) comments: - This attribute applies only to Specimens that are of type 'portion' or 'slide'. examples: - value: Top - value: Bottom - value: Unknown from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_section_location multivalued: false alias: section_location owner: Specimen domain_of: - Specimen range: SectionLocationEnum required: false derived_product: name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true identity: name: identity description: A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity owner: Specimen domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Specimen domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenCollectionMethodType/","text":"Enum: SpecimenCollectionMethodType URI: SpecimenCollectionMethodType Permissible Values Value Meaning Description ORCHIECTOMY None METASTASECTOMY None AUTOPSY None UNKNOWN None ASPIRATE None RIGHT_HEMICOLECTOMY None INCISIONAL_BIOPSY None BLOOD_DRAW None PERITONEAL_LAVAGE None OPEN_RADICAL_PROSTATECTOMY None ABDOMINO_PERINEAL_RESECTION_OF_RECTUM None SALPINGECTOMY None ENDO_RECTAL_TUMOR_RESECTION None BIOPSY None SALPINGO_OOPHORECTOMY None NOT_ALLOWED_TO_COLLECT None WHIPPLE_PROCEDURE None ENUCLEATION None MODIFIED_RADICAL_MASTECTOMY None PARACENTESIS None OPEN_CRANIOTOMY None WEDGE_RESECTION None LAPAROSCOPIC_RADICAL_NEPHRECTOMY None OPEN_PARTIAL_NEPHRECTOMY None TRANSURETHRAL_RESECTION None SIGMOID_COLECTOMY None OOPHORECTOMY None TOTAL_HEPATECTOMY None INDETERMINANT None SUBTOTAL_RESECTION None LEFT_HEMICOLECTOMY None NEEDLE_BIOPSY None OTHER None PANCREATECTOMY None THORACOSCOPIC_BIOPSY None TOTAL_MASTECTOMY None EXCISIONAL_BIOPSY None BONE_MARROW_ASPIRATE None LOCAL_RESECTION None LOBECTOMY None FINE_NEEDLE_ASPIRATION None OMENTECTOMY None TUMOR_RESECTION None CYSTECTOMY None GROSS_TOTAL_RESECTION None THORACENTESIS None ANTERIOR_RESECTION_OF_RECTUM None TRANSPLANT None LAPAROSCOPIC_PARTIAL_NEPHRECTOMY None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS None PNEUMONECTOMY None PAN_PROCTO_COLECTOMY None HYSTERECTOMY_NOS None CORE_BIOPSY None SIMPLE_MASTECTOMY None LUMPECTOMY None ENDOSCOPIC_BIOPSY None SIMPLE_HYSTERECTOMY None LYMPHADENECTOMY None LAPAROSCOPIC_BIOPSY None TUMOR_DEBULKING None ASCITES_DRAINAGE None ENDOSCOPIC_MUCOSAL_RESECTION None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS None TOTAL_COLECTOMY None LIQUID_BIOPSY None RADICAL_HYSTERECTOMY None SURGICAL_RESECTION None OPEN_RADICAL_NEPHRECTOMY None TRANSVERSE_COLECTOMY None HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY None PUNCH_BIOPSY None PARTIAL_HEPATECTOMY None SUPRACERVICAL_HYSTERECTOMY None OTHER_SURGICAL_RESECTION None NOT_REPORTED None FULL_HYSTERECTOMY None TONSILLECTOMY None SUPRAGLOTTIC_LARYNGECTOMY None SUPERFICIAL_PAROTIDECTOMY None LARYNGOPHARYNGECTOMY None MAXILLECTOMY None PARTIAL_NEPHRECTOMY None MANDIBULECTOMY None BUCCAL_MUCOSAL_RESECTION None VERTICAL_HEMILARYNGECTOMY None TOTAL_NEPHRECTOMY None TOTAL_LARYNGECTOMY None TRANSORAL_LASER_EXCISION None PAROTIDECTOMY_NOS None RADICAL_MAXILLECTOMY None ENDOLARYNGEAL_EXCISION None PALATECTOMY None GLOSSECTOMY None PARTIAL_LARYNGECTOMY None LYMPH_NODE_DISSECTION None RADICAL_PROSTATECTOMY None DEEP_PAROTIDECTOMY None SUBTOTAL_PROSTATECTOMY None RADICAL_NEPHRECTOMY None SUPRACRICOID_LARYNGECTOMY None PARTIAL_MAXILLECTOMY None Slots Name Description collection_method_type The type of method applied in collecting a sample from its original source Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenCollectionMethodType from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ORCHIECTOMY: text: ORCHIECTOMY METASTASECTOMY: text: METASTASECTOMY AUTOPSY: text: AUTOPSY UNKNOWN: text: UNKNOWN ASPIRATE: text: ASPIRATE RIGHT_HEMICOLECTOMY: text: RIGHT_HEMICOLECTOMY INCISIONAL_BIOPSY: text: INCISIONAL_BIOPSY BLOOD_DRAW: text: BLOOD_DRAW PERITONEAL_LAVAGE: text: PERITONEAL_LAVAGE OPEN_RADICAL_PROSTATECTOMY: text: OPEN_RADICAL_PROSTATECTOMY ABDOMINO_PERINEAL_RESECTION_OF_RECTUM: text: ABDOMINO_PERINEAL_RESECTION_OF_RECTUM SALPINGECTOMY: text: SALPINGECTOMY ENDO_RECTAL_TUMOR_RESECTION: text: ENDO_RECTAL_TUMOR_RESECTION BIOPSY: text: BIOPSY SALPINGO_OOPHORECTOMY: text: SALPINGO_OOPHORECTOMY NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT WHIPPLE_PROCEDURE: text: WHIPPLE_PROCEDURE ENUCLEATION: text: ENUCLEATION MODIFIED_RADICAL_MASTECTOMY: text: MODIFIED_RADICAL_MASTECTOMY PARACENTESIS: text: PARACENTESIS OPEN_CRANIOTOMY: text: OPEN_CRANIOTOMY WEDGE_RESECTION: text: WEDGE_RESECTION LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: LAPAROSCOPIC_RADICAL_NEPHRECTOMY OPEN_PARTIAL_NEPHRECTOMY: text: OPEN_PARTIAL_NEPHRECTOMY TRANSURETHRAL_RESECTION: text: TRANSURETHRAL_RESECTION SIGMOID_COLECTOMY: text: SIGMOID_COLECTOMY OOPHORECTOMY: text: OOPHORECTOMY TOTAL_HEPATECTOMY: text: TOTAL_HEPATECTOMY INDETERMINANT: text: INDETERMINANT SUBTOTAL_RESECTION: text: SUBTOTAL_RESECTION LEFT_HEMICOLECTOMY: text: LEFT_HEMICOLECTOMY NEEDLE_BIOPSY: text: NEEDLE_BIOPSY OTHER: text: OTHER PANCREATECTOMY: text: PANCREATECTOMY THORACOSCOPIC_BIOPSY: text: THORACOSCOPIC_BIOPSY TOTAL_MASTECTOMY: text: TOTAL_MASTECTOMY EXCISIONAL_BIOPSY: text: EXCISIONAL_BIOPSY BONE_MARROW_ASPIRATE: text: BONE_MARROW_ASPIRATE LOCAL_RESECTION: text: LOCAL_RESECTION LOBECTOMY: text: LOBECTOMY FINE_NEEDLE_ASPIRATION: text: FINE_NEEDLE_ASPIRATION OMENTECTOMY: text: OMENTECTOMY TUMOR_RESECTION: text: TUMOR_RESECTION CYSTECTOMY: text: CYSTECTOMY GROSS_TOTAL_RESECTION: text: GROSS_TOTAL_RESECTION THORACENTESIS: text: THORACENTESIS ANTERIOR_RESECTION_OF_RECTUM: text: ANTERIOR_RESECTION_OF_RECTUM TRANSPLANT: text: TRANSPLANT LAPAROSCOPIC_PARTIAL_NEPHRECTOMY: text: LAPAROSCOPIC_PARTIAL_NEPHRECTOMY LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS PNEUMONECTOMY: text: PNEUMONECTOMY PAN_PROCTO_COLECTOMY: text: PAN_PROCTO_COLECTOMY HYSTERECTOMY_NOS: text: HYSTERECTOMY_NOS CORE_BIOPSY: text: CORE_BIOPSY SIMPLE_MASTECTOMY: text: SIMPLE_MASTECTOMY LUMPECTOMY: text: LUMPECTOMY ENDOSCOPIC_BIOPSY: text: ENDOSCOPIC_BIOPSY SIMPLE_HYSTERECTOMY: text: SIMPLE_HYSTERECTOMY LYMPHADENECTOMY: text: LYMPHADENECTOMY LAPAROSCOPIC_BIOPSY: text: LAPAROSCOPIC_BIOPSY TUMOR_DEBULKING: text: TUMOR_DEBULKING ASCITES_DRAINAGE: text: ASCITES_DRAINAGE ENDOSCOPIC_MUCOSAL_RESECTION: text: ENDOSCOPIC_MUCOSAL_RESECTION LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS TOTAL_COLECTOMY: text: TOTAL_COLECTOMY LIQUID_BIOPSY: text: LIQUID_BIOPSY RADICAL_HYSTERECTOMY: text: RADICAL_HYSTERECTOMY SURGICAL_RESECTION: text: SURGICAL_RESECTION OPEN_RADICAL_NEPHRECTOMY: text: OPEN_RADICAL_NEPHRECTOMY TRANSVERSE_COLECTOMY: text: TRANSVERSE_COLECTOMY HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY PUNCH_BIOPSY: text: PUNCH_BIOPSY PARTIAL_HEPATECTOMY: text: PARTIAL_HEPATECTOMY SUPRACERVICAL_HYSTERECTOMY: text: SUPRACERVICAL_HYSTERECTOMY OTHER_SURGICAL_RESECTION: text: OTHER_SURGICAL_RESECTION NOT_REPORTED: text: NOT_REPORTED FULL_HYSTERECTOMY: text: FULL_HYSTERECTOMY TONSILLECTOMY: text: TONSILLECTOMY SUPRAGLOTTIC_LARYNGECTOMY: text: SUPRAGLOTTIC_LARYNGECTOMY SUPERFICIAL_PAROTIDECTOMY: text: SUPERFICIAL_PAROTIDECTOMY LARYNGOPHARYNGECTOMY: text: LARYNGOPHARYNGECTOMY MAXILLECTOMY: text: MAXILLECTOMY PARTIAL_NEPHRECTOMY: text: PARTIAL_NEPHRECTOMY MANDIBULECTOMY: text: MANDIBULECTOMY BUCCAL_MUCOSAL_RESECTION: text: BUCCAL_MUCOSAL_RESECTION VERTICAL_HEMILARYNGECTOMY: text: VERTICAL_HEMILARYNGECTOMY TOTAL_NEPHRECTOMY: text: TOTAL_NEPHRECTOMY TOTAL_LARYNGECTOMY: text: TOTAL_LARYNGECTOMY TRANSORAL_LASER_EXCISION: text: TRANSORAL_LASER_EXCISION PAROTIDECTOMY_NOS: text: PAROTIDECTOMY_NOS RADICAL_MAXILLECTOMY: text: RADICAL_MAXILLECTOMY ENDOLARYNGEAL_EXCISION: text: ENDOLARYNGEAL_EXCISION PALATECTOMY: text: PALATECTOMY GLOSSECTOMY: text: GLOSSECTOMY PARTIAL_LARYNGECTOMY: text: PARTIAL_LARYNGECTOMY LYMPH_NODE_DISSECTION: text: LYMPH_NODE_DISSECTION RADICAL_PROSTATECTOMY: text: RADICAL_PROSTATECTOMY DEEP_PAROTIDECTOMY: text: DEEP_PAROTIDECTOMY SUBTOTAL_PROSTATECTOMY: text: SUBTOTAL_PROSTATECTOMY RADICAL_NEPHRECTOMY: text: RADICAL_NEPHRECTOMY SUPRACRICOID_LARYNGECTOMY: text: SUPRACRICOID_LARYNGECTOMY PARTIAL_MAXILLECTOMY: text: PARTIAL_MAXILLECTOMY","title":"Enum: SpecimenCollectionMethodType"},{"location":"SpecimenCollectionMethodType/#enum-specimencollectionmethodtype","text":"URI: SpecimenCollectionMethodType","title":"Enum: SpecimenCollectionMethodType"},{"location":"SpecimenCollectionMethodType/#permissible-values","text":"Value Meaning Description ORCHIECTOMY None METASTASECTOMY None AUTOPSY None UNKNOWN None ASPIRATE None RIGHT_HEMICOLECTOMY None INCISIONAL_BIOPSY None BLOOD_DRAW None PERITONEAL_LAVAGE None OPEN_RADICAL_PROSTATECTOMY None ABDOMINO_PERINEAL_RESECTION_OF_RECTUM None SALPINGECTOMY None ENDO_RECTAL_TUMOR_RESECTION None BIOPSY None SALPINGO_OOPHORECTOMY None NOT_ALLOWED_TO_COLLECT None WHIPPLE_PROCEDURE None ENUCLEATION None MODIFIED_RADICAL_MASTECTOMY None PARACENTESIS None OPEN_CRANIOTOMY None WEDGE_RESECTION None LAPAROSCOPIC_RADICAL_NEPHRECTOMY None OPEN_PARTIAL_NEPHRECTOMY None TRANSURETHRAL_RESECTION None SIGMOID_COLECTOMY None OOPHORECTOMY None TOTAL_HEPATECTOMY None INDETERMINANT None SUBTOTAL_RESECTION None LEFT_HEMICOLECTOMY None NEEDLE_BIOPSY None OTHER None PANCREATECTOMY None THORACOSCOPIC_BIOPSY None TOTAL_MASTECTOMY None EXCISIONAL_BIOPSY None BONE_MARROW_ASPIRATE None LOCAL_RESECTION None LOBECTOMY None FINE_NEEDLE_ASPIRATION None OMENTECTOMY None TUMOR_RESECTION None CYSTECTOMY None GROSS_TOTAL_RESECTION None THORACENTESIS None ANTERIOR_RESECTION_OF_RECTUM None TRANSPLANT None LAPAROSCOPIC_PARTIAL_NEPHRECTOMY None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS None PNEUMONECTOMY None PAN_PROCTO_COLECTOMY None HYSTERECTOMY_NOS None CORE_BIOPSY None SIMPLE_MASTECTOMY None LUMPECTOMY None ENDOSCOPIC_BIOPSY None SIMPLE_HYSTERECTOMY None LYMPHADENECTOMY None LAPAROSCOPIC_BIOPSY None TUMOR_DEBULKING None ASCITES_DRAINAGE None ENDOSCOPIC_MUCOSAL_RESECTION None LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS None TOTAL_COLECTOMY None LIQUID_BIOPSY None RADICAL_HYSTERECTOMY None SURGICAL_RESECTION None OPEN_RADICAL_NEPHRECTOMY None TRANSVERSE_COLECTOMY None HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY None PUNCH_BIOPSY None PARTIAL_HEPATECTOMY None SUPRACERVICAL_HYSTERECTOMY None OTHER_SURGICAL_RESECTION None NOT_REPORTED None FULL_HYSTERECTOMY None TONSILLECTOMY None SUPRAGLOTTIC_LARYNGECTOMY None SUPERFICIAL_PAROTIDECTOMY None LARYNGOPHARYNGECTOMY None MAXILLECTOMY None PARTIAL_NEPHRECTOMY None MANDIBULECTOMY None BUCCAL_MUCOSAL_RESECTION None VERTICAL_HEMILARYNGECTOMY None TOTAL_NEPHRECTOMY None TOTAL_LARYNGECTOMY None TRANSORAL_LASER_EXCISION None PAROTIDECTOMY_NOS None RADICAL_MAXILLECTOMY None ENDOLARYNGEAL_EXCISION None PALATECTOMY None GLOSSECTOMY None PARTIAL_LARYNGECTOMY None LYMPH_NODE_DISSECTION None RADICAL_PROSTATECTOMY None DEEP_PAROTIDECTOMY None SUBTOTAL_PROSTATECTOMY None RADICAL_NEPHRECTOMY None SUPRACRICOID_LARYNGECTOMY None PARTIAL_MAXILLECTOMY None","title":"Permissible Values"},{"location":"SpecimenCollectionMethodType/#slots","text":"Name Description collection_method_type The type of method applied in collecting a sample from its original source","title":"Slots"},{"location":"SpecimenCollectionMethodType/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenCollectionMethodType/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenCollectionMethodType/#linkml-source","text":"name: SpecimenCollectionMethodType from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ORCHIECTOMY: text: ORCHIECTOMY METASTASECTOMY: text: METASTASECTOMY AUTOPSY: text: AUTOPSY UNKNOWN: text: UNKNOWN ASPIRATE: text: ASPIRATE RIGHT_HEMICOLECTOMY: text: RIGHT_HEMICOLECTOMY INCISIONAL_BIOPSY: text: INCISIONAL_BIOPSY BLOOD_DRAW: text: BLOOD_DRAW PERITONEAL_LAVAGE: text: PERITONEAL_LAVAGE OPEN_RADICAL_PROSTATECTOMY: text: OPEN_RADICAL_PROSTATECTOMY ABDOMINO_PERINEAL_RESECTION_OF_RECTUM: text: ABDOMINO_PERINEAL_RESECTION_OF_RECTUM SALPINGECTOMY: text: SALPINGECTOMY ENDO_RECTAL_TUMOR_RESECTION: text: ENDO_RECTAL_TUMOR_RESECTION BIOPSY: text: BIOPSY SALPINGO_OOPHORECTOMY: text: SALPINGO_OOPHORECTOMY NOT_ALLOWED_TO_COLLECT: text: NOT_ALLOWED_TO_COLLECT WHIPPLE_PROCEDURE: text: WHIPPLE_PROCEDURE ENUCLEATION: text: ENUCLEATION MODIFIED_RADICAL_MASTECTOMY: text: MODIFIED_RADICAL_MASTECTOMY PARACENTESIS: text: PARACENTESIS OPEN_CRANIOTOMY: text: OPEN_CRANIOTOMY WEDGE_RESECTION: text: WEDGE_RESECTION LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: LAPAROSCOPIC_RADICAL_NEPHRECTOMY OPEN_PARTIAL_NEPHRECTOMY: text: OPEN_PARTIAL_NEPHRECTOMY TRANSURETHRAL_RESECTION: text: TRANSURETHRAL_RESECTION SIGMOID_COLECTOMY: text: SIGMOID_COLECTOMY OOPHORECTOMY: text: OOPHORECTOMY TOTAL_HEPATECTOMY: text: TOTAL_HEPATECTOMY INDETERMINANT: text: INDETERMINANT SUBTOTAL_RESECTION: text: SUBTOTAL_RESECTION LEFT_HEMICOLECTOMY: text: LEFT_HEMICOLECTOMY NEEDLE_BIOPSY: text: NEEDLE_BIOPSY OTHER: text: OTHER PANCREATECTOMY: text: PANCREATECTOMY THORACOSCOPIC_BIOPSY: text: THORACOSCOPIC_BIOPSY TOTAL_MASTECTOMY: text: TOTAL_MASTECTOMY EXCISIONAL_BIOPSY: text: EXCISIONAL_BIOPSY BONE_MARROW_ASPIRATE: text: BONE_MARROW_ASPIRATE LOCAL_RESECTION: text: LOCAL_RESECTION LOBECTOMY: text: LOBECTOMY FINE_NEEDLE_ASPIRATION: text: FINE_NEEDLE_ASPIRATION OMENTECTOMY: text: OMENTECTOMY TUMOR_RESECTION: text: TUMOR_RESECTION CYSTECTOMY: text: CYSTECTOMY GROSS_TOTAL_RESECTION: text: GROSS_TOTAL_RESECTION THORACENTESIS: text: THORACENTESIS ANTERIOR_RESECTION_OF_RECTUM: text: ANTERIOR_RESECTION_OF_RECTUM TRANSPLANT: text: TRANSPLANT LAPAROSCOPIC_PARTIAL_NEPHRECTOMY: text: LAPAROSCOPIC_PARTIAL_NEPHRECTOMY LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS PNEUMONECTOMY: text: PNEUMONECTOMY PAN_PROCTO_COLECTOMY: text: PAN_PROCTO_COLECTOMY HYSTERECTOMY_NOS: text: HYSTERECTOMY_NOS CORE_BIOPSY: text: CORE_BIOPSY SIMPLE_MASTECTOMY: text: SIMPLE_MASTECTOMY LUMPECTOMY: text: LUMPECTOMY ENDOSCOPIC_BIOPSY: text: ENDOSCOPIC_BIOPSY SIMPLE_HYSTERECTOMY: text: SIMPLE_HYSTERECTOMY LYMPHADENECTOMY: text: LYMPHADENECTOMY LAPAROSCOPIC_BIOPSY: text: LAPAROSCOPIC_BIOPSY TUMOR_DEBULKING: text: TUMOR_DEBULKING ASCITES_DRAINAGE: text: ASCITES_DRAINAGE ENDOSCOPIC_MUCOSAL_RESECTION: text: ENDOSCOPIC_MUCOSAL_RESECTION LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS: text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS TOTAL_COLECTOMY: text: TOTAL_COLECTOMY LIQUID_BIOPSY: text: LIQUID_BIOPSY RADICAL_HYSTERECTOMY: text: RADICAL_HYSTERECTOMY SURGICAL_RESECTION: text: SURGICAL_RESECTION OPEN_RADICAL_NEPHRECTOMY: text: OPEN_RADICAL_NEPHRECTOMY TRANSVERSE_COLECTOMY: text: TRANSVERSE_COLECTOMY HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY: text: HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY PUNCH_BIOPSY: text: PUNCH_BIOPSY PARTIAL_HEPATECTOMY: text: PARTIAL_HEPATECTOMY SUPRACERVICAL_HYSTERECTOMY: text: SUPRACERVICAL_HYSTERECTOMY OTHER_SURGICAL_RESECTION: text: OTHER_SURGICAL_RESECTION NOT_REPORTED: text: NOT_REPORTED FULL_HYSTERECTOMY: text: FULL_HYSTERECTOMY TONSILLECTOMY: text: TONSILLECTOMY SUPRAGLOTTIC_LARYNGECTOMY: text: SUPRAGLOTTIC_LARYNGECTOMY SUPERFICIAL_PAROTIDECTOMY: text: SUPERFICIAL_PAROTIDECTOMY LARYNGOPHARYNGECTOMY: text: LARYNGOPHARYNGECTOMY MAXILLECTOMY: text: MAXILLECTOMY PARTIAL_NEPHRECTOMY: text: PARTIAL_NEPHRECTOMY MANDIBULECTOMY: text: MANDIBULECTOMY BUCCAL_MUCOSAL_RESECTION: text: BUCCAL_MUCOSAL_RESECTION VERTICAL_HEMILARYNGECTOMY: text: VERTICAL_HEMILARYNGECTOMY TOTAL_NEPHRECTOMY: text: TOTAL_NEPHRECTOMY TOTAL_LARYNGECTOMY: text: TOTAL_LARYNGECTOMY TRANSORAL_LASER_EXCISION: text: TRANSORAL_LASER_EXCISION PAROTIDECTOMY_NOS: text: PAROTIDECTOMY_NOS RADICAL_MAXILLECTOMY: text: RADICAL_MAXILLECTOMY ENDOLARYNGEAL_EXCISION: text: ENDOLARYNGEAL_EXCISION PALATECTOMY: text: PALATECTOMY GLOSSECTOMY: text: GLOSSECTOMY PARTIAL_LARYNGECTOMY: text: PARTIAL_LARYNGECTOMY LYMPH_NODE_DISSECTION: text: LYMPH_NODE_DISSECTION RADICAL_PROSTATECTOMY: text: RADICAL_PROSTATECTOMY DEEP_PAROTIDECTOMY: text: DEEP_PAROTIDECTOMY SUBTOTAL_PROSTATECTOMY: text: SUBTOTAL_PROSTATECTOMY RADICAL_NEPHRECTOMY: text: RADICAL_NEPHRECTOMY SUPRACRICOID_LARYNGECTOMY: text: SUPRACRICOID_LARYNGECTOMY PARTIAL_MAXILLECTOMY: text: PARTIAL_MAXILLECTOMY","title":"LinkML Source"},{"location":"SpecimenContainer/","text":"Class: SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:SpecimenContainer classDiagram class SpecimenContainer Entity <|-- SpecimenContainer SpecimenContainer : additive SpecimenContainer --> Substance : additive SpecimenContainer : container_number SpecimenContainer : container_type SpecimenContainer : id SpecimenContainer : parent_container SpecimenContainer --> SpecimenContainer : parent_container Inheritance Entity SpecimenContainer Slots Name Cardinality and Range Description Inheritance container_type 0..1 String The kind of the container direct container_number 0..1 String Informal number by which the container is referenced or identified (e direct additive 0..* Substance A material substance added to the container (typically to support the primary... direct parent_container 0..1 SpecimenContainer A larger container of which this container is a part (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen contained_in range SpecimenContainer SpecimenContainer parent_container range SpecimenContainer SpecimenStorageActivity container range SpecimenContainer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenContainer native bdchm:SpecimenContainer LinkML Source Direct name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false Induced name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: additive owner: SpecimenContainer domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: parent_container owner: SpecimenContainer domain_of: - SpecimenContainer range: SpecimenContainer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenContainer domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenContainer"},{"location":"SpecimenContainer/#class-specimencontainer","text":"A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:SpecimenContainer classDiagram class SpecimenContainer Entity <|-- SpecimenContainer SpecimenContainer : additive SpecimenContainer --> Substance : additive SpecimenContainer : container_number SpecimenContainer : container_type SpecimenContainer : id SpecimenContainer : parent_container SpecimenContainer --> SpecimenContainer : parent_container","title":"Class: SpecimenContainer"},{"location":"SpecimenContainer/#inheritance","text":"Entity SpecimenContainer","title":"Inheritance"},{"location":"SpecimenContainer/#slots","text":"Name Cardinality and Range Description Inheritance container_type 0..1 String The kind of the container direct container_number 0..1 String Informal number by which the container is referenced or identified (e direct additive 0..* Substance A material substance added to the container (typically to support the primary... direct parent_container 0..1 SpecimenContainer A larger container of which this container is a part (e direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenContainer/#usages","text":"used by used in type used Specimen contained_in range SpecimenContainer SpecimenContainer parent_container range SpecimenContainer SpecimenStorageActivity container range SpecimenContainer","title":"Usages"},{"location":"SpecimenContainer/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenContainer/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenContainer/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenContainer native bdchm:SpecimenContainer","title":"Mappings"},{"location":"SpecimenContainer/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenContainer/#direct","text":"name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenContainer required: false","title":"Direct"},{"location":"SpecimenContainer/#induced","text":"name: SpecimenContainer description: A vessel in which a specimen is held or to which it is attached - for storage or as a substrate for growth (e.g. a cell culture dish) or analysis (e.g. a microscope slide or 96-well plate) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: container_type: name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false container_number: name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false additive: name: additive description: A material substance added to the container (typically to support the primary contained object - e.g. culture media to support cell growth) examples: - value: DMEM - value: DMEM+Serum - value: RPMI - value: RPMI+Serum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: additive owner: SpecimenContainer domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false parent_container: name: parent_container description: A larger container of which this container is a part (e.g. the complete 96-well plate of which a single well is a part) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: parent_container owner: SpecimenContainer domain_of: - SpecimenContainer range: SpecimenContainer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenContainer domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenCreationActivity/","text":"Class: SpecimenCreationActivity The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). URI: bdchm:SpecimenCreationActivity classDiagram class SpecimenCreationActivity Entity <|-- SpecimenCreationActivity SpecimenCreationActivity : activity_type SpecimenCreationActivity --> SpecimenCreationActivityTypeEnum : activity_type SpecimenCreationActivity : additive SpecimenCreationActivity --> Substance : additive SpecimenCreationActivity : collection_method_type SpecimenCreationActivity --> SpecimenCollectionMethodType : collection_method_type SpecimenCreationActivity : collection_site SpecimenCreationActivity --> BodySite : collection_site SpecimenCreationActivity : date_ended SpecimenCreationActivity --> TimePoint : date_ended SpecimenCreationActivity : date_started SpecimenCreationActivity --> TimePoint : date_started SpecimenCreationActivity : derivation_method_type SpecimenCreationActivity : id SpecimenCreationActivity : performed_by SpecimenCreationActivity --> Organization : performed_by SpecimenCreationActivity : quantity_collected SpecimenCreationActivity --> Quantity : quantity_collected SpecimenCreationActivity : specimen_order Inheritance Entity SpecimenCreationActivity Slots Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenCreationActivityTypeEnum The high-level type of creation activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen creation event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a specimen creation event) direct performed_by 0..1 Organization The organization or group that performed the activity direct collection_method_type 0..1 SpecimenCollectionMethodType The type of method applied in collecting a sample from its original source direct derivation_method_type 0..1 String The type of method applied to derive a new specimen from an existing one direct additive 0..* Substance A type of material or reagent used applied as input when creating a specimen direct collection_site 0..1 BodySite The anatomic site from which a specimen was collected direct quantity_collected 0..1 Quantity The quantity of material in the specimen as originally collected from its ori... direct specimen_order 0..1 Integer A numeric value that represents the sequential order of this creation activit... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen creation_activity range SpecimenCreationActivity Comments A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenCreationActivity native bdchm:SpecimenCreationActivity LinkML Source Direct name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: integer required: false Induced name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: activity_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: performed_by owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenCreationActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: quantity_collected owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenCreationActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenCreationActivity"},{"location":"SpecimenCreationActivity/#class-specimencreationactivity","text":"The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). URI: bdchm:SpecimenCreationActivity classDiagram class SpecimenCreationActivity Entity <|-- SpecimenCreationActivity SpecimenCreationActivity : activity_type SpecimenCreationActivity --> SpecimenCreationActivityTypeEnum : activity_type SpecimenCreationActivity : additive SpecimenCreationActivity --> Substance : additive SpecimenCreationActivity : collection_method_type SpecimenCreationActivity --> SpecimenCollectionMethodType : collection_method_type SpecimenCreationActivity : collection_site SpecimenCreationActivity --> BodySite : collection_site SpecimenCreationActivity : date_ended SpecimenCreationActivity --> TimePoint : date_ended SpecimenCreationActivity : date_started SpecimenCreationActivity --> TimePoint : date_started SpecimenCreationActivity : derivation_method_type SpecimenCreationActivity : id SpecimenCreationActivity : performed_by SpecimenCreationActivity --> Organization : performed_by SpecimenCreationActivity : quantity_collected SpecimenCreationActivity --> Quantity : quantity_collected SpecimenCreationActivity : specimen_order","title":"Class: SpecimenCreationActivity"},{"location":"SpecimenCreationActivity/#inheritance","text":"Entity SpecimenCreationActivity","title":"Inheritance"},{"location":"SpecimenCreationActivity/#slots","text":"Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenCreationActivityTypeEnum The high-level type of creation activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen creation event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a specimen creation event) direct performed_by 0..1 Organization The organization or group that performed the activity direct collection_method_type 0..1 SpecimenCollectionMethodType The type of method applied in collecting a sample from its original source direct derivation_method_type 0..1 String The type of method applied to derive a new specimen from an existing one direct additive 0..* Substance A type of material or reagent used applied as input when creating a specimen direct collection_site 0..1 BodySite The anatomic site from which a specimen was collected direct quantity_collected 0..1 Quantity The quantity of material in the specimen as originally collected from its ori... direct specimen_order 0..1 Integer A numeric value that represents the sequential order of this creation activit... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenCreationActivity/#usages","text":"used by used in type used Specimen creation_activity range SpecimenCreationActivity","title":"Usages"},{"location":"SpecimenCreationActivity/#comments","text":"A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported.","title":"Comments"},{"location":"SpecimenCreationActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenCreationActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenCreationActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenCreationActivity native bdchm:SpecimenCreationActivity","title":"Mappings"},{"location":"SpecimenCreationActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenCreationActivity/#direct","text":"name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: integer required: false","title":"Direct"},{"location":"SpecimenCreationActivity/#induced","text":"name: SpecimenCreationActivity description: The process of creating a specimen. This may occur through observing and/or collecting material from an biological source or natural setting, or through derivation from an existing specimen (e.g. via portioning or aliquoting). comments: - A creation activity represents the entire process up to the point where the specimen is physically modified, stored, or transported. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of creation activity. comments: - At present our model collapses two types of processes through which specimens are created (initial collection from source, and derivation from an existing specimen). The 'category' is a flag to indicate which applies to a given instance, so that more specific recommendations about data entry in certain fields can be specified. examples: - value: Collection from Source - value: Derivation from Specimen from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: activity_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenCreationActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a specimen creation event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenCreationActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false performed_by: name: performed_by description: The organization or group that performed the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: performed_by owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false collection_method_type: name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: SpecimenCollectionMethodType required: false derivation_method_type: name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false additive: name: additive description: A type of material or reagent used applied as input when creating a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenCreationActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false collection_site: name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false quantity_collected: name: quantity_collected description: The quantity of material in the specimen as originally collected from its original source material (prior to downstream portioning or processing) comments: - This attribute applies only when Specimen.category='initial sample'. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: quantity_collected owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: Quantity required: false specimen_order: name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenCreationActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenCreationActivityTypeEnum/","text":"Enum: SpecimenCreationActivityTypeEnum The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) URI: SpecimenCreationActivityTypeEnum Permissible Values Value Meaning Description COLLECTION_FROM_SOURCE None An activity that collects an initial sample directly from a subject / source DERIVATION_FROM_SPECIMEN None An activity that derives a new specimen from an existing one Slots Name Description activity_type The high-level type of creation activity Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenCreationActivityTypeEnum description: The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: COLLECTION_FROM_SOURCE: text: COLLECTION_FROM_SOURCE description: An activity that collects an initial sample directly from a subject / source. DERIVATION_FROM_SPECIMEN: text: DERIVATION_FROM_SPECIMEN description: An activity that derives a new specimen from an existing one.","title":"Enum: SpecimenCreationActivityTypeEnum"},{"location":"SpecimenCreationActivityTypeEnum/#enum-specimencreationactivitytypeenum","text":"The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) URI: SpecimenCreationActivityTypeEnum","title":"Enum: SpecimenCreationActivityTypeEnum"},{"location":"SpecimenCreationActivityTypeEnum/#permissible-values","text":"Value Meaning Description COLLECTION_FROM_SOURCE None An activity that collects an initial sample directly from a subject / source DERIVATION_FROM_SPECIMEN None An activity that derives a new specimen from an existing one","title":"Permissible Values"},{"location":"SpecimenCreationActivityTypeEnum/#slots","text":"Name Description activity_type The high-level type of creation activity","title":"Slots"},{"location":"SpecimenCreationActivityTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenCreationActivityTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenCreationActivityTypeEnum/#linkml-source","text":"name: SpecimenCreationActivityTypeEnum description: The high-level type of activity through which the specimen was generated (i.e. via collection from the original source, or via derivation from an existing specimen) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: COLLECTION_FROM_SOURCE: text: COLLECTION_FROM_SOURCE description: An activity that collects an initial sample directly from a subject / source. DERIVATION_FROM_SPECIMEN: text: DERIVATION_FROM_SPECIMEN description: An activity that derives a new specimen from an existing one.","title":"LinkML Source"},{"location":"SpecimenProcessingActivity/","text":"Class: SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. URI: bdchm:SpecimenProcessingActivity classDiagram class SpecimenProcessingActivity Entity <|-- SpecimenProcessingActivity SpecimenProcessingActivity : activity_type SpecimenProcessingActivity --> SpecimenProcessingActivityTypeEnum : activity_type SpecimenProcessingActivity : additive SpecimenProcessingActivity --> Substance : additive SpecimenProcessingActivity : date_ended SpecimenProcessingActivity --> TimePoint : date_ended SpecimenProcessingActivity : date_started SpecimenProcessingActivity --> TimePoint : date_started SpecimenProcessingActivity : duration SpecimenProcessingActivity --> Quantity : duration SpecimenProcessingActivity : id SpecimenProcessingActivity : method_type Inheritance Entity SpecimenProcessingActivity Slots Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenProcessingActivityTypeEnum The high-level type of processing activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct date_ended 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct duration 0..* Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to process the specimen direct additive 0..* Substance A type of material or reagent used as input when processing the specimen direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen processing_activity range SpecimenProcessingActivity Comments \"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied). Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenProcessingActivity native bdchm:SpecimenProcessingActivity LinkML Source Direct name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false inlined: true inlined_as_list: true Induced name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: activity_type owner: SpecimenProcessingActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: duration owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false alias: method_type owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenProcessingActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenProcessingActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenProcessingActivity"},{"location":"SpecimenProcessingActivity/#class-specimenprocessingactivity","text":"An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. URI: bdchm:SpecimenProcessingActivity classDiagram class SpecimenProcessingActivity Entity <|-- SpecimenProcessingActivity SpecimenProcessingActivity : activity_type SpecimenProcessingActivity --> SpecimenProcessingActivityTypeEnum : activity_type SpecimenProcessingActivity : additive SpecimenProcessingActivity --> Substance : additive SpecimenProcessingActivity : date_ended SpecimenProcessingActivity --> TimePoint : date_ended SpecimenProcessingActivity : date_started SpecimenProcessingActivity --> TimePoint : date_started SpecimenProcessingActivity : duration SpecimenProcessingActivity --> Quantity : duration SpecimenProcessingActivity : id SpecimenProcessingActivity : method_type","title":"Class: SpecimenProcessingActivity"},{"location":"SpecimenProcessingActivity/#inheritance","text":"Entity SpecimenProcessingActivity","title":"Inheritance"},{"location":"SpecimenProcessingActivity/#slots","text":"Name Cardinality and Range Description Inheritance activity_type 0..1 SpecimenProcessingActivityTypeEnum The high-level type of processing activity direct date_started 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct date_ended 0..1 TimePoint The date when the activity began (in this case, a specimen processing event) direct duration 0..* Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to process the specimen direct additive 0..* Substance A type of material or reagent used as input when processing the specimen direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenProcessingActivity/#usages","text":"used by used in type used Specimen processing_activity range SpecimenProcessingActivity","title":"Usages"},{"location":"SpecimenProcessingActivity/#comments","text":"\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).","title":"Comments"},{"location":"SpecimenProcessingActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenProcessingActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenProcessingActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenProcessingActivity native bdchm:SpecimenProcessingActivity","title":"Mappings"},{"location":"SpecimenProcessingActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenProcessingActivity/#direct","text":"name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: Substance required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"SpecimenProcessingActivity/#induced","text":"name: SpecimenProcessingActivity description: An activity that modifies the physical structure, composition, or state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities do not result in the generation of new entities - they take a single specimen as input, and output that same specimen. comments: - '\"Processing\" as defined here alters the physical nature of a specimen, such that storage or transport activities do not qualify as processing activities. When instantiating this class, create a separate instances for each type/method of processing performed (e.g. each method of fixation, freezing, labeling, etc. that is applied).' from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: activity_type: name: activity_type description: The high-level type of processing activity examples: - value: Fixation - value: Freezing - value: Mounting - value: Preservation from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: activity_type owner: SpecimenProcessingActivity domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: SpecimenProcessingActivityTypeEnum required: false date_started: name: date_started description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity began (in this case, a specimen processing event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenProcessingActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: duration owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false inlined: true inlined_as_list: true method_type: name: method_type description: A specific type of method or procedure performed to process the specimen examples: - value: Snap Freezing - value: Cryopreservation in liquid nitrogen (dead tissue) - value: Cryopreservation in dry ice (dead tissue) - value: Formalin fixed paraffin embedded (FFPE) - value: Formalin fixed-unbuffered - value: Formalin fixed-buffered - value: OCT from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenProcessingActivity_method_type multivalued: false alias: method_type owner: SpecimenProcessingActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false additive: name: additive description: A type of material or reagent used as input when processing the specimen examples: - value: Formalin from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: additive owner: SpecimenProcessingActivity domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: Substance required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenProcessingActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenProcessingActivityTypeEnum/","text":"Enum: SpecimenProcessingActivityTypeEnum The high-level type of processing activity performed. URI: SpecimenProcessingActivityTypeEnum Permissible Values Value Meaning Description FIXATION None A processing activity that applies chemicals to preserve biological tissues f... FREEZING None A processing activity that aims to freeze a specimen MOUNTING None A processing activity that aims to secure a specimen or slide in place in pre... PRESERVATION None A processing activity that aims to preserve a specimen Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenProcessingActivityTypeEnum description: The high-level type of processing activity performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FIXATION: text: FIXATION description: A processing activity that applies chemicals to preserve biological tissues from decay due to autolysis or putrefaction FREEZING: text: FREEZING description: A processing activity that aims to freeze a specimen. MOUNTING: text: MOUNTING description: A processing activity that aims to secure a specimen or slide in place in preparation for further examination (usually via microscopy) PRESERVATION: text: PRESERVATION description: A processing activity that aims to preserve a specimen.","title":"Enum: SpecimenProcessingActivityTypeEnum"},{"location":"SpecimenProcessingActivityTypeEnum/#enum-specimenprocessingactivitytypeenum","text":"The high-level type of processing activity performed. URI: SpecimenProcessingActivityTypeEnum","title":"Enum: SpecimenProcessingActivityTypeEnum"},{"location":"SpecimenProcessingActivityTypeEnum/#permissible-values","text":"Value Meaning Description FIXATION None A processing activity that applies chemicals to preserve biological tissues f... FREEZING None A processing activity that aims to freeze a specimen MOUNTING None A processing activity that aims to secure a specimen or slide in place in pre... PRESERVATION None A processing activity that aims to preserve a specimen","title":"Permissible Values"},{"location":"SpecimenProcessingActivityTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenProcessingActivityTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenProcessingActivityTypeEnum/#linkml-source","text":"name: SpecimenProcessingActivityTypeEnum description: The high-level type of processing activity performed. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: FIXATION: text: FIXATION description: A processing activity that applies chemicals to preserve biological tissues from decay due to autolysis or putrefaction FREEZING: text: FREEZING description: A processing activity that aims to freeze a specimen. MOUNTING: text: MOUNTING description: A processing activity that aims to secure a specimen or slide in place in preparation for further examination (usually via microscopy) PRESERVATION: text: PRESERVATION description: A processing activity that aims to preserve a specimen.","title":"LinkML Source"},{"location":"SpecimenQualityObservation/","text":"Class: SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQualityObservation classDiagram class SpecimenQualityObservation Observation <|-- SpecimenQualityObservation SpecimenQualityObservation : age_at_observation SpecimenQualityObservation : associated_participant SpecimenQualityObservation --> Participant : associated_participant SpecimenQualityObservation : associated_visit SpecimenQualityObservation --> Visit : associated_visit SpecimenQualityObservation : category SpecimenQualityObservation : focus SpecimenQualityObservation --> Entity : focus SpecimenQualityObservation : id SpecimenQualityObservation : method_type SpecimenQualityObservation : observation_type SpecimenQualityObservation : performed_by SpecimenQualityObservation --> Organization : performed_by SpecimenQualityObservation : value SpecimenQualityObservation --> ObservationValueString : value Inheritance Entity Observation SpecimenQualityObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueString The result of the observation, encoded as a free-text Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen quality_measure range SpecimenQualityObservation Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenQualityObservation native bdchm:SpecimenQualityObservation LinkML Source Direct name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true Induced name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQualityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQualityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQualityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQualityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQualityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQualityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQualityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQualityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQualityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQualityObservation domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenQualityObservation"},{"location":"SpecimenQualityObservation/#class-specimenqualityobservation","text":"A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQualityObservation classDiagram class SpecimenQualityObservation Observation <|-- SpecimenQualityObservation SpecimenQualityObservation : age_at_observation SpecimenQualityObservation : associated_participant SpecimenQualityObservation --> Participant : associated_participant SpecimenQualityObservation : associated_visit SpecimenQualityObservation --> Visit : associated_visit SpecimenQualityObservation : category SpecimenQualityObservation : focus SpecimenQualityObservation --> Entity : focus SpecimenQualityObservation : id SpecimenQualityObservation : method_type SpecimenQualityObservation : observation_type SpecimenQualityObservation : performed_by SpecimenQualityObservation --> Organization : performed_by SpecimenQualityObservation : value SpecimenQualityObservation --> ObservationValueString : value","title":"Class: SpecimenQualityObservation"},{"location":"SpecimenQualityObservation/#inheritance","text":"Entity Observation SpecimenQualityObservation","title":"Inheritance"},{"location":"SpecimenQualityObservation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueString The result of the observation, encoded as a free-text Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenQualityObservation/#usages","text":"used by used in type used Specimen quality_measure range SpecimenQualityObservation","title":"Usages"},{"location":"SpecimenQualityObservation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQualityObservation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQualityObservation/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenQualityObservation native bdchm:SpecimenQualityObservation","title":"Mappings"},{"location":"SpecimenQualityObservation/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenQualityObservation/#direct","text":"name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true","title":"Direct"},{"location":"SpecimenQualityObservation/#induced","text":"name: SpecimenQualityObservation description: A structured object that describes a characteristic of a specimen indicative of its quality or suitability for use, as generated through a point-in-time observation or measurement. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQualityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQualityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQualityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQualityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQualityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQualityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQualityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQualityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a free-text Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQualityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueString required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQualityObservation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenQualityObservationMethodEnum/","text":"Enum: SpecimenQualityObservationMethodEnum A type of method used in determining the quantity of a specimen. URI: SpecimenQualityObservationMethodEnum Permissible Values Value Meaning Description UV_SPEC None A technique used to measure light absorbance across the ultraviolet and visib... PICO_GREEN None A technique applying the Pico488 fluorescent sensor dye that is used for quan... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenQualityObservationMethodEnum description: A type of method used in determining the quantity of a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: UV_SPEC: text: UV_SPEC description: A technique used to measure light absorbance across the ultraviolet and visible ranges of the electromagnetic spectrum. PICO_GREEN: text: PICO_GREEN description: A technique applying the Pico488 fluorescent sensor dye that is used for quantifying the amount of double-stranded DNA (dsDNA) present in a given sample.","title":"Enum: SpecimenQualityObservationMethodEnum"},{"location":"SpecimenQualityObservationMethodEnum/#enum-specimenqualityobservationmethodenum","text":"A type of method used in determining the quantity of a specimen. URI: SpecimenQualityObservationMethodEnum","title":"Enum: SpecimenQualityObservationMethodEnum"},{"location":"SpecimenQualityObservationMethodEnum/#permissible-values","text":"Value Meaning Description UV_SPEC None A technique used to measure light absorbance across the ultraviolet and visib... PICO_GREEN None A technique applying the Pico488 fluorescent sensor dye that is used for quan...","title":"Permissible Values"},{"location":"SpecimenQualityObservationMethodEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQualityObservationMethodEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQualityObservationMethodEnum/#linkml-source","text":"name: SpecimenQualityObservationMethodEnum description: A type of method used in determining the quantity of a specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: UV_SPEC: text: UV_SPEC description: A technique used to measure light absorbance across the ultraviolet and visible ranges of the electromagnetic spectrum. PICO_GREEN: text: PICO_GREEN description: A technique applying the Pico488 fluorescent sensor dye that is used for quantifying the amount of double-stranded DNA (dsDNA) present in a given sample.","title":"LinkML Source"},{"location":"SpecimenQualityObservationTypeEnum/","text":"Enum: SpecimenQualityObservationTypeEnum Types of measurements that reflect the quality of a specimen or its suitability for use. URI: SpecimenQualityObservationTypeEnum Permissible Values Value Meaning Description A260_A280_RATIO None Ratio of absorbance measured at a wavelength of 260 over that at a wavelength... RIBOSOMAL_RNA_28S_16S_RATIO None Ratio of quantity of 28s RNA over that of 16s RNA Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenQualityObservationTypeEnum description: Types of measurements that reflect the quality of a specimen or its suitability for use. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: A260_A280_RATIO: text: A260_A280_RATIO description: Ratio of absorbance measured at a wavelength of 260 over that at a wavelength of 280. RIBOSOMAL_RNA_28S_16S_RATIO: text: RIBOSOMAL_RNA_28S_16S_RATIO description: Ratio of quantity of 28s RNA over that of 16s RNA.","title":"Enum: SpecimenQualityObservationTypeEnum"},{"location":"SpecimenQualityObservationTypeEnum/#enum-specimenqualityobservationtypeenum","text":"Types of measurements that reflect the quality of a specimen or its suitability for use. URI: SpecimenQualityObservationTypeEnum","title":"Enum: SpecimenQualityObservationTypeEnum"},{"location":"SpecimenQualityObservationTypeEnum/#permissible-values","text":"Value Meaning Description A260_A280_RATIO None Ratio of absorbance measured at a wavelength of 260 over that at a wavelength... RIBOSOMAL_RNA_28S_16S_RATIO None Ratio of quantity of 28s RNA over that of 16s RNA","title":"Permissible Values"},{"location":"SpecimenQualityObservationTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQualityObservationTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQualityObservationTypeEnum/#linkml-source","text":"name: SpecimenQualityObservationTypeEnum description: Types of measurements that reflect the quality of a specimen or its suitability for use. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: A260_A280_RATIO: text: A260_A280_RATIO description: Ratio of absorbance measured at a wavelength of 260 over that at a wavelength of 280. RIBOSOMAL_RNA_28S_16S_RATIO: text: RIBOSOMAL_RNA_28S_16S_RATIO description: Ratio of quantity of 28s RNA over that of 16s RNA.","title":"LinkML Source"},{"location":"SpecimenQuantityObservation/","text":"Class: SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQuantityObservation classDiagram class SpecimenQuantityObservation Observation <|-- SpecimenQuantityObservation SpecimenQuantityObservation : age_at_observation SpecimenQuantityObservation : associated_participant SpecimenQuantityObservation --> Participant : associated_participant SpecimenQuantityObservation : associated_visit SpecimenQuantityObservation --> Visit : associated_visit SpecimenQuantityObservation : category SpecimenQuantityObservation : focus SpecimenQuantityObservation --> Entity : focus SpecimenQuantityObservation : id SpecimenQuantityObservation : method_type SpecimenQuantityObservation : observation_type SpecimenQuantityObservation : performed_by SpecimenQuantityObservation --> Organization : performed_by SpecimenQuantityObservation : value SpecimenQuantityObservation --> ObservationValueQuantity : value Inheritance Entity Observation SpecimenQuantityObservation Slots Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen quantity_measure range SpecimenQuantityObservation Comments At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenQuantityObservation native bdchm:SpecimenQuantityObservation LinkML Source Direct name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true Induced name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQuantityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQuantityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQuantityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQuantityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQuantityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQuantityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQuantityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQuantityObservation domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenQuantityObservation"},{"location":"SpecimenQuantityObservation/#class-specimenquantityobservation","text":"A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. URI: bdchm:SpecimenQuantityObservation classDiagram class SpecimenQuantityObservation Observation <|-- SpecimenQuantityObservation SpecimenQuantityObservation : age_at_observation SpecimenQuantityObservation : associated_participant SpecimenQuantityObservation --> Participant : associated_participant SpecimenQuantityObservation : associated_visit SpecimenQuantityObservation --> Visit : associated_visit SpecimenQuantityObservation : category SpecimenQuantityObservation : focus SpecimenQuantityObservation --> Entity : focus SpecimenQuantityObservation : id SpecimenQuantityObservation : method_type SpecimenQuantityObservation : observation_type SpecimenQuantityObservation : performed_by SpecimenQuantityObservation --> Organization : performed_by SpecimenQuantityObservation : value SpecimenQuantityObservation --> ObservationValueQuantity : value","title":"Class: SpecimenQuantityObservation"},{"location":"SpecimenQuantityObservation/#inheritance","text":"Entity Observation SpecimenQuantityObservation","title":"Inheritance"},{"location":"SpecimenQuantityObservation/#slots","text":"Name Cardinality and Range Description Inheritance age_at_observation 0..1 Integer The Participant's age (expressed in days) when the Observation was made Observation category 0..1 String The general category of observation described Observation observation_type 1..1 String The type of Observation being represented (e Observation method_type 0..1 String A type of method used in generating the Observation result Observation focus 0..1 Entity The entity or entities directly observed/measured in generating an observatio... Observation associated_participant 0..1 Participant The patient that the observation is about (if not the direct focus) Observation associated_visit 0..1 Visit A reference to the Visit during which this Observation was recorded Observation performed_by 0..1 Organization The organization or group that performed the observation activity Observation value 1..1 ObservationValueQuantity The result of the observation, encoded as a Quantity Observation id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenQuantityObservation/#usages","text":"used by used in type used Specimen quantity_measure range SpecimenQuantityObservation","title":"Usages"},{"location":"SpecimenQuantityObservation/#comments","text":"At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data.","title":"Comments"},{"location":"SpecimenQuantityObservation/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQuantityObservation/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQuantityObservation/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenQuantityObservation native bdchm:SpecimenQuantityObservation","title":"Mappings"},{"location":"SpecimenQuantityObservation/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenQuantityObservation/#direct","text":"name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true","title":"Direct"},{"location":"SpecimenQuantityObservation/#induced","text":"name: SpecimenQuantityObservation description: A structured object that describes a single data item about the quantity of a Specimen, as generated through a point-in-time observation or measurement. comments: - At the core of an Observation is a flexible key-value pair (or a structured collection of key-value pairs), where a \"key\" field defines the type of observation made, and the \"value\" field describes the value or outcome of the observation. The fact that the type of observation captured is defined in the data allow Observation to convey a broad range of observation data. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Observation slot_usage: value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. multivalued: false domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true attributes: age_at_observation: name: age_at_observation description: The Participant's age (expressed in days) when the Observation was made. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_observation owner: SpecimenQuantityObservation domain_of: - Observation range: integer unit: ucum_code: d category: name: category description: The general category of observation described from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_category multivalued: false alias: category owner: SpecimenQuantityObservation domain_of: - ObservationSet - Observation range: string required: false observation_type: name: observation_type description: The type of Observation being represented (e.g. 'diastolic blood pressure') comments: - This field holds the \"key\" in the core key-value pair comprised of the observation_type field and the relevant value(s) field. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Observation_observation_type multivalued: false alias: observation_type owner: SpecimenQuantityObservation domain_of: - Observation range: string required: true method_type: name: method_type description: A type of method used in generating the Observation result. comments: - This may be a type of observational, measurement, experimental, or computational method specifying how to generate data (e.g. \"manual counting\", \"bright field microscopy\",). Or a Guideline or SOP specifying how to interpret data and/or encode the result of an Observation (e.g. a Cancer Staging system such as that defined by the AJCC, or variant interpretation guideline such as that provided by the ACMG). from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_Observation_method_type multivalued: false alias: method_type owner: SpecimenQuantityObservation domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false focus: name: focus description: The entity or entities directly observed/measured in generating an observation result. comments: - The \"focus\", \"subject\", and \"specimen\" fields are useful when data creators want an Observation object to stand on its own, so it can point back to the entities it is about. These fields are not needed when an Observation is embedded in a Specimen or other entity, where focus, subject, and specimen can be determined from context. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: focus owner: SpecimenQuantityObservation domain_of: - Document - ObservationSet - Observation range: Entity required: false associated_participant: name: associated_participant description: The patient that the observation is about (if not the direct focus). e.g. observations are often made on specimens derived from a patient, or other entities related to a patient, that ultimately tell us something about the patient of interest. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: associated_participant owner: SpecimenQuantityObservation domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant required: false associated_visit: name: associated_visit description: A reference to the Visit during which this Observation was recorded. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_visit owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: Visit performed_by: name: performed_by description: The organization or group that performed the observation activity. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: performed_by owner: SpecimenQuantityObservation domain_of: - SpecimenCreationActivity - ObservationSet - Observation range: Organization required: false value: name: value description: The result of the observation, encoded as a Quantity. comments: - One and only one of the value(x) fields must be populated. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: value owner: SpecimenQuantityObservation domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: ObservationValueQuantity required: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenQuantityObservation domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenQuantityObservationTypeEnum/","text":"Enum: SpecimenQuantityObservationTypeEnum Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. URI: SpecimenQuantityObservationTypeEnum Permissible Values Value Meaning Description WEIGHT None The current weight of the specimen, at the time of recording (as opposed to a... VOLUME None The current total volume of the specimen, at the time of recording CONCENTRATION None The concentration of an extracted analyte that is present in a specimen (spec... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenQuantityObservationTypeEnum description: Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: WEIGHT: text: WEIGHT description: The current weight of the specimen, at the time of recording (as opposed to an initial weight before its processing or portioning). VOLUME: text: VOLUME description: The current total volume of the specimen, at the time of recording. CONCENTRATION: text: CONCENTRATION description: The concentration of an extracted analyte that is present in a specimen (specifically, in a specimen of type 'analyte', or an 'aliquot' derived from an analyte). For example, the concentration of DNA in a specimen created through extracting DNA from a blood sample.","title":"Enum: SpecimenQuantityObservationTypeEnum"},{"location":"SpecimenQuantityObservationTypeEnum/#enum-specimenquantityobservationtypeenum","text":"Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. URI: SpecimenQuantityObservationTypeEnum","title":"Enum: SpecimenQuantityObservationTypeEnum"},{"location":"SpecimenQuantityObservationTypeEnum/#permissible-values","text":"Value Meaning Description WEIGHT None The current weight of the specimen, at the time of recording (as opposed to a... VOLUME None The current total volume of the specimen, at the time of recording CONCENTRATION None The concentration of an extracted analyte that is present in a specimen (spec...","title":"Permissible Values"},{"location":"SpecimenQuantityObservationTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenQuantityObservationTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenQuantityObservationTypeEnum/#linkml-source","text":"name: SpecimenQuantityObservationTypeEnum description: Measures related to the quantity of a specimen or analyte it currently contains - e.g. its weight, volume, or concentration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: WEIGHT: text: WEIGHT description: The current weight of the specimen, at the time of recording (as opposed to an initial weight before its processing or portioning). VOLUME: text: VOLUME description: The current total volume of the specimen, at the time of recording. CONCENTRATION: text: CONCENTRATION description: The concentration of an extracted analyte that is present in a specimen (specifically, in a specimen of type 'analyte', or an 'aliquot' derived from an analyte). For example, the concentration of DNA in a specimen created through extracting DNA from a blood sample.","title":"LinkML Source"},{"location":"SpecimenStorageActivity/","text":"Class: SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. URI: bdchm:SpecimenStorageActivity classDiagram class SpecimenStorageActivity Entity <|-- SpecimenStorageActivity SpecimenStorageActivity : container SpecimenStorageActivity --> SpecimenContainer : container SpecimenStorageActivity : date_ended SpecimenStorageActivity --> TimePoint : date_ended SpecimenStorageActivity : date_started SpecimenStorageActivity --> TimePoint : date_started SpecimenStorageActivity : duration SpecimenStorageActivity --> Quantity : duration SpecimenStorageActivity : id SpecimenStorageActivity : method_type Inheritance Entity SpecimenStorageActivity Slots Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a storage event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a storage event) direct duration 0..1 Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to store the specimen direct container 0..* SpecimenContainer A container in which the specimen is held or affixed during its storage direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen storage_activity range SpecimenStorageActivity Comments Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenStorageActivity native bdchm:SpecimenStorageActivity LinkML Source Direct name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenContainer required: false inlined: true inlined_as_list: true Induced name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: duration owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false alias: method_type owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenStorageActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenStorageActivity"},{"location":"SpecimenStorageActivity/#class-specimenstorageactivity","text":"An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. URI: bdchm:SpecimenStorageActivity classDiagram class SpecimenStorageActivity Entity <|-- SpecimenStorageActivity SpecimenStorageActivity : container SpecimenStorageActivity --> SpecimenContainer : container SpecimenStorageActivity : date_ended SpecimenStorageActivity --> TimePoint : date_ended SpecimenStorageActivity : date_started SpecimenStorageActivity --> TimePoint : date_started SpecimenStorageActivity : duration SpecimenStorageActivity --> Quantity : duration SpecimenStorageActivity : id SpecimenStorageActivity : method_type","title":"Class: SpecimenStorageActivity"},{"location":"SpecimenStorageActivity/#inheritance","text":"Entity SpecimenStorageActivity","title":"Inheritance"},{"location":"SpecimenStorageActivity/#slots","text":"Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a storage event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a storage event) direct duration 0..1 Quantity The length of time over which the activity was performed direct method_type 0..1 String A specific type of method or procedure performed to store the specimen direct container 0..* SpecimenContainer A container in which the specimen is held or affixed during its storage direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenStorageActivity/#usages","text":"used by used in type used Specimen storage_activity range SpecimenStorageActivity","title":"Usages"},{"location":"SpecimenStorageActivity/#comments","text":"Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each.","title":"Comments"},{"location":"SpecimenStorageActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenStorageActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenStorageActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenStorageActivity native bdchm:SpecimenStorageActivity","title":"Mappings"},{"location":"SpecimenStorageActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenStorageActivity/#direct","text":"name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true range: SpecimenContainer required: false inlined: true inlined_as_list: true","title":"Direct"},{"location":"SpecimenStorageActivity/#induced","text":"name: SpecimenStorageActivity description: An activity in which a specimen is stored or maintained in a particular location, container, or state. Unlike 'processing' activities, storage does not alter the \\nintrinsic physical nature of a specimen. comments: - Think of the StorageActivity as being one of many possible periods when the specimen was stored at some location and in some state or condition. We may want to capture storage dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a storage event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenStorageActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. comments: - 'Quantity.unit MUST be a unit of time. ' from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: duration owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: Quantity required: false method_type: name: method_type description: A specific type of method or procedure performed to store the specimen examples: - value: ambient temperature - value: cut slide - value: fresh - value: frozen at -70C - value: frozen at -150C - value: frozen in liquid nitrogen - value: frozen in vapor phase - value: paraffin block - value: RNAlater at 4C from_schema: https://w3id.org/nhlbidatastage/bdchm values_from: - crdch:enum_CRDCH_SpecimenStorageActivity_method_type multivalued: false alias: method_type owner: SpecimenStorageActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - ObservationSet - Observation range: string required: false container: name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenStorageActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenTransportActivity/","text":"Class: SpecimenTransportActivity An activity through which a specimen is transported between locations or organizations. URI: bdchm:SpecimenTransportActivity classDiagram class SpecimenTransportActivity Entity <|-- SpecimenTransportActivity SpecimenTransportActivity : date_ended SpecimenTransportActivity --> TimePoint : date_ended SpecimenTransportActivity : date_started SpecimenTransportActivity --> TimePoint : date_started SpecimenTransportActivity : duration SpecimenTransportActivity : id SpecimenTransportActivity : transport_destination SpecimenTransportActivity --> Organization : transport_destination SpecimenTransportActivity : transport_origin SpecimenTransportActivity --> Organization : transport_origin Inheritance Entity SpecimenTransportActivity Slots Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a transport event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a transport event) direct duration 0..* String The length of time over which the activity was performed direct transport_origin 0..1 Organization An organization (facility, site, lab, etc) from which the specimen was transp... direct transport_destination 0..1 Organization An organization (facility, site, lab, etc) to which the specimen is delivered... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used Specimen transport_activity range SpecimenTransportActivity Comments Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:SpecimenTransportActivity native bdchm:SpecimenTransportActivity LinkML Source Direct name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false Induced name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: duration owner: SpecimenTransportActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_origin owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenTransportActivity domain_of: - Entity range: uriorcurie required: true","title":"Class: SpecimenTransportActivity"},{"location":"SpecimenTransportActivity/#class-specimentransportactivity","text":"An activity through which a specimen is transported between locations or organizations. URI: bdchm:SpecimenTransportActivity classDiagram class SpecimenTransportActivity Entity <|-- SpecimenTransportActivity SpecimenTransportActivity : date_ended SpecimenTransportActivity --> TimePoint : date_ended SpecimenTransportActivity : date_started SpecimenTransportActivity --> TimePoint : date_started SpecimenTransportActivity : duration SpecimenTransportActivity : id SpecimenTransportActivity : transport_destination SpecimenTransportActivity --> Organization : transport_destination SpecimenTransportActivity : transport_origin SpecimenTransportActivity --> Organization : transport_origin","title":"Class: SpecimenTransportActivity"},{"location":"SpecimenTransportActivity/#inheritance","text":"Entity SpecimenTransportActivity","title":"Inheritance"},{"location":"SpecimenTransportActivity/#slots","text":"Name Cardinality and Range Description Inheritance date_started 0..1 TimePoint The date when the activity began (in this case, a transport event) direct date_ended 0..1 TimePoint The date when the activity ended (in this case, a transport event) direct duration 0..* String The length of time over which the activity was performed direct transport_origin 0..1 Organization An organization (facility, site, lab, etc) from which the specimen was transp... direct transport_destination 0..1 Organization An organization (facility, site, lab, etc) to which the specimen is delivered... direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"SpecimenTransportActivity/#usages","text":"used by used in type used Specimen transport_activity range SpecimenTransportActivity","title":"Usages"},{"location":"SpecimenTransportActivity/#comments","text":"Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each.","title":"Comments"},{"location":"SpecimenTransportActivity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenTransportActivity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenTransportActivity/#mappings","text":"Mapping Type Mapped Value self bdchm:SpecimenTransportActivity native bdchm:SpecimenTransportActivity","title":"Mappings"},{"location":"SpecimenTransportActivity/#linkml-source","text":"","title":"LinkML Source"},{"location":"SpecimenTransportActivity/#direct","text":"name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Organization required: false","title":"Direct"},{"location":"SpecimenTransportActivity/#induced","text":"name: SpecimenTransportActivity description: An activity through which a specimen is transported between locations or organizations. comments: - Think of the TransportActivity as being one of many possible occasions when the specimen was moved from one location to another, in some state or condition. We may want to capture dates and conditions for each. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_started: name: date_started description: The date when the activity began (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_started owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false date_ended: name: date_ended description: The date when the activity ended (in this case, a transport event). comments: - To allow for more precise specification of dates when an activity was performed, we provide date_started and date_ended attributes. If source data only provides a single date, it SHOULD be entered as both the date_started and date_ended. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: false alias: date_ended owner: SpecimenTransportActivity domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: TimePoint required: false duration: name: duration description: The length of time over which the activity was performed. from_schema: https://w3id.org/nhlbidatastage/bdchm multivalued: true alias: duration owner: SpecimenTransportActivity domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string required: false inlined: true inlined_as_list: true transport_origin: name: transport_origin description: An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_origin owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false transport_destination: name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: SpecimenTransportActivity domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"SpecimenTypeEnum/","text":"Enum: SpecimenTypeEnum A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: SpecimenTypeEnum Permissible Values Value Meaning Description ALIQUOT None A specimen that results from the division of some parent specimen into equal ... ANALYTE None A specimen generated through the extraction of a specified class of substance... FRESH_SPECIMEN None A specimen representing the material that was directly collected from a subje... PORTION None A physical sub-part taken from an existing specimen SLIDE None A specimen that is mounted on a slide or coverslip for microscopic analysis Slots Name Description specimen_type The high-level type of the specimen, based on its derivation provenance (i Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: SpecimenTypeEnum description: A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIQUOT: text: ALIQUOT description: A specimen that results from the division of some parent specimen into equal amounts for downstream analysis. ANALYTE: text: ANALYTE description: A specimen generated through the extraction of a specified class of substance/chemical (e.g. DNA, RNA, protein) from a parent specimen, which is stored in solution as an analyte. FRESH_SPECIMEN: text: FRESH_SPECIMEN description: A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen). PORTION: text: PORTION description: A physical sub-part taken from an existing specimen. SLIDE: text: SLIDE description: A specimen that is mounted on a slide or coverslip for microscopic analysis.","title":"Enum: SpecimenTypeEnum"},{"location":"SpecimenTypeEnum/#enum-specimentypeenum","text":"A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: SpecimenTypeEnum","title":"Enum: SpecimenTypeEnum"},{"location":"SpecimenTypeEnum/#permissible-values","text":"Value Meaning Description ALIQUOT None A specimen that results from the division of some parent specimen into equal ... ANALYTE None A specimen generated through the extraction of a specified class of substance... FRESH_SPECIMEN None A specimen representing the material that was directly collected from a subje... PORTION None A physical sub-part taken from an existing specimen SLIDE None A specimen that is mounted on a slide or coverslip for microscopic analysis","title":"Permissible Values"},{"location":"SpecimenTypeEnum/#slots","text":"Name Description specimen_type The high-level type of the specimen, based on its derivation provenance (i","title":"Slots"},{"location":"SpecimenTypeEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"SpecimenTypeEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"SpecimenTypeEnum/#linkml-source","text":"name: SpecimenTypeEnum description: A high-level type of specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIQUOT: text: ALIQUOT description: A specimen that results from the division of some parent specimen into equal amounts for downstream analysis. ANALYTE: text: ANALYTE description: A specimen generated through the extraction of a specified class of substance/chemical (e.g. DNA, RNA, protein) from a parent specimen, which is stored in solution as an analyte. FRESH_SPECIMEN: text: FRESH_SPECIMEN description: A specimen representing the material that was directly collected from a subject (i.e. not generated through portioning, aliquoting, or analyte extraction from an existing specimen). PORTION: text: PORTION description: A physical sub-part taken from an existing specimen. SLIDE: text: SLIDE description: A specimen that is mounted on a slide or coverslip for microscopic analysis.","title":"LinkML Source"},{"location":"String/","text":"Type: String A character string URI: xsd:string base : str uri : xsd:string Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: String"},{"location":"String/#type-string","text":"A character string URI: xsd:string base : str uri : xsd:string","title":"Type: String"},{"location":"String/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"String/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Substance/","text":"Class: Substance A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. URI: bdchm:Substance classDiagram class Substance Entity <|-- Substance Substance : id Substance : role Substance : substance_quantity Substance --> Quantity : substance_quantity Substance : substance_type Inheritance Entity Substance Slots Name Cardinality and Range Description Inheritance substance_type 0..1 String The specific type of the substance - at as granular a level as possible direct role 0..* String A role played by the substance in a particular application (e direct substance_quantity 0..1 Quantity The quantity of substance this instance stands for direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used SpecimenContainer additive range Substance SpecimenCreationActivity additive range Substance SpecimenProcessingActivity additive range Substance Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Substance native bdchm:Substance LinkML Source Direct name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false Induced name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: substance_quantity owner: Substance domain_of: - Substance range: Quantity required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Substance domain_of: - Entity range: uriorcurie required: true","title":"Class: Substance"},{"location":"Substance/#class-substance","text":"A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. URI: bdchm:Substance classDiagram class Substance Entity <|-- Substance Substance : id Substance : role Substance : substance_quantity Substance --> Quantity : substance_quantity Substance : substance_type","title":"Class: Substance"},{"location":"Substance/#inheritance","text":"Entity Substance","title":"Inheritance"},{"location":"Substance/#slots","text":"Name Cardinality and Range Description Inheritance substance_type 0..1 String The specific type of the substance - at as granular a level as possible direct role 0..* String A role played by the substance in a particular application (e direct substance_quantity 0..1 Quantity The quantity of substance this instance stands for direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Substance/#usages","text":"used by used in type used SpecimenContainer additive range Substance SpecimenCreationActivity additive range Substance SpecimenProcessingActivity additive range Substance","title":"Usages"},{"location":"Substance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Substance/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Substance/#mappings","text":"Mapping Type Mapped Value self bdchm:Substance native bdchm:Substance","title":"Mappings"},{"location":"Substance/#linkml-source","text":"","title":"LinkML Source"},{"location":"Substance/#direct","text":"name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false range: Quantity required: false","title":"Direct"},{"location":"Substance/#induced","text":"name: Substance description: A type of material substance, or instance thereof, as used in a particular application. May include information about the role the substance played in a particular application. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: substance_type: name: substance_type description: The specific type of the substance - at as granular a level as possible. May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false role: name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false substance_quantity: name: substance_quantity description: The quantity of substance this instance stands for. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: substance_quantity owner: Substance domain_of: - Substance range: Quantity required: false id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Substance domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"Time/","text":"Type: Time A time object represents a (local) time of day, independent of any particular day URI: xsd:time base : XSDTime uri : xsd:time repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Time"},{"location":"Time/#type-time","text":"A time object represents a (local) time of day, independent of any particular day URI: xsd:time base : XSDTime uri : xsd:time repr : str","title":"Type: Time"},{"location":"Time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Time/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"TimePeriod/","text":"Class: TimePeriod A period of time between a start and end time point. URI: bdchm:TimePeriod classDiagram class TimePeriod TimePeriod : period_end TimePeriod --> TimePoint : period_end TimePeriod : period_start TimePeriod --> TimePoint : period_start Slots Name Cardinality and Range Description Inheritance period_start 0..1 TimePoint When a period of time started direct period_end 0..1 TimePoint When a period of time ended direct Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:TimePeriod native bdchm:TimePeriod LinkML Source Direct name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint Induced name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_start owner: TimePeriod domain_of: - TimePeriod range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_end owner: TimePeriod domain_of: - TimePeriod range: TimePoint","title":"Class: TimePeriod"},{"location":"TimePeriod/#class-timeperiod","text":"A period of time between a start and end time point. URI: bdchm:TimePeriod classDiagram class TimePeriod TimePeriod : period_end TimePeriod --> TimePoint : period_end TimePeriod : period_start TimePeriod --> TimePoint : period_start","title":"Class: TimePeriod"},{"location":"TimePeriod/#slots","text":"Name Cardinality and Range Description Inheritance period_start 0..1 TimePoint When a period of time started direct period_end 0..1 TimePoint When a period of time ended direct","title":"Slots"},{"location":"TimePeriod/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"TimePeriod/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"TimePeriod/#mappings","text":"Mapping Type Mapped Value self bdchm:TimePeriod native bdchm:TimePeriod","title":"Mappings"},{"location":"TimePeriod/#linkml-source","text":"","title":"LinkML Source"},{"location":"TimePeriod/#direct","text":"name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint","title":"Direct"},{"location":"TimePeriod/#induced","text":"name: TimePeriod description: A period of time between a start and end time point. from_schema: https://w3id.org/nhlbidatastage/bdchm attributes: period_start: name: period_start description: When a period of time started. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_start owner: TimePeriod domain_of: - TimePeriod range: TimePoint period_end: name: period_end description: When a period of time ended. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: period_end owner: TimePeriod domain_of: - TimePeriod range: TimePoint","title":"Induced"},{"location":"TimePoint/","text":"Class: TimePoint A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. URI: bdchm:TimePoint classDiagram class TimePoint Entity <|-- TimePoint TimePoint : date_time TimePoint : event_type TimePoint : id TimePoint : index_time_point TimePoint --> TimePoint : index_time_point TimePoint : offset_from_index Inheritance Entity TimePoint Slots Name Cardinality and Range Description Inheritance date_time 0..1 Datetime An explicitly specified timepoint described in terms of a date and optionally... direct index_time_point 0..1 TimePoint Another TimePoint from which this point is offset direct offset_from_index 0..1 Integer A quantity of time that, together with the index date or event, can be used t... direct event_type 0..1 String An event that occurred at the point in time specified by this TimePoint direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used ResearchStudy date_started range TimePoint ResearchStudy date_ended range TimePoint ResearchStudy associated_timepoint range TimePoint Consent valid_from range TimePoint Consent valid_to range TimePoint TimePoint index_time_point range TimePoint TimePeriod period_start range TimePoint TimePeriod period_end range TimePoint QuestionnaireResponseValueTimePoint value range TimePoint SpecimenCreationActivity date_started range TimePoint SpecimenCreationActivity date_ended range TimePoint SpecimenProcessingActivity date_started range TimePoint SpecimenProcessingActivity date_ended range TimePoint SpecimenStorageActivity date_started range TimePoint SpecimenStorageActivity date_ended range TimePoint SpecimenTransportActivity date_started range TimePoint SpecimenTransportActivity date_ended range TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:TimePoint native bdchm:TimePoint LinkML Source Direct name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string Induced name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_time_point owner: TimePoint domain_of: - TimePoint range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: offset_from_index owner: TimePoint domain_of: - TimePoint range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: TimePoint domain_of: - Entity range: uriorcurie required: true","title":"Class: TimePoint"},{"location":"TimePoint/#class-timepoint","text":"A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. URI: bdchm:TimePoint classDiagram class TimePoint Entity <|-- TimePoint TimePoint : date_time TimePoint : event_type TimePoint : id TimePoint : index_time_point TimePoint --> TimePoint : index_time_point TimePoint : offset_from_index","title":"Class: TimePoint"},{"location":"TimePoint/#inheritance","text":"Entity TimePoint","title":"Inheritance"},{"location":"TimePoint/#slots","text":"Name Cardinality and Range Description Inheritance date_time 0..1 Datetime An explicitly specified timepoint described in terms of a date and optionally... direct index_time_point 0..1 TimePoint Another TimePoint from which this point is offset direct offset_from_index 0..1 Integer A quantity of time that, together with the index date or event, can be used t... direct event_type 0..1 String An event that occurred at the point in time specified by this TimePoint direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"TimePoint/#usages","text":"used by used in type used ResearchStudy date_started range TimePoint ResearchStudy date_ended range TimePoint ResearchStudy associated_timepoint range TimePoint Consent valid_from range TimePoint Consent valid_to range TimePoint TimePoint index_time_point range TimePoint TimePeriod period_start range TimePoint TimePeriod period_end range TimePoint QuestionnaireResponseValueTimePoint value range TimePoint SpecimenCreationActivity date_started range TimePoint SpecimenCreationActivity date_ended range TimePoint SpecimenProcessingActivity date_started range TimePoint SpecimenProcessingActivity date_ended range TimePoint SpecimenStorageActivity date_started range TimePoint SpecimenStorageActivity date_ended range TimePoint SpecimenTransportActivity date_started range TimePoint SpecimenTransportActivity date_ended range TimePoint","title":"Usages"},{"location":"TimePoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"TimePoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"TimePoint/#mappings","text":"Mapping Type Mapped Value self bdchm:TimePoint native bdchm:TimePoint","title":"Mappings"},{"location":"TimePoint/#linkml-source","text":"","title":"LinkML Source"},{"location":"TimePoint/#direct","text":"name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: string","title":"Direct"},{"location":"TimePoint/#induced","text":"name: TimePoint description: A structured representation of a single point in time that allows direct/explicit declaration as a dateTime, specification in terms of offset from a defined index, or description of an event type as a proxy for the time point when it occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: date_time: name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime index_time_point: name: index_time_point description: Another TimePoint from which this point is offset. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: index_time_point owner: TimePoint domain_of: - TimePoint range: TimePoint offset_from_index: name: offset_from_index description: A quantity of time that, together with the index date or event, can be used to derive a specific timepoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: offset_from_index owner: TimePoint domain_of: - TimePoint range: integer event_type: name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: TimePoint domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"UnitOfMeasurementEnum/","text":"Enum: UnitOfMeasurementEnum Standard units of measurement from the Units of Measurement (UOM) ontology . Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. URI: UnitOfMeasurementEnum This is a dynamic enum Slots Name Description unit A coded or free text (in the Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: UnitOfMeasurementEnum description: Standard units of measurement from the [Units of Measurement (UOM) ontology](https://units-of-measurement.org/). Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: UOM","title":"Enum: UnitOfMeasurementEnum"},{"location":"UnitOfMeasurementEnum/#enum-unitofmeasurementenum","text":"Standard units of measurement from the Units of Measurement (UOM) ontology . Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. URI: UnitOfMeasurementEnum This is a dynamic enum","title":"Enum: UnitOfMeasurementEnum"},{"location":"UnitOfMeasurementEnum/#slots","text":"Name Description unit A coded or free text (in the","title":"Slots"},{"location":"UnitOfMeasurementEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"UnitOfMeasurementEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"UnitOfMeasurementEnum/#linkml-source","text":"name: UnitOfMeasurementEnum description: Standard units of measurement from the [Units of Measurement (UOM) ontology](https://units-of-measurement.org/). Units-of-measurement (UOM) provides URLs for Unified Code for Units of Measure (UCUM) codes, and mappings to a number of units ontologies and systems, in human- and machine-readable linked data formats. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: UOM","title":"LinkML Source"},{"location":"Uri/","text":"Type: Uri a complete URI URI: xsd:anyURI base : URI uri : xsd:anyURI repr : str Comments in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Uri"},{"location":"Uri/#type-uri","text":"a complete URI URI: xsd:anyURI base : URI uri : xsd:anyURI repr : str","title":"Type: Uri"},{"location":"Uri/#comments","text":"in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node","title":"Comments"},{"location":"Uri/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uri/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Uriorcurie/","text":"Type: Uriorcurie a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#type-uriorcurie","text":"a URI or a CURIE URI: xsd:anyURI base : URIorCURIE uri : xsd:anyURI repr : str","title":"Type: Uriorcurie"},{"location":"Uriorcurie/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Uriorcurie/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VertebrateBreedEnum/","text":"Enum: VertebrateBreedEnum A constrained set of enumerative values containing the VBO values for vertebrate breeds. URI: VertebrateBreedEnum This is a dynamic enum Slots Name Description breed A label given to a group of animals homogeneous in appearance and other chara... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VertebrateBreedEnum description: A constrained set of enumerative values containing the VBO values for vertebrate breeds. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:vbo source_nodes: - VBO:0400000 relationship_types: - rdfs:subClassOf include_self: false","title":"Enum: VertebrateBreedEnum"},{"location":"VertebrateBreedEnum/#enum-vertebratebreedenum","text":"A constrained set of enumerative values containing the VBO values for vertebrate breeds. URI: VertebrateBreedEnum This is a dynamic enum","title":"Enum: VertebrateBreedEnum"},{"location":"VertebrateBreedEnum/#slots","text":"Name Description breed A label given to a group of animals homogeneous in appearance and other chara...","title":"Slots"},{"location":"VertebrateBreedEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VertebrateBreedEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VertebrateBreedEnum/#linkml-source","text":"name: VertebrateBreedEnum description: A constrained set of enumerative values containing the VBO values for vertebrate breeds. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 reachable_from: source_ontology: obo:vbo source_nodes: - VBO:0400000 relationship_types: - rdfs:subClassOf include_self: false","title":"LinkML Source"},{"location":"Visit/","text":"Class: Visit Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) URI: bdchm:Visit classDiagram class Visit Entity <|-- Visit Visit : age_at_visit_end Visit : age_at_visit_start Visit : associated_participant Visit --> Participant : associated_participant Visit : id Visit : visit_category Visit --> VisitCategoryEnum : visit_category Visit : visit_provenance Visit --> VisitProvenanceEnum : visit_provenance Inheritance Entity Visit Slots Name Cardinality and Range Description Inheritance visit_category 0..1 VisitCategoryEnum A value representing the kind (or category) of visit, like inpatient or outpa... direct age_at_visit_start 0..1 Integer The age of the Participant (in days) at the start of the Visit direct age_at_visit_end 0..1 Integer The age of the Participant (in days) at the end of the Visit direct visit_provenance 0..1 VisitProvenanceEnum A value representing the provenance of the visit record, or where the record ... direct associated_participant 0..1 Participant A reference to the Participant for whom this Visit occurred direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity Usages used by used in type used QuestionnaireResponse associated_visit range Visit Condition associated_visit range Visit Procedure associated_visit range Visit DrugExposure associated_visit range Visit DeviceExposure associated_visit range Visit DimensionalObservation associated_visit range Visit SpecimenQualityObservation associated_visit range Visit SpecimenQuantityObservation associated_visit range Visit Observation associated_visit range Visit Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm Mappings Mapping Type Mapped Value self bdchm:Visit native bdchm:Visit LinkML Source Direct name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant Induced name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_start owner: Visit domain_of: - Visit range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_end owner: Visit domain_of: - Visit range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Visit domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Visit domain_of: - Entity range: uriorcurie required: true","title":"Class: Visit"},{"location":"Visit/#class-visit","text":"Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) URI: bdchm:Visit classDiagram class Visit Entity <|-- Visit Visit : age_at_visit_end Visit : age_at_visit_start Visit : associated_participant Visit --> Participant : associated_participant Visit : id Visit : visit_category Visit --> VisitCategoryEnum : visit_category Visit : visit_provenance Visit --> VisitProvenanceEnum : visit_provenance","title":"Class: Visit"},{"location":"Visit/#inheritance","text":"Entity Visit","title":"Inheritance"},{"location":"Visit/#slots","text":"Name Cardinality and Range Description Inheritance visit_category 0..1 VisitCategoryEnum A value representing the kind (or category) of visit, like inpatient or outpa... direct age_at_visit_start 0..1 Integer The age of the Participant (in days) at the start of the Visit direct age_at_visit_end 0..1 Integer The age of the Participant (in days) at the end of the Visit direct visit_provenance 0..1 VisitProvenanceEnum A value representing the provenance of the visit record, or where the record ... direct associated_participant 0..1 Participant A reference to the Participant for whom this Visit occurred direct id 1..1 Uriorcurie The 'logical' identifier of the entity within the system of record Entity","title":"Slots"},{"location":"Visit/#usages","text":"used by used in type used QuestionnaireResponse associated_visit range Visit Condition associated_visit range Visit Procedure associated_visit range Visit DrugExposure associated_visit range Visit DeviceExposure associated_visit range Visit DimensionalObservation associated_visit range Visit SpecimenQualityObservation associated_visit range Visit SpecimenQuantityObservation associated_visit range Visit Observation associated_visit range Visit","title":"Usages"},{"location":"Visit/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"Visit/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"Visit/#mappings","text":"Mapping Type Mapped Value self bdchm:Visit native bdchm:Visit","title":"Mappings"},{"location":"Visit/#linkml-source","text":"","title":"LinkML Source"},{"location":"Visit/#direct","text":"name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm range: Participant","title":"Direct"},{"location":"Visit/#induced","text":"name: Visit description: Events where Persons engage with the healthcare system for a duration of time. They are often also called \u201cEncounters\u201d. Visits are defined by a configuration of circumstances under which they occur, such as (i) whether the patient comes to a healthcare institution, the other way around, or the interaction is remote, (ii) whether and what kind of trained medical staff is delivering the service during the Visit, and (iii) whether the Visit is transient or for a longer period involving a stay in bed. (OMOP) from_schema: https://w3id.org/nhlbidatastage/bdchm is_a: Entity attributes: visit_category: name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum age_at_visit_start: name: age_at_visit_start description: The age of the Participant (in days) at the start of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_start owner: Visit domain_of: - Visit range: integer unit: ucum_code: d age_at_visit_end: name: age_at_visit_end description: The age of the Participant (in days) at the end of the Visit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: age_at_visit_end owner: Visit domain_of: - Visit range: integer unit: ucum_code: d visit_provenance: name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum associated_participant: name: associated_participant description: A reference to the Participant for whom this Visit occurred. from_schema: https://w3id.org/nhlbidatastage/bdchm alias: associated_participant owner: Visit domain_of: - Demography - Visit - Condition - Procedure - DrugExposure - DeviceExposure - File - ObservationSet - Observation range: Participant id: name: id description: The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id owner: Visit domain_of: - Entity range: uriorcurie required: true","title":"Induced"},{"location":"VisitCategoryEnum/","text":"Enum: VisitCategoryEnum A constrained set of enumerative values containing the OMOP values for visit categories. URI: VisitCategoryEnum Permissible Values Value Meaning Description INPATIENT OMOP:9201 Person visiting hospital, at a care stie, in bed, for duration of more than o... EMERGENCY_ROOM OMOP:9203 Person visiting dedicated healthcare institution for treating emergencies, at... EMERGENCY_ROOM_AND_INPATIENT OMOP:262 Person visiting ER followed by a subsequent Inpatient Visit, where Emergency ... NON_HOSPITAL_INSTITUTION OMOP:42898160 Person visiting dedicated institution for reasons of poor health, at a Care S... OUTPATIENT OMOP:9202 Person visiting dedicated ambulatory healthcare institution, at a Care Site, ... HOME OMOP:581476 Provider visiting Person, without a Care Site, within one day, delivering ser... TELEHEALTH OMOP:5083 Patient engages with Provider through communication media PHARMACY OMOP:581458 Person visiting pharmacy for dispensing of Drug, at a Care Site, within one d... LABORATORY OMOP:32036 Patient visiting dedicated institution, at a Care Site, within one day, for t... AMBULANCE OMOP:581478 Person using transportation service for the purpose of initiating one of the ... CASE_MANAGEMENT OMOP:38004193 Person interacting with healthcare system, without a Care Site, within a day,... Slots Name Description visit_category A value representing the kind (or category) of visit, like inpatient or outpa... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VisitCategoryEnum description: A constrained set of enumerative values containing the OMOP values for visit categories. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: INPATIENT: text: INPATIENT description: Person visiting hospital, at a care stie, in bed, for duration of more than one day, with physicians and other Providers permanently available to deliver service around the clock meaning: OMOP:9201 EMERGENCY_ROOM: text: EMERGENCY_ROOM description: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within one day, with physicians and Providers permanently available to deliver service around the clock meaning: OMOP:9203 EMERGENCY_ROOM_AND_INPATIENT: text: EMERGENCY_ROOM_AND_INPATIENT description: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of hospital, and transition from the ER to other hospital departments is undefined meaning: OMOP:262 NON_HOSPITAL_INSTITUTION: text: NON_HOSPITAL_INSTITUTION description: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock meaning: OMOP:42898160 OUTPATIENT: text: OUTPATIENT description: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, without bed, with physicians or medical Providers delivering service during Visit meaning: OMOP:9202 HOME: text: HOME description: Provider visiting Person, without a Care Site, within one day, delivering service meaning: OMOP:581476 TELEHEALTH: text: TELEHEALTH description: Patient engages with Provider through communication media meaning: OMOP:5083 PHARMACY: text: PHARMACY description: Person visiting pharmacy for dispensing of Drug, at a Care Site, within one day meaning: OMOP:581458 LABORATORY: text: LABORATORY description: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a Measurement. meaning: OMOP:32036 AMBULANCE: text: AMBULANCE description: Person using transportation service for the purpose of initiating one of the other Visits, without a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service meaning: OMOP:581478 CASE_MANAGEMENT: text: CASE_MANAGEMENT description: Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes meaning: OMOP:38004193","title":"Enum: VisitCategoryEnum"},{"location":"VisitCategoryEnum/#enum-visitcategoryenum","text":"A constrained set of enumerative values containing the OMOP values for visit categories. URI: VisitCategoryEnum","title":"Enum: VisitCategoryEnum"},{"location":"VisitCategoryEnum/#permissible-values","text":"Value Meaning Description INPATIENT OMOP:9201 Person visiting hospital, at a care stie, in bed, for duration of more than o... EMERGENCY_ROOM OMOP:9203 Person visiting dedicated healthcare institution for treating emergencies, at... EMERGENCY_ROOM_AND_INPATIENT OMOP:262 Person visiting ER followed by a subsequent Inpatient Visit, where Emergency ... NON_HOSPITAL_INSTITUTION OMOP:42898160 Person visiting dedicated institution for reasons of poor health, at a Care S... OUTPATIENT OMOP:9202 Person visiting dedicated ambulatory healthcare institution, at a Care Site, ... HOME OMOP:581476 Provider visiting Person, without a Care Site, within one day, delivering ser... TELEHEALTH OMOP:5083 Patient engages with Provider through communication media PHARMACY OMOP:581458 Person visiting pharmacy for dispensing of Drug, at a Care Site, within one d... LABORATORY OMOP:32036 Patient visiting dedicated institution, at a Care Site, within one day, for t... AMBULANCE OMOP:581478 Person using transportation service for the purpose of initiating one of the ... CASE_MANAGEMENT OMOP:38004193 Person interacting with healthcare system, without a Care Site, within a day,...","title":"Permissible Values"},{"location":"VisitCategoryEnum/#slots","text":"Name Description visit_category A value representing the kind (or category) of visit, like inpatient or outpa...","title":"Slots"},{"location":"VisitCategoryEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VisitCategoryEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VisitCategoryEnum/#linkml-source","text":"name: VisitCategoryEnum description: A constrained set of enumerative values containing the OMOP values for visit categories. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: INPATIENT: text: INPATIENT description: Person visiting hospital, at a care stie, in bed, for duration of more than one day, with physicians and other Providers permanently available to deliver service around the clock meaning: OMOP:9201 EMERGENCY_ROOM: text: EMERGENCY_ROOM description: Person visiting dedicated healthcare institution for treating emergencies, at a Care Site, within one day, with physicians and Providers permanently available to deliver service around the clock meaning: OMOP:9203 EMERGENCY_ROOM_AND_INPATIENT: text: EMERGENCY_ROOM_AND_INPATIENT description: Person visiting ER followed by a subsequent Inpatient Visit, where Emergency department is part of hospital, and transition from the ER to other hospital departments is undefined meaning: OMOP:262 NON_HOSPITAL_INSTITUTION: text: NON_HOSPITAL_INSTITUTION description: Person visiting dedicated institution for reasons of poor health, at a Care Site, long-term or permanently, with no physician but possibly other Providers permanently available to deliver service around the clock meaning: OMOP:42898160 OUTPATIENT: text: OUTPATIENT description: Person visiting dedicated ambulatory healthcare institution, at a Care Site, within one day, without bed, with physicians or medical Providers delivering service during Visit meaning: OMOP:9202 HOME: text: HOME description: Provider visiting Person, without a Care Site, within one day, delivering service meaning: OMOP:581476 TELEHEALTH: text: TELEHEALTH description: Patient engages with Provider through communication media meaning: OMOP:5083 PHARMACY: text: PHARMACY description: Person visiting pharmacy for dispensing of Drug, at a Care Site, within one day meaning: OMOP:581458 LABORATORY: text: LABORATORY description: Patient visiting dedicated institution, at a Care Site, within one day, for the purpose of a Measurement. meaning: OMOP:32036 AMBULANCE: text: AMBULANCE description: Person using transportation service for the purpose of initiating one of the other Visits, without a Care Site, within one day, potentially with Providers accompanying the Visit and delivering service meaning: OMOP:581478 CASE_MANAGEMENT: text: CASE_MANAGEMENT description: Person interacting with healthcare system, without a Care Site, within a day, with no Providers involved, for administrative purposes meaning: OMOP:38004193","title":"LinkML Source"},{"location":"VisitProvenanceEnum/","text":"Enum: VisitProvenanceEnum A constrained set of enumerative values containing the OMOP values for visit provenance. URI: VisitProvenanceEnum Permissible Values Value Meaning Description CASE_REPORT_FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM_AUTHORIZATION OMOP:32811 Claim authorization CLAIM_DISCHARGE_RECORD OMOP:32812 Claim discharge record CLAIM_ENROLMENT_RECORD OMOP:32813 Claim enrolment record COST_RECORD OMOP:32814 Cost record DEATH_CERTIFICATE OMOP:32815 Death Certificate DENTAL_CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR_PATHOLOGY_REPORT OMOP:32835 EHR Pathology report EHR_ADMINISTRATION_RECORD OMOP:32818 EHR administration record EHR_ADMISSION_NOTE OMOP:32819 EHR admission note EHR_ANCILLARY_REPORT OMOP:32820 EHR ancillary report EHR_BILLING_RECORD OMOP:32821 EHR billing record EHR_CHIEF_COMPLAINT OMOP:32822 EHR chief complaint EHR_DISCHARGE_RECORD OMOP:32823 EHR discharge record EHR_DISCHARGE_SUMMARY OMOP:32824 EHR discharge summary EHR_DISPENSING_RECORD OMOP:32825 EHR dispensing record EHR_EMERGENCY_ROOM_NOTE OMOP:32826 EHR emergency room note EHR_ENCOUNTER_RECORD OMOP:32827 EHR encounter record EHR_EPISODE_RECORD OMOP:32828 EHR episode record EHR_INPATIENT_NOTE OMOP:32829 EHR inpatient note EHR_MEDICATION_LIST OMOP:32830 EHR medication list EHR_NOTE OMOP:32831 EHR note EHR_NURSING_REPORT OMOP:32832 EHR nursing report EHR_ORDER OMOP:32833 EHR order EHR_OUTPATIENT_NOTE OMOP:32834 EHR outpatient note EHR_PHYSICAL_EXAMINATION OMOP:32836 EHR physical examination EHR_PLANNED_DISPENSING_RECORD OMOP:32837 EHR planned dispensing record EHR_PRESCRIPTION OMOP:32838 EHR prescription EHR_PRESCRIPTION_ISSUE_RECORD OMOP:32839 EHR prescription issue record EHR_PROBLEM_LIST OMOP:32840 EHR problem list EHR_RADIOLOGY_REPORT OMOP:32841 EHR radiology report EHR_REFERRAL_RECORD OMOP:32842 EHR referral record EXTERNAL_CDM_INSTANCE OMOP:32843 External CDM instance FACILITY_CLAIM OMOP:32844 Facility claim FACILITY_CLAIM_DETAIL OMOP:32845 Facility claim detail FACILITY_CLAIM_HEADER OMOP:32846 Facility claim header GEOGRAPHIC_ISOLATION_RECORD OMOP:32847 Geographic isolation record GOVERNMENT_REPORT OMOP:32848 Government report HEALTH_INFORMATION_EXCHANGE_RECORD OMOP:32849 Health Information Exchange record HEALTH_RISK_ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE_PROFESSIONAL_FILLED_SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL_COST OMOP:32852 Hospital cost INPATIENT_CLAIM OMOP:32853 Inpatient claim INPATIENT_CLAIM_DETAIL OMOP:32854 Inpatient claim detail INPATIENT_CLAIM_HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL_ORDER_RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT_CLAIM OMOP:32859 Outpatient claim OUTPATIENT_CLAIM_DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT_CLAIM_HEADER OMOP:32861 Outpatient claim header PATIENT_FILLED_SURVEY OMOP:32862 Patient filled survey PATIENT_OR_PAYER_PAID_RECORD OMOP:32863 Patient or payer paid record PATIENT_REPORTED_COST OMOP:32864 Patient reported cost PATIENT_SELF-REPORT OMOP:32865 Patient self-report PATIENT_SELF-TESTED OMOP:705183 Patient self-tested PAYER_SYSTEM_RECORD_(PAID_PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) OMOP:32867 Payer system record (primary payer) PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY_CLAIM OMOP:32869 Pharmacy claim POINT_OF_CARE/EXPRESS_LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION_TIME_PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL_CLAIM OMOP:32871 Professional claim PROFESSIONAL_CLAIM_DETAIL OMOP:32872 Professional claim detail PROFESSIONAL_CLAIM_HEADER OMOP:32873 Professional claim header PROVIDER_CHARGE_LIST_PRICE OMOP:32874 Provider charge list price PROVIDER_FINANCIAL_SYSTEM OMOP:32875 Provider financial system PROVIDER_INCURRED_COST_RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION_RECORD OMOP:32877 Randomization record REFERENCE_LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD_ALGORITHM OMOP:32880 Standard algorithm STANDARD_ALGORITHM_FROM_EHR OMOP:32882 Standard algorithm from EHR STANDARD_ALGORITHM_FROM_CLAIMS OMOP:32881 Standard algorithm from claims SURVEY OMOP:32883 Survey US_SOCIAL_SECURITY_DEATH_MASTER_FILE OMOP:32885 US Social Security Death Master File URGENT_LAB OMOP:32884 Urgent lab VISION_CLAIM OMOP:32886 Vision claim Slots Name Description visit_provenance A value representing the provenance of the visit record, or where the record ... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VisitProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for visit provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE_REPORT_FORM: text: CASE_REPORT_FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM_AUTHORIZATION: text: CLAIM_AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM_DISCHARGE_RECORD: text: CLAIM_DISCHARGE_RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM_ENROLMENT_RECORD: text: CLAIM_ENROLMENT_RECORD description: Claim enrolment record meaning: OMOP:32813 COST_RECORD: text: COST_RECORD description: Cost record meaning: OMOP:32814 DEATH_CERTIFICATE: text: DEATH_CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL_CLAIM: text: DENTAL_CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR_PATHOLOGY_REPORT: text: EHR_PATHOLOGY_REPORT description: EHR Pathology report meaning: OMOP:32835 EHR_ADMINISTRATION_RECORD: text: EHR_ADMINISTRATION_RECORD description: EHR administration record meaning: OMOP:32818 EHR_ADMISSION_NOTE: text: EHR_ADMISSION_NOTE description: EHR admission note meaning: OMOP:32819 EHR_ANCILLARY_REPORT: text: EHR_ANCILLARY_REPORT description: EHR ancillary report meaning: OMOP:32820 EHR_BILLING_RECORD: text: EHR_BILLING_RECORD description: EHR billing record meaning: OMOP:32821 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR_DISCHARGE_RECORD: text: EHR_DISCHARGE_RECORD description: EHR discharge record meaning: OMOP:32823 EHR_DISCHARGE_SUMMARY: text: EHR_DISCHARGE_SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR_DISPENSING_RECORD: text: EHR_DISPENSING_RECORD description: EHR dispensing record meaning: OMOP:32825 EHR_EMERGENCY_ROOM_NOTE: text: EHR_EMERGENCY_ROOM_NOTE description: EHR emergency room note meaning: OMOP:32826 EHR_ENCOUNTER_RECORD: text: EHR_ENCOUNTER_RECORD description: EHR encounter record meaning: OMOP:32827 EHR_EPISODE_RECORD: text: EHR_EPISODE_RECORD description: EHR episode record meaning: OMOP:32828 EHR_INPATIENT_NOTE: text: EHR_INPATIENT_NOTE description: EHR inpatient note meaning: OMOP:32829 EHR_MEDICATION_LIST: text: EHR_MEDICATION_LIST description: EHR medication list meaning: OMOP:32830 EHR_NOTE: text: EHR_NOTE description: EHR note meaning: OMOP:32831 EHR_NURSING_REPORT: text: EHR_NURSING_REPORT description: EHR nursing report meaning: OMOP:32832 EHR_ORDER: text: EHR_ORDER description: EHR order meaning: OMOP:32833 EHR_OUTPATIENT_NOTE: text: EHR_OUTPATIENT_NOTE description: EHR outpatient note meaning: OMOP:32834 EHR_PHYSICAL_EXAMINATION: text: EHR_PHYSICAL_EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR_PLANNED_DISPENSING_RECORD: text: EHR_PLANNED_DISPENSING_RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR_PRESCRIPTION: text: EHR_PRESCRIPTION description: EHR prescription meaning: OMOP:32838 EHR_PRESCRIPTION_ISSUE_RECORD: text: EHR_PRESCRIPTION_ISSUE_RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR_PROBLEM_LIST: text: EHR_PROBLEM_LIST description: EHR problem list meaning: OMOP:32840 EHR_RADIOLOGY_REPORT: text: EHR_RADIOLOGY_REPORT description: EHR radiology report meaning: OMOP:32841 EHR_REFERRAL_RECORD: text: EHR_REFERRAL_RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL_CDM_INSTANCE: text: EXTERNAL_CDM_INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY_CLAIM: text: FACILITY_CLAIM description: Facility claim meaning: OMOP:32844 FACILITY_CLAIM_DETAIL: text: FACILITY_CLAIM_DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY_CLAIM_HEADER: text: FACILITY_CLAIM_HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC_ISOLATION_RECORD: text: GEOGRAPHIC_ISOLATION_RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT_REPORT: text: GOVERNMENT_REPORT description: Government report meaning: OMOP:32848 HEALTH_INFORMATION_EXCHANGE_RECORD: text: HEALTH_INFORMATION_EXCHANGE_RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH_RISK_ASSESSMENT: text: HEALTH_RISK_ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE_PROFESSIONAL_FILLED_SURVEY: text: HEALTHCARE_PROFESSIONAL_FILLED_SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL_COST: text: HOSPITAL_COST description: Hospital cost meaning: OMOP:32852 INPATIENT_CLAIM: text: INPATIENT_CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT_CLAIM_DETAIL: text: INPATIENT_CLAIM_DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT_CLAIM_HEADER: text: INPATIENT_CLAIM_HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL_ORDER_RECORD: text: MAIL_ORDER_RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT_CLAIM: text: OUTPATIENT_CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT_CLAIM_DETAIL: text: OUTPATIENT_CLAIM_DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT_CLAIM_HEADER: text: OUTPATIENT_CLAIM_HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT_FILLED_SURVEY: text: PATIENT_FILLED_SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT_OR_PAYER_PAID_RECORD: text: PATIENT_OR_PAYER_PAID_RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT_REPORTED_COST: text: PATIENT_REPORTED_COST description: Patient reported cost meaning: OMOP:32864 PATIENT_SELF-REPORT: text: PATIENT_SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT_SELF-TESTED: text: PATIENT_SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER_SYSTEM_RECORD_(PAID_PREMIUM): text: PAYER_SYSTEM_RECORD_(PAID_PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER_SYSTEM_RECORD_(PRIMARY_PAYER): text: PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER_SYSTEM_RECORD_(SECONDARY_PAYER): text: PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY_CLAIM: text: PHARMACY_CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT_OF_CARE/EXPRESS_LAB: text: POINT_OF_CARE/EXPRESS_LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION_TIME_PERIOD: text: PRE-QUALIFICATION_TIME_PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL_CLAIM: text: PROFESSIONAL_CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL_CLAIM_DETAIL: text: PROFESSIONAL_CLAIM_DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL_CLAIM_HEADER: text: PROFESSIONAL_CLAIM_HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER_CHARGE_LIST_PRICE: text: PROVIDER_CHARGE_LIST_PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER_FINANCIAL_SYSTEM: text: PROVIDER_FINANCIAL_SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER_INCURRED_COST_RECORD: text: PROVIDER_INCURRED_COST_RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION_RECORD: text: RANDOMIZATION_RECORD description: Randomization record meaning: OMOP:32877 REFERENCE_LAB: text: REFERENCE_LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD_ALGORITHM: text: STANDARD_ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD_ALGORITHM_FROM_EHR: text: STANDARD_ALGORITHM_FROM_EHR description: Standard algorithm from EHR meaning: OMOP:32882 STANDARD_ALGORITHM_FROM_CLAIMS: text: STANDARD_ALGORITHM_FROM_CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 US_SOCIAL_SECURITY_DEATH_MASTER_FILE: text: US_SOCIAL_SECURITY_DEATH_MASTER_FILE description: US Social Security Death Master File meaning: OMOP:32885 URGENT_LAB: text: URGENT_LAB description: Urgent lab meaning: OMOP:32884 VISION_CLAIM: text: VISION_CLAIM description: Vision claim meaning: OMOP:32886","title":"Enum: VisitProvenanceEnum"},{"location":"VisitProvenanceEnum/#enum-visitprovenanceenum","text":"A constrained set of enumerative values containing the OMOP values for visit provenance. URI: VisitProvenanceEnum","title":"Enum: VisitProvenanceEnum"},{"location":"VisitProvenanceEnum/#permissible-values","text":"Value Meaning Description CASE_REPORT_FORM OMOP:32809 Case Report Form CLAIM OMOP:32810 Claim CLAIM_AUTHORIZATION OMOP:32811 Claim authorization CLAIM_DISCHARGE_RECORD OMOP:32812 Claim discharge record CLAIM_ENROLMENT_RECORD OMOP:32813 Claim enrolment record COST_RECORD OMOP:32814 Cost record DEATH_CERTIFICATE OMOP:32815 Death Certificate DENTAL_CLAIM OMOP:32816 Dental claim EHR OMOP:32817 EHR EHR_PATHOLOGY_REPORT OMOP:32835 EHR Pathology report EHR_ADMINISTRATION_RECORD OMOP:32818 EHR administration record EHR_ADMISSION_NOTE OMOP:32819 EHR admission note EHR_ANCILLARY_REPORT OMOP:32820 EHR ancillary report EHR_BILLING_RECORD OMOP:32821 EHR billing record EHR_CHIEF_COMPLAINT OMOP:32822 EHR chief complaint EHR_DISCHARGE_RECORD OMOP:32823 EHR discharge record EHR_DISCHARGE_SUMMARY OMOP:32824 EHR discharge summary EHR_DISPENSING_RECORD OMOP:32825 EHR dispensing record EHR_EMERGENCY_ROOM_NOTE OMOP:32826 EHR emergency room note EHR_ENCOUNTER_RECORD OMOP:32827 EHR encounter record EHR_EPISODE_RECORD OMOP:32828 EHR episode record EHR_INPATIENT_NOTE OMOP:32829 EHR inpatient note EHR_MEDICATION_LIST OMOP:32830 EHR medication list EHR_NOTE OMOP:32831 EHR note EHR_NURSING_REPORT OMOP:32832 EHR nursing report EHR_ORDER OMOP:32833 EHR order EHR_OUTPATIENT_NOTE OMOP:32834 EHR outpatient note EHR_PHYSICAL_EXAMINATION OMOP:32836 EHR physical examination EHR_PLANNED_DISPENSING_RECORD OMOP:32837 EHR planned dispensing record EHR_PRESCRIPTION OMOP:32838 EHR prescription EHR_PRESCRIPTION_ISSUE_RECORD OMOP:32839 EHR prescription issue record EHR_PROBLEM_LIST OMOP:32840 EHR problem list EHR_RADIOLOGY_REPORT OMOP:32841 EHR radiology report EHR_REFERRAL_RECORD OMOP:32842 EHR referral record EXTERNAL_CDM_INSTANCE OMOP:32843 External CDM instance FACILITY_CLAIM OMOP:32844 Facility claim FACILITY_CLAIM_DETAIL OMOP:32845 Facility claim detail FACILITY_CLAIM_HEADER OMOP:32846 Facility claim header GEOGRAPHIC_ISOLATION_RECORD OMOP:32847 Geographic isolation record GOVERNMENT_REPORT OMOP:32848 Government report HEALTH_INFORMATION_EXCHANGE_RECORD OMOP:32849 Health Information Exchange record HEALTH_RISK_ASSESSMENT OMOP:32850 Health Risk Assessment HEALTHCARE_PROFESSIONAL_FILLED_SURVEY OMOP:32851 Healthcare professional filled survey HOSPITAL_COST OMOP:32852 Hospital cost INPATIENT_CLAIM OMOP:32853 Inpatient claim INPATIENT_CLAIM_DETAIL OMOP:32854 Inpatient claim detail INPATIENT_CLAIM_HEADER OMOP:32855 Inpatient claim header LAB OMOP:32856 Lab MAIL_ORDER_RECORD OMOP:32857 Mail order record NLP OMOP:32858 NLP OUTPATIENT_CLAIM OMOP:32859 Outpatient claim OUTPATIENT_CLAIM_DETAIL OMOP:32860 Outpatient claim detail OUTPATIENT_CLAIM_HEADER OMOP:32861 Outpatient claim header PATIENT_FILLED_SURVEY OMOP:32862 Patient filled survey PATIENT_OR_PAYER_PAID_RECORD OMOP:32863 Patient or payer paid record PATIENT_REPORTED_COST OMOP:32864 Patient reported cost PATIENT_SELF-REPORT OMOP:32865 Patient self-report PATIENT_SELF-TESTED OMOP:705183 Patient self-tested PAYER_SYSTEM_RECORD_(PAID_PREMIUM) OMOP:32866 Payer system record (paid premium) PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) OMOP:32867 Payer system record (primary payer) PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) OMOP:32868 Payer system record (secondary payer) PHARMACY_CLAIM OMOP:32869 Pharmacy claim POINT_OF_CARE/EXPRESS_LAB OMOP:703249 Point of care/express lab PRE-QUALIFICATION_TIME_PERIOD OMOP:32870 Pre-qualification time period PROFESSIONAL_CLAIM OMOP:32871 Professional claim PROFESSIONAL_CLAIM_DETAIL OMOP:32872 Professional claim detail PROFESSIONAL_CLAIM_HEADER OMOP:32873 Professional claim header PROVIDER_CHARGE_LIST_PRICE OMOP:32874 Provider charge list price PROVIDER_FINANCIAL_SYSTEM OMOP:32875 Provider financial system PROVIDER_INCURRED_COST_RECORD OMOP:32876 Provider incurred cost record RANDOMIZATION_RECORD OMOP:32877 Randomization record REFERENCE_LAB OMOP:32878 Reference lab REGISTRY OMOP:32879 Registry STANDARD_ALGORITHM OMOP:32880 Standard algorithm STANDARD_ALGORITHM_FROM_EHR OMOP:32882 Standard algorithm from EHR STANDARD_ALGORITHM_FROM_CLAIMS OMOP:32881 Standard algorithm from claims SURVEY OMOP:32883 Survey US_SOCIAL_SECURITY_DEATH_MASTER_FILE OMOP:32885 US Social Security Death Master File URGENT_LAB OMOP:32884 Urgent lab VISION_CLAIM OMOP:32886 Vision claim","title":"Permissible Values"},{"location":"VisitProvenanceEnum/#slots","text":"Name Description visit_provenance A value representing the provenance of the visit record, or where the record ...","title":"Slots"},{"location":"VisitProvenanceEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VisitProvenanceEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VisitProvenanceEnum/#linkml-source","text":"name: VisitProvenanceEnum description: A constrained set of enumerative values containing the OMOP values for visit provenance. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: CASE_REPORT_FORM: text: CASE_REPORT_FORM description: Case Report Form meaning: OMOP:32809 CLAIM: text: CLAIM description: Claim meaning: OMOP:32810 CLAIM_AUTHORIZATION: text: CLAIM_AUTHORIZATION description: Claim authorization meaning: OMOP:32811 CLAIM_DISCHARGE_RECORD: text: CLAIM_DISCHARGE_RECORD description: Claim discharge record meaning: OMOP:32812 CLAIM_ENROLMENT_RECORD: text: CLAIM_ENROLMENT_RECORD description: Claim enrolment record meaning: OMOP:32813 COST_RECORD: text: COST_RECORD description: Cost record meaning: OMOP:32814 DEATH_CERTIFICATE: text: DEATH_CERTIFICATE description: Death Certificate meaning: OMOP:32815 DENTAL_CLAIM: text: DENTAL_CLAIM description: Dental claim meaning: OMOP:32816 EHR: text: EHR description: EHR meaning: OMOP:32817 EHR_PATHOLOGY_REPORT: text: EHR_PATHOLOGY_REPORT description: EHR Pathology report meaning: OMOP:32835 EHR_ADMINISTRATION_RECORD: text: EHR_ADMINISTRATION_RECORD description: EHR administration record meaning: OMOP:32818 EHR_ADMISSION_NOTE: text: EHR_ADMISSION_NOTE description: EHR admission note meaning: OMOP:32819 EHR_ANCILLARY_REPORT: text: EHR_ANCILLARY_REPORT description: EHR ancillary report meaning: OMOP:32820 EHR_BILLING_RECORD: text: EHR_BILLING_RECORD description: EHR billing record meaning: OMOP:32821 EHR_CHIEF_COMPLAINT: text: EHR_CHIEF_COMPLAINT description: EHR chief complaint meaning: OMOP:32822 EHR_DISCHARGE_RECORD: text: EHR_DISCHARGE_RECORD description: EHR discharge record meaning: OMOP:32823 EHR_DISCHARGE_SUMMARY: text: EHR_DISCHARGE_SUMMARY description: EHR discharge summary meaning: OMOP:32824 EHR_DISPENSING_RECORD: text: EHR_DISPENSING_RECORD description: EHR dispensing record meaning: OMOP:32825 EHR_EMERGENCY_ROOM_NOTE: text: EHR_EMERGENCY_ROOM_NOTE description: EHR emergency room note meaning: OMOP:32826 EHR_ENCOUNTER_RECORD: text: EHR_ENCOUNTER_RECORD description: EHR encounter record meaning: OMOP:32827 EHR_EPISODE_RECORD: text: EHR_EPISODE_RECORD description: EHR episode record meaning: OMOP:32828 EHR_INPATIENT_NOTE: text: EHR_INPATIENT_NOTE description: EHR inpatient note meaning: OMOP:32829 EHR_MEDICATION_LIST: text: EHR_MEDICATION_LIST description: EHR medication list meaning: OMOP:32830 EHR_NOTE: text: EHR_NOTE description: EHR note meaning: OMOP:32831 EHR_NURSING_REPORT: text: EHR_NURSING_REPORT description: EHR nursing report meaning: OMOP:32832 EHR_ORDER: text: EHR_ORDER description: EHR order meaning: OMOP:32833 EHR_OUTPATIENT_NOTE: text: EHR_OUTPATIENT_NOTE description: EHR outpatient note meaning: OMOP:32834 EHR_PHYSICAL_EXAMINATION: text: EHR_PHYSICAL_EXAMINATION description: EHR physical examination meaning: OMOP:32836 EHR_PLANNED_DISPENSING_RECORD: text: EHR_PLANNED_DISPENSING_RECORD description: EHR planned dispensing record meaning: OMOP:32837 EHR_PRESCRIPTION: text: EHR_PRESCRIPTION description: EHR prescription meaning: OMOP:32838 EHR_PRESCRIPTION_ISSUE_RECORD: text: EHR_PRESCRIPTION_ISSUE_RECORD description: EHR prescription issue record meaning: OMOP:32839 EHR_PROBLEM_LIST: text: EHR_PROBLEM_LIST description: EHR problem list meaning: OMOP:32840 EHR_RADIOLOGY_REPORT: text: EHR_RADIOLOGY_REPORT description: EHR radiology report meaning: OMOP:32841 EHR_REFERRAL_RECORD: text: EHR_REFERRAL_RECORD description: EHR referral record meaning: OMOP:32842 EXTERNAL_CDM_INSTANCE: text: EXTERNAL_CDM_INSTANCE description: External CDM instance meaning: OMOP:32843 FACILITY_CLAIM: text: FACILITY_CLAIM description: Facility claim meaning: OMOP:32844 FACILITY_CLAIM_DETAIL: text: FACILITY_CLAIM_DETAIL description: Facility claim detail meaning: OMOP:32845 FACILITY_CLAIM_HEADER: text: FACILITY_CLAIM_HEADER description: Facility claim header meaning: OMOP:32846 GEOGRAPHIC_ISOLATION_RECORD: text: GEOGRAPHIC_ISOLATION_RECORD description: Geographic isolation record meaning: OMOP:32847 GOVERNMENT_REPORT: text: GOVERNMENT_REPORT description: Government report meaning: OMOP:32848 HEALTH_INFORMATION_EXCHANGE_RECORD: text: HEALTH_INFORMATION_EXCHANGE_RECORD description: Health Information Exchange record meaning: OMOP:32849 HEALTH_RISK_ASSESSMENT: text: HEALTH_RISK_ASSESSMENT description: Health Risk Assessment meaning: OMOP:32850 HEALTHCARE_PROFESSIONAL_FILLED_SURVEY: text: HEALTHCARE_PROFESSIONAL_FILLED_SURVEY description: Healthcare professional filled survey meaning: OMOP:32851 HOSPITAL_COST: text: HOSPITAL_COST description: Hospital cost meaning: OMOP:32852 INPATIENT_CLAIM: text: INPATIENT_CLAIM description: Inpatient claim meaning: OMOP:32853 INPATIENT_CLAIM_DETAIL: text: INPATIENT_CLAIM_DETAIL description: Inpatient claim detail meaning: OMOP:32854 INPATIENT_CLAIM_HEADER: text: INPATIENT_CLAIM_HEADER description: Inpatient claim header meaning: OMOP:32855 LAB: text: LAB description: Lab meaning: OMOP:32856 MAIL_ORDER_RECORD: text: MAIL_ORDER_RECORD description: Mail order record meaning: OMOP:32857 NLP: text: NLP description: NLP meaning: OMOP:32858 OUTPATIENT_CLAIM: text: OUTPATIENT_CLAIM description: Outpatient claim meaning: OMOP:32859 OUTPATIENT_CLAIM_DETAIL: text: OUTPATIENT_CLAIM_DETAIL description: Outpatient claim detail meaning: OMOP:32860 OUTPATIENT_CLAIM_HEADER: text: OUTPATIENT_CLAIM_HEADER description: Outpatient claim header meaning: OMOP:32861 PATIENT_FILLED_SURVEY: text: PATIENT_FILLED_SURVEY description: Patient filled survey meaning: OMOP:32862 PATIENT_OR_PAYER_PAID_RECORD: text: PATIENT_OR_PAYER_PAID_RECORD description: Patient or payer paid record meaning: OMOP:32863 PATIENT_REPORTED_COST: text: PATIENT_REPORTED_COST description: Patient reported cost meaning: OMOP:32864 PATIENT_SELF-REPORT: text: PATIENT_SELF-REPORT description: Patient self-report meaning: OMOP:32865 PATIENT_SELF-TESTED: text: PATIENT_SELF-TESTED description: Patient self-tested meaning: OMOP:705183 PAYER_SYSTEM_RECORD_(PAID_PREMIUM): text: PAYER_SYSTEM_RECORD_(PAID_PREMIUM) description: Payer system record (paid premium) meaning: OMOP:32866 PAYER_SYSTEM_RECORD_(PRIMARY_PAYER): text: PAYER_SYSTEM_RECORD_(PRIMARY_PAYER) description: Payer system record (primary payer) meaning: OMOP:32867 PAYER_SYSTEM_RECORD_(SECONDARY_PAYER): text: PAYER_SYSTEM_RECORD_(SECONDARY_PAYER) description: Payer system record (secondary payer) meaning: OMOP:32868 PHARMACY_CLAIM: text: PHARMACY_CLAIM description: Pharmacy claim meaning: OMOP:32869 POINT_OF_CARE/EXPRESS_LAB: text: POINT_OF_CARE/EXPRESS_LAB description: Point of care/express lab meaning: OMOP:703249 PRE-QUALIFICATION_TIME_PERIOD: text: PRE-QUALIFICATION_TIME_PERIOD description: Pre-qualification time period meaning: OMOP:32870 PROFESSIONAL_CLAIM: text: PROFESSIONAL_CLAIM description: Professional claim meaning: OMOP:32871 PROFESSIONAL_CLAIM_DETAIL: text: PROFESSIONAL_CLAIM_DETAIL description: Professional claim detail meaning: OMOP:32872 PROFESSIONAL_CLAIM_HEADER: text: PROFESSIONAL_CLAIM_HEADER description: Professional claim header meaning: OMOP:32873 PROVIDER_CHARGE_LIST_PRICE: text: PROVIDER_CHARGE_LIST_PRICE description: Provider charge list price meaning: OMOP:32874 PROVIDER_FINANCIAL_SYSTEM: text: PROVIDER_FINANCIAL_SYSTEM description: Provider financial system meaning: OMOP:32875 PROVIDER_INCURRED_COST_RECORD: text: PROVIDER_INCURRED_COST_RECORD description: Provider incurred cost record meaning: OMOP:32876 RANDOMIZATION_RECORD: text: RANDOMIZATION_RECORD description: Randomization record meaning: OMOP:32877 REFERENCE_LAB: text: REFERENCE_LAB description: Reference lab meaning: OMOP:32878 REGISTRY: text: REGISTRY description: Registry meaning: OMOP:32879 STANDARD_ALGORITHM: text: STANDARD_ALGORITHM description: Standard algorithm meaning: OMOP:32880 STANDARD_ALGORITHM_FROM_EHR: text: STANDARD_ALGORITHM_FROM_EHR description: Standard algorithm from EHR meaning: OMOP:32882 STANDARD_ALGORITHM_FROM_CLAIMS: text: STANDARD_ALGORITHM_FROM_CLAIMS description: Standard algorithm from claims meaning: OMOP:32881 SURVEY: text: SURVEY description: Survey meaning: OMOP:32883 US_SOCIAL_SECURITY_DEATH_MASTER_FILE: text: US_SOCIAL_SECURITY_DEATH_MASTER_FILE description: US Social Security Death Master File meaning: OMOP:32885 URGENT_LAB: text: URGENT_LAB description: Urgent lab meaning: OMOP:32884 VISION_CLAIM: text: VISION_CLAIM description: Vision claim meaning: OMOP:32886","title":"LinkML Source"},{"location":"VitalStatusEnum/","text":"Enum: VitalStatusEnum A constrained set of enumerative values containing the OMOP values for vital status. URI: VitalStatusEnum Permissible Values Value Meaning Description ALIVE OMOP:4230556 Showing characteristics of life; displaying signs of life DEAD OMOP:434489 The cessation of life Slots Name Description vital_status Coded value indicating the state or condition of being living or deceased; al... Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: VitalStatusEnum description: A constrained set of enumerative values containing the OMOP values for vital status. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIVE: text: ALIVE description: Showing characteristics of life; displaying signs of life. (NCIt) meaning: OMOP:4230556 DEAD: text: DEAD description: The cessation of life. (NCIt) meaning: OMOP:434489","title":"Enum: VitalStatusEnum"},{"location":"VitalStatusEnum/#enum-vitalstatusenum","text":"A constrained set of enumerative values containing the OMOP values for vital status. URI: VitalStatusEnum","title":"Enum: VitalStatusEnum"},{"location":"VitalStatusEnum/#permissible-values","text":"Value Meaning Description ALIVE OMOP:4230556 Showing characteristics of life; displaying signs of life DEAD OMOP:434489 The cessation of life","title":"Permissible Values"},{"location":"VitalStatusEnum/#slots","text":"Name Description vital_status Coded value indicating the state or condition of being living or deceased; al...","title":"Slots"},{"location":"VitalStatusEnum/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"VitalStatusEnum/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"VitalStatusEnum/#linkml-source","text":"name: VitalStatusEnum description: A constrained set of enumerative values containing the OMOP values for vital status. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 permissible_values: ALIVE: text: ALIVE description: Showing characteristics of life; displaying signs of life. (NCIt) meaning: OMOP:4230556 DEAD: text: DEAD description: The cessation of life. (NCIt) meaning: OMOP:434489","title":"LinkML Source"},{"location":"about/","text":"BDCHM Model Overview This is a high-level class diagram of the core entities present in the BioData Catalyst Harmonized Model (BDCHM). classDiagram Participant \"1..*\" --> \"1\" Person : associated_person Demography \"1..*\" --> \"1\" Participant : associated_participant ResearchStudy \"1..*\" <-- \"1\" Participant : member_of_research_study ResearchStudy \"0..1\" <-- \"1\" ResearchStudy : part_of Visit \"0..*\" --> \"1\" Participant : associated_participant QuestionnaireResponse \"0..*\" --> \"1\" Visit : associated_visit QuestionnaireResponseItem \"1..*\" <-- \"1\" QuestionnaireResponse : items QuestionnaireResponseValue \"1\" <-- \"1\" QuestionnaireResponseItem : response_value QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireItem \"0..1\" <-- \"1\" QuestionnaireResponseItem : has_questionnaire_item Questionnaire \"1\" --> \"1..*\" QuestionnaireItem : items QuestionnaireItem \"1\" --> \"0..1\" QuestionnaireItem : part_of Condition \"0..*\" --> \"0..1\" Visit : associated_visit Condition \"0..*\" --> \"1\" Participant : associated_participant Person : id Person : identity Person : species Person : breed Person : year_of_birth Person : vital_status Person : age_at_death Person : cause_of_death Demography : id Demography : identity Demography : sex Demography : race Demography : ethnicity Participant : id Participant : identity Participant : description Participant : age_at_enrollment Participant : index_timepoint Participant : originating_site Participant : study_arm ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : sponsor ResearchStudy : date_started ResearchStudy : date_ended ResearchStudy : url ResearchStudy : research_project_type ResearchStudy : associated_timepoint ResearchStudy : principal_investigator ResearchStudy : principal_investigator Visit : id Visit : age_at_visit_start Visit : age_at_visit_end Visit : visit_category Visit : visit_provenance Questionnaire : id Questionnaire : identity Questionnaire : name Questionnaire : title Questionnaire : description Questionnaire : url Questionnaire : version Questionnaire : publisher Questionnaire : copyright Questionnaire : copyright_label Questionnaire : language QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : text QuestionnaireItem : code QuestionnaireResponse : id QuestionnaireResponse : age_at_response QuestionnaireResponseItem : id QuestionnaireResponseItem : text QuestionnaireResponseValue : type QuestionnaireResponseValue : name QuestionnaireResponseValueDecimal : value QuestionnaireResponseValueBoolean : value QuestionnaireResponseValueString : value Condition : id Condition : identity Condition : condition_concept Condition : age_at_condition_start Condition : age_at_condition_end Condition : condition_provenance Condition : condition_status Condition : relationship_to_participant","title":"About"},{"location":"about/#bdchm-model-overview","text":"This is a high-level class diagram of the core entities present in the BioData Catalyst Harmonized Model (BDCHM). classDiagram Participant \"1..*\" --> \"1\" Person : associated_person Demography \"1..*\" --> \"1\" Participant : associated_participant ResearchStudy \"1..*\" <-- \"1\" Participant : member_of_research_study ResearchStudy \"0..1\" <-- \"1\" ResearchStudy : part_of Visit \"0..*\" --> \"1\" Participant : associated_participant QuestionnaireResponse \"0..*\" --> \"1\" Visit : associated_visit QuestionnaireResponseItem \"1..*\" <-- \"1\" QuestionnaireResponse : items QuestionnaireResponseValue \"1\" <-- \"1\" QuestionnaireResponseItem : response_value QuestionnaireResponseValue <|-- QuestionnaireResponseValueDecimal QuestionnaireResponseValue <|-- QuestionnaireResponseValueBoolean QuestionnaireResponseValue <|-- QuestionnaireResponseValueString QuestionnaireItem \"0..1\" <-- \"1\" QuestionnaireResponseItem : has_questionnaire_item Questionnaire \"1\" --> \"1..*\" QuestionnaireItem : items QuestionnaireItem \"1\" --> \"0..1\" QuestionnaireItem : part_of Condition \"0..*\" --> \"0..1\" Visit : associated_visit Condition \"0..*\" --> \"1\" Participant : associated_participant Person : id Person : identity Person : species Person : breed Person : year_of_birth Person : vital_status Person : age_at_death Person : cause_of_death Demography : id Demography : identity Demography : sex Demography : race Demography : ethnicity Participant : id Participant : identity Participant : description Participant : age_at_enrollment Participant : index_timepoint Participant : originating_site Participant : study_arm ResearchStudy : id ResearchStudy : identity ResearchStudy : name ResearchStudy : name_shortened ResearchStudy : description ResearchStudy : description_shortened ResearchStudy : sponsor ResearchStudy : date_started ResearchStudy : date_ended ResearchStudy : url ResearchStudy : research_project_type ResearchStudy : associated_timepoint ResearchStudy : principal_investigator ResearchStudy : principal_investigator Visit : id Visit : age_at_visit_start Visit : age_at_visit_end Visit : visit_category Visit : visit_provenance Questionnaire : id Questionnaire : identity Questionnaire : name Questionnaire : title Questionnaire : description Questionnaire : url Questionnaire : version Questionnaire : publisher Questionnaire : copyright Questionnaire : copyright_label Questionnaire : language QuestionnaireItem : id QuestionnaireItem : identity QuestionnaireItem : text QuestionnaireItem : code QuestionnaireResponse : id QuestionnaireResponse : age_at_response QuestionnaireResponseItem : id QuestionnaireResponseItem : text QuestionnaireResponseValue : type QuestionnaireResponseValue : name QuestionnaireResponseValueDecimal : value QuestionnaireResponseValueBoolean : value QuestionnaireResponseValueString : value Condition : id Condition : identity Condition : condition_concept Condition : age_at_condition_start Condition : age_at_condition_end Condition : condition_provenance Condition : condition_status Condition : relationship_to_participant","title":"BDCHM Model Overview"},{"location":"activity_type/","text":"Slot: activity_type URI: bdchm:activity_type Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no Properties Range: String Identifier and Mapping Information LinkML Source name: activity_type alias: activity_type domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: string","title":"Slot: activity_type"},{"location":"activity_type/#slot-activity_type","text":"URI: bdchm:activity_type","title":"Slot: activity_type"},{"location":"activity_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no","title":"Applicable Classes"},{"location":"activity_type/#properties","text":"Range: String","title":"Properties"},{"location":"activity_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"activity_type/#linkml-source","text":"name: activity_type alias: activity_type domain_of: - SpecimenCreationActivity - SpecimenProcessingActivity range: string","title":"LinkML Source"},{"location":"additive/","text":"Slot: additive URI: bdchm:additive Applicable Classes Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no Properties Range: String Identifier and Mapping Information LinkML Source name: additive alias: additive domain_of: - SpecimenContainer - SpecimenCreationActivity - SpecimenProcessingActivity range: string","title":"Slot: additive"},{"location":"additive/#slot-additive","text":"URI: bdchm:additive","title":"Slot: additive"},{"location":"additive/#applicable-classes","text":"Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no","title":"Applicable Classes"},{"location":"additive/#properties","text":"Range: 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URI: bdchm:associated_person","title":"Slot: associated_person"},{"location":"associated_person/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no","title":"Applicable Classes"},{"location":"associated_person/#properties","text":"Range: Person","title":"Properties"},{"location":"associated_person/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"associated_person/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"associated_person/#linkml-source","text":"name: associated_person description: A reference to the Person that is associated with this record. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: associated_person domain_of: - Participant range: Person","title":"LinkML Source"},{"location":"associated_timepoint/","text":"Slot: associated_timepoint A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) URI: bdchm:associated_timepoint Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: TimePoint Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint","title":"Slot: associated_timepoint"},{"location":"associated_timepoint/#slot-associated_timepoint","text":"A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) URI: bdchm:associated_timepoint","title":"Slot: associated_timepoint"},{"location":"associated_timepoint/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"associated_timepoint/#properties","text":"Range: TimePoint Multivalued: True","title":"Properties"},{"location":"associated_timepoint/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"associated_timepoint/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"associated_timepoint/#linkml-source","text":"name: associated_timepoint description: A collection of timepoint observations that are relevant to research projects (e.g. date of IACUC approval, date of IRB approval, date of embargo end, etc.) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: associated_timepoint owner: ResearchStudy domain_of: - ResearchStudy range: TimePoint","title":"LinkML Source"},{"location":"associated_visit/","text":"Slot: associated_visit URI: bdchm:associated_visit Applicable Classes Name Description Modifies Slot QuestionnaireResponse QuestionnaireResponse provides a complete or partial list of answers to a set... no Condition Conditions are records of a Person suggesting the presence of a disease or me... no Procedure Procedure contains records of activities or processes ordered by, or carried ... no DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no DimensionalObservation A structured object that describes a single data item about the physical dime... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no Observation A data structure with key (observation_type) and value (value) attributes tha... no Properties Range: String Identifier and Mapping Information LinkML Source name: associated_visit alias: associated_visit domain_of: - 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QuestionnaireResponse - Condition - Procedure - DrugExposure - DeviceExposure - Observation range: string","title":"LinkML Source"},{"location":"bdchm/","text":"bdchm This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm","title":"bdchm"},{"location":"bdchm/#bdchm","text":"This is the harmonized data model for use in the BioData Catalyst project. URI: https://w3id.org/nhlbidatastage/bdchm","title":"bdchm"},{"location":"breed/","text":"Slot: breed A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). URI: bdchm:breed Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: VertebrateBreedEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum","title":"Slot: breed"},{"location":"breed/#slot-breed","text":"A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). URI: bdchm:breed","title":"Slot: breed"},{"location":"breed/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"breed/#properties","text":"Range: VertebrateBreedEnum","title":"Properties"},{"location":"breed/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"breed/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"breed/#linkml-source","text":"name: breed description: A label given to a group of animals homogeneous in appearance and other characteristics that distinguish it from other animals of the same species. Values should be derived from the Vertebrate Breed Ontology (http://purl.obolibrary.org/obo/vbo.owl). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: breed owner: Person domain_of: - Person range: VertebrateBreedEnum","title":"LinkML Source"},{"location":"category/","text":"Slot: category URI: bdchm:category Applicable Classes Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no Properties Range: String Identifier and Mapping Information LinkML Source name: category alias: category domain_of: - ObservationSet - Observation range: string","title":"Slot: category"},{"location":"category/#slot-category","text":"URI: bdchm:category","title":"Slot: category"},{"location":"category/#applicable-classes","text":"Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no","title":"Applicable Classes"},{"location":"category/#properties","text":"Range: String","title":"Properties"},{"location":"category/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"category/#linkml-source","text":"name: category alias: category domain_of: - ObservationSet - Observation range: string","title":"LinkML Source"},{"location":"cause_of_death/","text":"Slot: cause_of_death Coded value indicating the circumstance or condition that results in the death of the individual. URI: bdchm:cause_of_death Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string","title":"Slot: cause_of_death"},{"location":"cause_of_death/#slot-cause_of_death","text":"Coded value indicating the circumstance or condition that results in the death of the individual. URI: bdchm:cause_of_death","title":"Slot: cause_of_death"},{"location":"cause_of_death/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"cause_of_death/#properties","text":"Range: String","title":"Properties"},{"location":"cause_of_death/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cause_of_death/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"cause_of_death/#linkml-source","text":"name: cause_of_death description: Coded value indicating the circumstance or condition that results in the death of the individual. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: cause_of_death owner: Person domain_of: - Person range: string","title":"LinkML Source"},{"location":"cellular_composition_type/","text":"Slot: cellular_composition_type A term describing the type of cell or cellular material comprising a specimen. URI: bdchm:cellular_composition_type Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: String Examples Value 2D Classical Conditionally Reprogrammed Cells Adherent Cell Line Bone Marrow Components Buccal Cells Buffy Coat Derived Cell Line Granulocytes Pleural Effusion Human Original Cells Liquid Suspension Cell Line Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false","title":"Slot: cellular_composition_type"},{"location":"cellular_composition_type/#slot-cellular_composition_type","text":"A term describing the type of cell or cellular material comprising a specimen. URI: bdchm:cellular_composition_type","title":"Slot: cellular_composition_type"},{"location":"cellular_composition_type/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"cellular_composition_type/#properties","text":"Range: String","title":"Properties"},{"location":"cellular_composition_type/#examples","text":"Value 2D Classical Conditionally Reprogrammed Cells Adherent Cell Line Bone Marrow Components Buccal Cells Buffy Coat Derived Cell Line Granulocytes Pleural Effusion Human Original Cells Liquid Suspension Cell Line","title":"Examples"},{"location":"cellular_composition_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"cellular_composition_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"cellular_composition_type/#linkml-source","text":"name: cellular_composition_type description: A term describing the type of cell or cellular material comprising a specimen. examples: - value: 2D Classical Conditionally Reprogrammed Cells - value: Adherent Cell Line - value: Bone Marrow Components - value: Buccal Cells - value: Buffy Coat - value: Derived Cell Line - value: Granulocytes - value: Pleural Effusion - value: Human Original Cells - value: Liquid Suspension Cell Line from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_cellular_composition_type multivalued: false alias: cellular_composition_type owner: Specimen domain_of: - Specimen range: string required: false","title":"LinkML Source"},{"location":"code/","text":"Slot: code Corresponding concept for this item in a terminology URI: bdchm:code Applicable Classes Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string","title":"Slot: code"},{"location":"code/#slot-code","text":"Corresponding concept for this item in a terminology URI: bdchm:code","title":"Slot: code"},{"location":"code/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no","title":"Applicable Classes"},{"location":"code/#properties","text":"Range: String","title":"Properties"},{"location":"code/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"code/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"code/#linkml-source","text":"name: code description: Corresponding concept for this item in a terminology from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: code owner: QuestionnaireItem domain_of: - QuestionnaireItem range: string","title":"LinkML Source"},{"location":"collection_method_type/","text":"Slot: collection_method_type The type of method applied in collecting a sample from its original source. URI: bdchm:collection_method_type Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: SpecimenCollectionMethodType Examples Value Anterior Resection of Rectum Ascites Drainage Excisional Biopsy Specimen Pooling Comments This attribute applies only when the Specimen.category = 'original'. 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URI: bdchm:collection_method_type","title":"Slot: collection_method_type"},{"location":"collection_method_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"collection_method_type/#properties","text":"Range: SpecimenCollectionMethodType","title":"Properties"},{"location":"collection_method_type/#examples","text":"Value Anterior Resection of Rectum Ascites Drainage Excisional Biopsy Specimen Pooling","title":"Examples"},{"location":"collection_method_type/#comments","text":"This attribute applies only when the Specimen.category = 'original'.","title":"Comments"},{"location":"collection_method_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"collection_method_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"collection_method_type/#linkml-source","text":"name: collection_method_type description: The type of method applied in collecting a sample from its original source. comments: - This attribute applies only when the Specimen.category = 'original'. examples: - value: Anterior Resection of Rectum - value: Ascites Drainage - value: Excisional Biopsy - value: Specimen Pooling from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: SpecimenCollectionMethodType required: false","title":"LinkML Source"},{"location":"collection_site/","text":"Slot: collection_site The anatomic site from which a specimen was collected. URI: bdchm:collection_site Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: BodySite Examples Value Abdomen Abdominal Wall Acetabulum Comments This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false","title":"Slot: collection_site"},{"location":"collection_site/#slot-collection_site","text":"The anatomic site from which a specimen was collected. URI: bdchm:collection_site","title":"Slot: collection_site"},{"location":"collection_site/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"collection_site/#properties","text":"Range: BodySite","title":"Properties"},{"location":"collection_site/#examples","text":"Value Abdomen Abdominal Wall Acetabulum","title":"Examples"},{"location":"collection_site/#comments","text":"This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'.","title":"Comments"},{"location":"collection_site/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"collection_site/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"collection_site/#linkml-source","text":"name: collection_site description: The anatomic site from which a specimen was collected. comments: - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection from Source'. examples: - value: Abdomen - value: Abdominal Wall - value: Acetabulum from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: collection_site owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: BodySite required: false","title":"LinkML Source"},{"location":"condition_concept/","text":"Slot: condition_concept The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. URI: bdchm:condition_concept Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: ConditionConceptEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum","title":"Slot: condition_concept"},{"location":"condition_concept/#slot-condition_concept","text":"The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. URI: bdchm:condition_concept","title":"Slot: condition_concept"},{"location":"condition_concept/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"condition_concept/#properties","text":"Range: ConditionConceptEnum","title":"Properties"},{"location":"condition_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"condition_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"condition_concept/#linkml-source","text":"name: condition_concept description: The coded value for the presence of a disease or medical condition stated as a diagnosis, a sign or a symptom, coded to the Human Phenotype Ontology or MONDO. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_concept owner: Condition domain_of: - Condition range: ConditionConceptEnum","title":"LinkML Source"},{"location":"condition_provenance/","text":"Slot: condition_provenance A value representing the provenance of the Condition record URI: bdchm:condition_provenance Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: ProvenanceEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum","title":"Slot: condition_provenance"},{"location":"condition_provenance/#slot-condition_provenance","text":"A value representing the provenance of the Condition record URI: bdchm:condition_provenance","title":"Slot: condition_provenance"},{"location":"condition_provenance/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"condition_provenance/#properties","text":"Range: ProvenanceEnum","title":"Properties"},{"location":"condition_provenance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"condition_provenance/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"condition_provenance/#linkml-source","text":"name: condition_provenance description: A value representing the provenance of the Condition record from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_provenance owner: Condition domain_of: - Condition range: ProvenanceEnum","title":"LinkML Source"},{"location":"condition_status/","text":"Slot: condition_status A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. URI: bdchm:condition_status Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: ConditionStatusEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum","title":"Slot: condition_status"},{"location":"condition_status/#slot-condition_status","text":"A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. URI: bdchm:condition_status","title":"Slot: condition_status"},{"location":"condition_status/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"condition_status/#properties","text":"Range: ConditionStatusEnum","title":"Properties"},{"location":"condition_status/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"condition_status/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"condition_status/#linkml-source","text":"name: condition_status description: A value indicating whether the medical condition described in this record is present, absent, or unknown for this individual patient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: condition_status owner: Condition domain_of: - Condition range: ConditionStatusEnum","title":"LinkML Source"},{"location":"consent_code/","text":"Slot: consent_code Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html URI: bdchm:consent_code Applicable Classes Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no Properties Range: DataUseEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum","title":"Slot: consent_code"},{"location":"consent_code/#slot-consent_code","text":"Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html URI: bdchm:consent_code","title":"Slot: consent_code"},{"location":"consent_code/#applicable-classes","text":"Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no","title":"Applicable Classes"},{"location":"consent_code/#properties","text":"Range: DataUseEnum","title":"Properties"},{"location":"consent_code/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"consent_code/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"consent_code/#linkml-source","text":"name: consent_code description: 'Data Use Restrictions that are used to indicate permissions/restrictions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Based on the Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html' from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: consent_code owner: Consent domain_of: - Consent range: DataUseEnum","title":"LinkML Source"},{"location":"consents/","text":"Slot: consents URI: bdchm:consents Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information LinkML Source name: consents alias: consents domain_of: - Participant - ResearchStudy range: string","title":"Slot: consents"},{"location":"consents/#slot-consents","text":"URI: bdchm:consents","title":"Slot: consents"},{"location":"consents/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"consents/#properties","text":"Range: String","title":"Properties"},{"location":"consents/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"consents/#linkml-source","text":"name: consents alias: consents domain_of: - Participant - ResearchStudy range: string","title":"LinkML Source"},{"location":"contained_in/","text":"Slot: contained_in A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:contained_in Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenContainer Comments The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false","title":"Slot: contained_in"},{"location":"contained_in/#slot-contained_in","text":"A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) URI: bdchm:contained_in","title":"Slot: contained_in"},{"location":"contained_in/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"contained_in/#properties","text":"Range: SpecimenContainer","title":"Properties"},{"location":"contained_in/#comments","text":"The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity.","title":"Comments"},{"location":"contained_in/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"contained_in/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"contained_in/#linkml-source","text":"name: contained_in description: A physical container in which a specimen is presently held or attached - as storage for future use, a substrate for growth (e.g. a cell culture dish), or a vessel to enable analysis (e.g. a microscope slide or 96-well plate) comments: - The 0..1 cardinality on this attribute means that you cannot directly references multiple nested containers holding a sample. To capture this scenario, use the \"parent_container\" attribute of the Container entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: contained_in owner: Specimen domain_of: - Specimen range: SpecimenContainer required: false","title":"LinkML Source"},{"location":"container/","text":"Slot: container A container in which the specimen is held or affixed during its storage. URI: bdchm:container Applicable Classes Name Description Modifies Slot SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no Properties Range: SpecimenContainer Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true","title":"Slot: container"},{"location":"container/#slot-container","text":"A container in which the specimen is held or affixed during its storage. URI: bdchm:container","title":"Slot: container"},{"location":"container/#applicable-classes","text":"Name Description Modifies Slot SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no","title":"Applicable Classes"},{"location":"container/#properties","text":"Range: SpecimenContainer Multivalued: True","title":"Properties"},{"location":"container/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"container/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"container/#linkml-source","text":"name: container description: A container in which the specimen is held or affixed during its storage. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: container owner: SpecimenStorageActivity domain_of: - SpecimenStorageActivity range: SpecimenContainer required: false inlined: true inlined_as_list: true","title":"LinkML Source"},{"location":"container_number/","text":"Slot: container_number Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) URI: bdchm:container_number Applicable Classes Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"Slot: container_number"},{"location":"container_number/#slot-container_number","text":"Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) URI: bdchm:container_number","title":"Slot: container_number"},{"location":"container_number/#applicable-classes","text":"Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no","title":"Applicable Classes"},{"location":"container_number/#properties","text":"Range: String","title":"Properties"},{"location":"container_number/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"container_number/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"container_number/#linkml-source","text":"name: container_number description: Informal number by which the container is referenced or identified (e.g. a slide number, or a well number in a plate) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: container_number owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"LinkML Source"},{"location":"container_type/","text":"Slot: container_type The kind of the container. URI: bdchm:container_type Applicable Classes Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no Properties Range: String Examples Value Capillary blood collection tube Sputum specimen container Cell culture flask Glass slide Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"Slot: container_type"},{"location":"container_type/#slot-container_type","text":"The kind of the container. URI: bdchm:container_type","title":"Slot: container_type"},{"location":"container_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenContainer A vessel in which a specimen is held or to which it is attached - for storage... no","title":"Applicable Classes"},{"location":"container_type/#properties","text":"Range: String","title":"Properties"},{"location":"container_type/#examples","text":"Value Capillary blood collection tube Sputum specimen container Cell culture flask Glass slide","title":"Examples"},{"location":"container_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"container_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"container_type/#linkml-source","text":"name: container_type description: The kind of the container. examples: - value: Capillary blood collection tube - value: Sputum specimen container - value: Cell culture flask - value: Glass slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenContainer_container_type multivalued: false alias: container_type owner: SpecimenContainer domain_of: - SpecimenContainer range: string required: false","title":"LinkML Source"},{"location":"copyright/","text":"Slot: copyright Textual description of any use and/or publishing restrictions URI: bdchm:copyright Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: copyright"},{"location":"copyright/#slot-copyright","text":"Textual description of any use and/or publishing restrictions URI: bdchm:copyright","title":"Slot: copyright"},{"location":"copyright/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"copyright/#properties","text":"Range: String","title":"Properties"},{"location":"copyright/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"copyright/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"copyright/#linkml-source","text":"name: copyright description: Textual description of any use and/or publishing restrictions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"copyright_label/","text":"Slot: copyright_label Copyright holder and year(s) URI: bdchm:copyright_label Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: copyright_label"},{"location":"copyright_label/#slot-copyright_label","text":"Copyright holder and year(s) URI: bdchm:copyright_label","title":"Slot: copyright_label"},{"location":"copyright_label/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"copyright_label/#properties","text":"Range: String","title":"Properties"},{"location":"copyright_label/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"copyright_label/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"copyright_label/#linkml-source","text":"name: copyright_label description: Copyright holder and year(s) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: copyright_label owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"creation_activity/","text":"Slot: creation_activity The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. URI: bdchm:creation_activity Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenCreationActivity Comments Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false","title":"Slot: creation_activity"},{"location":"creation_activity/#slot-creation_activity","text":"The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. URI: bdchm:creation_activity","title":"Slot: creation_activity"},{"location":"creation_activity/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"creation_activity/#properties","text":"Range: SpecimenCreationActivity","title":"Properties"},{"location":"creation_activity/#comments","text":"Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it.","title":"Comments"},{"location":"creation_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"creation_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"creation_activity/#linkml-source","text":"name: creation_activity description: The activity through which a specimen was created, by removing material from an biological subject, or deriving material from an existing specimen. comments: - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, but may be subject to many processing events that subsequently modify or derive new specimens from it. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: creation_activity owner: Specimen domain_of: - Specimen range: SpecimenCreationActivity required: false","title":"LinkML Source"},{"location":"data_category/","text":"Slot: data_category A broad categorization of the contents of the data file. URI: bdchm:data_category Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string","title":"Slot: data_category"},{"location":"data_category/#slot-data_category","text":"A broad categorization of the contents of the data file. URI: bdchm:data_category","title":"Slot: data_category"},{"location":"data_category/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"data_category/#properties","text":"Range: String","title":"Properties"},{"location":"data_category/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"data_category/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"data_category/#linkml-source","text":"name: data_category description: A broad categorization of the contents of the data file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_category owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"data_type/","text":"Slot: data_type The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary DCMI-TYPE . To describe the file format, physical medium, or dimensions of the resource, use the Format element. URI: bdchm:data_type Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Comments Called 'type' in Dublin Core. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string","title":"Slot: data_type"},{"location":"data_type/#slot-data_type","text":"The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary DCMI-TYPE . To describe the file format, physical medium, or dimensions of the resource, use the Format element. URI: bdchm:data_type","title":"Slot: data_type"},{"location":"data_type/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"data_type/#properties","text":"Range: String","title":"Properties"},{"location":"data_type/#comments","text":"Called 'type' in Dublin Core.","title":"Comments"},{"location":"data_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"data_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"data_type/#linkml-source","text":"name: data_type description: The nature or genre of the resource. Recommended best practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [DCMI-TYPE](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/#section-7). To describe the file format, physical medium, or dimensions of the resource, use the Format element. comments: - Called 'type' in Dublin Core. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: data_type owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"date_ended/","text":"Slot: date_ended URI: bdchm:date_ended Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: String Identifier and Mapping Information LinkML Source name: date_ended alias: date_ended domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"Slot: date_ended"},{"location":"date_ended/#slot-date_ended","text":"URI: bdchm:date_ended","title":"Slot: date_ended"},{"location":"date_ended/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"date_ended/#properties","text":"Range: String","title":"Properties"},{"location":"date_ended/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_ended/#linkml-source","text":"name: date_ended alias: date_ended domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"LinkML Source"},{"location":"date_started/","text":"Slot: date_started URI: bdchm:date_started Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: String Identifier and Mapping Information LinkML Source name: date_started alias: date_started domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"Slot: date_started"},{"location":"date_started/#slot-date_started","text":"URI: bdchm:date_started","title":"Slot: date_started"},{"location":"date_started/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no SpecimenCreationActivity The process of creating a specimen no SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"date_started/#properties","text":"Range: String","title":"Properties"},{"location":"date_started/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_started/#linkml-source","text":"name: date_started alias: date_started domain_of: - ResearchStudy - SpecimenCreationActivity - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"LinkML Source"},{"location":"date_time/","text":"Slot: date_time An explicitly specified timepoint described in terms of a date and optionally a time on that date. URI: bdchm:date_time Applicable Classes Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no Properties Range: Datetime Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime","title":"Slot: date_time"},{"location":"date_time/#slot-date_time","text":"An explicitly specified timepoint described in terms of a date and optionally a time on that date. URI: bdchm:date_time","title":"Slot: date_time"},{"location":"date_time/#applicable-classes","text":"Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no","title":"Applicable Classes"},{"location":"date_time/#properties","text":"Range: Datetime","title":"Properties"},{"location":"date_time/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"date_time/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"date_time/#linkml-source","text":"name: date_time description: An explicitly specified timepoint described in terms of a date and optionally a time on that date. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: date_time owner: TimePoint domain_of: - TimePoint range: datetime","title":"LinkML Source"},{"location":"days_supply/","text":"Slot: days_supply The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). URI: bdchm:days_supply Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no Properties Range: Integer Comments The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"Slot: days_supply"},{"location":"days_supply/#slot-days_supply","text":"The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). URI: bdchm:days_supply","title":"Slot: days_supply"},{"location":"days_supply/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"days_supply/#properties","text":"Range: Integer","title":"Properties"},{"location":"days_supply/#comments","text":"The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras.","title":"Comments"},{"location":"days_supply/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"days_supply/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"days_supply/#linkml-source","text":"name: days_supply description: The number of days of supply of the medication as recorded in the original prescription or dispensing record. Days supply can differ from actual drug duration (i.e. prescribed days supply vs actual exposure). comments: - The field should be left empty if the source data does not contain a verbatim days_supply, and should not be calculated from other fields. Negative values are not allowed. If the source has negative days supply the record should be dropped as it is unknown if the patient actually took the drug. Several actions are possible -- record is not trustworthy and we remove the record entirely; we trust the record and leave days_supply empty; or record needs to be combined with other record (e.g. reversal of prescription). High values (>365 days) should be investigated. If considered an error in the source data (e.g. typo), the value needs to be excluded to prevent creation of unrealistic long eras. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: days_supply owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"LinkML Source"},{"location":"derivation_method_type/","text":"Slot: derivation_method_type The type of method applied to derive a new specimen from an existing one. URI: bdchm:derivation_method_type Applicable Classes Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no Properties Range: String Examples Value Vibratome Cryosectioning Tissuemolds Slidingmicrotome Sectioning Other Unknown NotReported Comments This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false","title":"Slot: derivation_method_type"},{"location":"derivation_method_type/#slot-derivation_method_type","text":"The type of method applied to derive a new specimen from an existing one. URI: bdchm:derivation_method_type","title":"Slot: derivation_method_type"},{"location":"derivation_method_type/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"derivation_method_type/#properties","text":"Range: String","title":"Properties"},{"location":"derivation_method_type/#examples","text":"Value Vibratome Cryosectioning Tissuemolds Slidingmicrotome Sectioning Other Unknown NotReported","title":"Examples"},{"location":"derivation_method_type/#comments","text":"This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'.","title":"Comments"},{"location":"derivation_method_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"derivation_method_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"derivation_method_type/#linkml-source","text":"name: derivation_method_type description: The type of method applied to derive a new specimen from an existing one. comments: - This attribute applies only when Specimen.category = 'portion', 'aliquot', 'analyte', or 'slide'. examples: - value: Vibratome - value: Cryosectioning - value: Tissuemolds - value: Slidingmicrotome - value: Sectioning - value: Other - value: Unknown - value: NotReported from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type multivalued: false alias: derivation_method_type owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: string required: false","title":"LinkML Source"},{"location":"derived_from/","text":"Slot: derived_from A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. URI: bdchm:derived_from Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: File Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: derived_from description: A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: derived_from owner: File domain_of: - File range: File","title":"Slot: derived_from"},{"location":"derived_from/#slot-derived_from","text":"A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. URI: bdchm:derived_from","title":"Slot: derived_from"},{"location":"derived_from/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"derived_from/#properties","text":"Range: File","title":"Properties"},{"location":"derived_from/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"derived_from/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"derived_from/#linkml-source","text":"name: derived_from description: A File from which this File is derived. A derivation is a transformation of an entity into another, an update of an entity resulting in a new one, or the construction of a new entity based on a pre-existing entity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: derived_from owner: File domain_of: - File range: File","title":"LinkML Source"},{"location":"derived_product/","text":"Slot: derived_product A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) URI: bdchm:derived_product Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: BiologicProduct Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true","title":"Slot: derived_product"},{"location":"derived_product/#slot-derived_product","text":"A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) URI: bdchm:derived_product","title":"Slot: derived_product"},{"location":"derived_product/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"derived_product/#properties","text":"Range: BiologicProduct Multivalued: True","title":"Properties"},{"location":"derived_product/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"derived_product/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"derived_product/#linkml-source","text":"name: derived_product description: A 'living' biologically active product that was derived from the specimen (e.g. a cell culture, tissue culture, or organoid) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: derived_product owner: Specimen domain_of: - Specimen range: BiologicProduct required: false inlined: true inlined_as_list: true","title":"LinkML Source"},{"location":"description/","text":"Slot: description URI: bdchm:description Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no File Abstract class for various kinds of files no Document A collection of information intented to be understood together as a whole, an... no Specimen Any material taken as a sample from a biological entity (living or dead), or ... no BiologicProduct A living organism, or a metabolically active biological system such as a cell... no Properties Range: String Identifier and Mapping Information LinkML Source name: description alias: description domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string","title":"Slot: description"},{"location":"description/#slot-description","text":"URI: bdchm:description","title":"Slot: description"},{"location":"description/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no ResearchStudy A process where a researcher or organization plans and then executes a series... no Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no File Abstract class for various kinds of files no Document A collection of information intented to be understood together as a whole, an... no Specimen Any material taken as a sample from a biological entity (living or dead), or ... no BiologicProduct A living organism, or a metabolically active biological system such as a cell... no","title":"Applicable Classes"},{"location":"description/#properties","text":"Range: String","title":"Properties"},{"location":"description/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"description/#linkml-source","text":"name: description alias: description domain_of: - Participant - ResearchStudy - Questionnaire - File - Document - Specimen - BiologicProduct range: string","title":"LinkML Source"},{"location":"description_shortened/","text":"Slot: description_shortened An abbreviated description of a research program, project, or study. URI: bdchm:description_shortened Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"Slot: description_shortened"},{"location":"description_shortened/#slot-description_shortened","text":"An abbreviated description of a research program, project, or study. URI: bdchm:description_shortened","title":"Slot: description_shortened"},{"location":"description_shortened/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"description_shortened/#properties","text":"Range: String","title":"Properties"},{"location":"description_shortened/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"description_shortened/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"description_shortened/#linkml-source","text":"name: description_shortened description: An abbreviated description of a research program, project, or study. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: description_shortened owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"LinkML Source"},{"location":"device_concept/","text":"Slot: device_concept The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. URI: bdchm:device_concept Applicable Classes Name Description Modifies Slot DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no Properties Range: DeviceExposureConceptEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum","title":"Slot: device_concept"},{"location":"device_concept/#slot-device_concept","text":"The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. URI: bdchm:device_concept","title":"Slot: device_concept"},{"location":"device_concept/#applicable-classes","text":"Name Description Modifies Slot DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no","title":"Applicable Classes"},{"location":"device_concept/#properties","text":"Range: DeviceExposureConceptEnum","title":"Properties"},{"location":"device_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"device_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"device_concept/#linkml-source","text":"name: device_concept description: The coded value for a device. Primarily SNOMED. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: device_concept owner: DeviceExposure domain_of: - DeviceExposure range: DeviceExposureConceptEnum","title":"LinkML Source"},{"location":"dimensional_measures/","text":"Slot: dimensional_measures Observations about the current physical dimensions of an object (e.g. length, width, area). URI: bdchm:dimensional_measures Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: DimensionalObservationSet Comments Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false","title":"Slot: dimensional_measures"},{"location":"dimensional_measures/#slot-dimensional_measures","text":"Observations about the current physical dimensions of an object (e.g. length, width, area). URI: bdchm:dimensional_measures","title":"Slot: dimensional_measures"},{"location":"dimensional_measures/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"dimensional_measures/#properties","text":"Range: DimensionalObservationSet","title":"Properties"},{"location":"dimensional_measures/#comments","text":"Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object.","title":"Comments"},{"location":"dimensional_measures/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"dimensional_measures/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"dimensional_measures/#linkml-source","text":"name: dimensional_measures description: Observations about the current physical dimensions of an object (e.g. length, width, area). comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: dimensional_measures owner: Specimen domain_of: - Specimen range: DimensionalObservationSet required: false","title":"LinkML Source"},{"location":"document_type/","text":"Slot: document_type The high-level type of the document (e.g. 'publication', 'pathology report') URI: bdchm:document_type Applicable Classes Name Description Modifies Slot Document A collection of information intented to be understood together as a whole, an... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false","title":"Slot: document_type"},{"location":"document_type/#slot-document_type","text":"The high-level type of the document (e.g. 'publication', 'pathology report') URI: bdchm:document_type","title":"Slot: document_type"},{"location":"document_type/#applicable-classes","text":"Name Description Modifies Slot Document A collection of information intented to be understood together as a whole, an... no","title":"Applicable Classes"},{"location":"document_type/#properties","text":"Range: String","title":"Properties"},{"location":"document_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"document_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"document_type/#linkml-source","text":"name: document_type description: The high-level type of the document (e.g. 'publication', 'pathology report') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Document_document_type multivalued: false alias: document_type owner: Document domain_of: - Document range: string required: false","title":"LinkML Source"},{"location":"drug_concept/","text":"Slot: drug_concept The coded value for a drug. From RxNorm. The syntax for the enum may need work. URI: bdchm:drug_concept Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no Properties Range: DrugExposureConceptEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum","title":"Slot: drug_concept"},{"location":"drug_concept/#slot-drug_concept","text":"The coded value for a drug. From RxNorm. The syntax for the enum may need work. URI: bdchm:drug_concept","title":"Slot: drug_concept"},{"location":"drug_concept/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"drug_concept/#properties","text":"Range: DrugExposureConceptEnum","title":"Properties"},{"location":"drug_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"drug_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"drug_concept/#linkml-source","text":"name: drug_concept description: The coded value for a drug. From RxNorm. The syntax for the enum may need work. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: drug_concept owner: DrugExposure domain_of: - DrugExposure range: DrugExposureConceptEnum","title":"LinkML Source"},{"location":"duration/","text":"Slot: duration URI: bdchm:duration Applicable Classes Name Description Modifies Slot SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no Properties Range: String Identifier and Mapping Information LinkML Source name: duration alias: duration domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"Slot: duration"},{"location":"duration/#slot-duration","text":"URI: bdchm:duration","title":"Slot: duration"},{"location":"duration/#applicable-classes","text":"Name Description Modifies Slot SpecimenProcessingActivity An activity that modifies the physical structure, composition, or state of a ... no SpecimenStorageActivity An activity in which a specimen is stored or maintained in a particular locat... no SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"duration/#properties","text":"Range: String","title":"Properties"},{"location":"duration/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"duration/#linkml-source","text":"name: duration alias: duration domain_of: - SpecimenProcessingActivity - SpecimenStorageActivity - SpecimenTransportActivity range: string","title":"LinkML Source"},{"location":"entries/","text":"Slot: entries URI: bdchm:entries Applicable Classes Name Description Modifies Slot ResearchStudyCollection A holder for ResearchStudy objects no Properties Range: ResearchStudy Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true","title":"Slot: entries"},{"location":"entries/#slot-entries","text":"URI: bdchm:entries","title":"Slot: entries"},{"location":"entries/#applicable-classes","text":"Name Description Modifies Slot ResearchStudyCollection A holder for ResearchStudy objects no","title":"Applicable Classes"},{"location":"entries/#properties","text":"Range: ResearchStudy Multivalued: True","title":"Properties"},{"location":"entries/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"entries/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"entries/#linkml-source","text":"name: entries from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: entries owner: ResearchStudyCollection domain_of: - ResearchStudyCollection range: ResearchStudy inlined: true","title":"LinkML Source"},{"location":"ethnicity/","text":"Slot: ethnicity An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau URI: bdchm:ethnicity Applicable Classes Name Description Modifies Slot Demography Demographics about an individual or animal receiving care or other health-rel... no Properties Range: EthnicityEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum","title":"Slot: ethnicity"},{"location":"ethnicity/#slot-ethnicity","text":"An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau URI: bdchm:ethnicity","title":"Slot: ethnicity"},{"location":"ethnicity/#applicable-classes","text":"Name Description Modifies Slot Demography Demographics about an individual or animal receiving care or other health-rel... no","title":"Applicable Classes"},{"location":"ethnicity/#properties","text":"Range: EthnicityEnum","title":"Properties"},{"location":"ethnicity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"ethnicity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"ethnicity/#linkml-source","text":"name: ethnicity description: An individual's self-described social and cultural grouping, specifically whether an individual describes themselves as Hispanic or Latino. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: ethnicity owner: Demography domain_of: - Demography range: EthnicityEnum","title":"LinkML Source"},{"location":"event_type/","text":"Slot: event_type An event that occurred at the point in time specified by this TimePoint. URI: bdchm:event_type Applicable Classes Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string","title":"Slot: event_type"},{"location":"event_type/#slot-event_type","text":"An event that occurred at the point in time specified by this TimePoint. URI: bdchm:event_type","title":"Slot: event_type"},{"location":"event_type/#applicable-classes","text":"Name Description Modifies Slot TimePoint A structured representation of a single point in time that allows direct/expl... no","title":"Applicable Classes"},{"location":"event_type/#properties","text":"Range: String","title":"Properties"},{"location":"event_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"event_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"event_type/#linkml-source","text":"name: event_type description: An event that occurred at the point in time specified by this TimePoint. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: event_type owner: TimePoint domain_of: - TimePoint range: string","title":"LinkML Source"},{"location":"exposure_provenance/","text":"Slot: exposure_provenance URI: bdchm:exposure_provenance Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no Properties Range: String Identifier and Mapping Information LinkML Source name: exposure_provenance alias: exposure_provenance domain_of: - DrugExposure - DeviceExposure range: string","title":"Slot: exposure_provenance"},{"location":"exposure_provenance/#slot-exposure_provenance","text":"URI: bdchm:exposure_provenance","title":"Slot: exposure_provenance"},{"location":"exposure_provenance/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no DeviceExposure DeviceExposures are records of a Person suggesting exposure to a foreign obje... no","title":"Applicable Classes"},{"location":"exposure_provenance/#properties","text":"Range: String","title":"Properties"},{"location":"exposure_provenance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"exposure_provenance/#linkml-source","text":"name: exposure_provenance alias: exposure_provenance domain_of: - DrugExposure - DeviceExposure range: string","title":"LinkML Source"},{"location":"file_location/","text":"Slot: file_location A unique identifier or url for identifying or locating the file. URI: bdchm:file_location Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: Uriorcurie Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: file_location description: A unique identifier or url for identifying or locating the file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: file_location owner: File domain_of: - File range: uriorcurie","title":"Slot: file_location"},{"location":"file_location/#slot-file_location","text":"A unique identifier or url for identifying or locating the file. URI: bdchm:file_location","title":"Slot: file_location"},{"location":"file_location/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"file_location/#properties","text":"Range: Uriorcurie Multivalued: True","title":"Properties"},{"location":"file_location/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"file_location/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"file_location/#linkml-source","text":"name: file_location description: A unique identifier or url for identifying or locating the file. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: file_location owner: File domain_of: - File range: uriorcurie","title":"LinkML Source"},{"location":"file_name/","text":"Slot: file_name The name (or part of a name) of a file (of any type). URI: bdchm:file_name Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string","title":"Slot: file_name"},{"location":"file_name/#slot-file_name","text":"The name (or part of a name) of a file (of any type). URI: bdchm:file_name","title":"Slot: file_name"},{"location":"file_name/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"file_name/#properties","text":"Range: String","title":"Properties"},{"location":"file_name/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"file_name/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"file_name/#linkml-source","text":"name: file_name description: The name (or part of a name) of a file (of any type). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_name owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"file_size/","text":"Slot: file_size The size of the data file (object) in bytes. URI: bdchm:file_size Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer","title":"Slot: file_size"},{"location":"file_size/#slot-file_size","text":"The size of the data file (object) in bytes. URI: bdchm:file_size","title":"Slot: file_size"},{"location":"file_size/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"file_size/#properties","text":"Range: Integer","title":"Properties"},{"location":"file_size/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"file_size/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"file_size/#linkml-source","text":"name: file_size description: The size of the data file (object) in bytes. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: file_size owner: File domain_of: - File range: integer","title":"LinkML Source"},{"location":"focus/","text":"Slot: focus URI: bdchm:focus Applicable Classes Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no Document A collection of information intented to be understood together as a whole, an... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no Properties Range: String Identifier and Mapping Information LinkML Source name: focus alias: focus domain_of: - Document - ObservationSet - Observation range: string","title":"Slot: focus"},{"location":"focus/#slot-focus","text":"URI: bdchm:focus","title":"Slot: focus"},{"location":"focus/#applicable-classes","text":"Name Description Modifies Slot DimensionalObservation A structured object that describes a single data item about the physical dime... no DimensionalObservationSet A set of one or more discrete observations about the physical dimensions of a... no Document A collection of information intented to be understood together as a whole, an... no SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... no SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... no ObservationSet A structured object to hold related Observations in a set no Observation A data structure with key (observation_type) and value (value) attributes tha... no","title":"Applicable Classes"},{"location":"focus/#properties","text":"Range: String","title":"Properties"},{"location":"focus/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"focus/#linkml-source","text":"name: focus alias: focus domain_of: - Document - ObservationSet - Observation range: string","title":"LinkML Source"},{"location":"format/","text":"Slot: format The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). URI: bdchm:format Applicable Classes Name Description Modifies Slot File Abstract class for various kinds of files no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string","title":"Slot: format"},{"location":"format/#slot-format","text":"The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). URI: bdchm:format","title":"Slot: format"},{"location":"format/#applicable-classes","text":"Name Description Modifies Slot File Abstract class for various kinds of files no","title":"Applicable Classes"},{"location":"format/#properties","text":"Range: String","title":"Properties"},{"location":"format/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"format/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"format/#linkml-source","text":"name: format description: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME] (http://www.iana.org/assignments/media-types/). from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: format owner: File domain_of: - File range: string","title":"LinkML Source"},{"location":"growth_rate/","text":"Slot: growth_rate When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. URI: bdchm:growth_rate Applicable Classes Name Description Modifies Slot BiologicProduct A living organism, or a metabolically active biological system such as a cell... no Properties Range: String Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false","title":"Slot: growth_rate"},{"location":"growth_rate/#slot-growth_rate","text":"When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. URI: bdchm:growth_rate","title":"Slot: growth_rate"},{"location":"growth_rate/#applicable-classes","text":"Name Description Modifies Slot BiologicProduct A living organism, or a metabolically active biological system such as a cell... no","title":"Applicable Classes"},{"location":"growth_rate/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"growth_rate/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"growth_rate/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"growth_rate/#linkml-source","text":"name: growth_rate description: When the specimen an actively growing model system, such as a cell or tissue culture, this property captures its rate of growth. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: growth_rate owner: BiologicProduct domain_of: - BiologicProduct range: string required: false","title":"LinkML Source"},{"location":"has_questionnaire_item/","text":"Slot: has_questionnaire_item A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. URI: bdchm:has_questionnaire_item Applicable Classes Name Description Modifies Slot QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no Properties Range: QuestionnaireItem Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem","title":"Slot: has_questionnaire_item"},{"location":"has_questionnaire_item/#slot-has_questionnaire_item","text":"A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. URI: bdchm:has_questionnaire_item","title":"Slot: has_questionnaire_item"},{"location":"has_questionnaire_item/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no","title":"Applicable Classes"},{"location":"has_questionnaire_item/#properties","text":"Range: QuestionnaireItem","title":"Properties"},{"location":"has_questionnaire_item/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"has_questionnaire_item/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"has_questionnaire_item/#linkml-source","text":"name: has_questionnaire_item description: A reference to the QuestionnaireItem that this QuestionnaireResponseItem responds to. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: has_questionnaire_item owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireItem","title":"LinkML Source"},{"location":"id/","text":"Slot: id The 'logical' identifier of the entity within the system of record. The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. 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The simple value of this attribute stands for an identifier of this data object within the system, it can be used as a reference from other objects within the same system (i.e. primary and foreign keys), and it should be unique per type of object. The same data object copied to a different system will likely have a different \"id\" in the new system since \"id\" values are system specific and do not represent persistent business identifiers. Business identifiers are assigned outside the information system and are captured in the \"identifier\" field. The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. 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The \"id\" field is more likely to be a serially or randomly generated value that is assigned to the data object as it is created in a system. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier identifier: true alias: id domain_of: - Entity range: uriorcurie required: true","title":"LinkML Source"},{"location":"identity/","text":"Slot: identity A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. 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Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie","title":"Slot: identity"},{"location":"identity/#slot-identity","text":"A 'business' identifier or accession number for the entity, typically as provided by an external system or authority, that are globally unique and persist across implementing systems. Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. 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Also, since these identifiers are created outside the information system through a specific business process, the Identifier type has additional attributes to capture this additional metadata so the actual identifier values are qualified by the context that created those values. This additional context allows \"identifier\" instances to be transmitted as business data across systems while still being able to trace them back to the system of origin. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 slot_uri: schema:identifier multivalued: true alias: identity domain_of: - Person - Demography - Participant - ResearchStudy - Organization - Questionnaire - QuestionnaireItem - Condition - Procedure - DrugExposure - DeviceExposure - File - Document - Specimen - BiologicProduct range: uriorcurie","title":"LinkML Source"},{"location":"index_time_point/","text":"Slot: index_time_point Another TimePoint from which this point is offset. 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URI: bdchm:quantity_measure Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenQuantityObservation Multivalued: True Comments Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quantity_measure owner: Specimen domain_of: - Specimen range: SpecimenQuantityObservation required: false","title":"Slot: quantity_measure"},{"location":"quantity_measure/#slot-quantity_measure","text":"An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. URI: bdchm:quantity_measure","title":"Slot: quantity_measure"},{"location":"quantity_measure/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"quantity_measure/#properties","text":"Range: SpecimenQuantityObservation Multivalued: True","title":"Properties"},{"location":"quantity_measure/#comments","text":"Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object.","title":"Comments"},{"location":"quantity_measure/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"quantity_measure/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"quantity_measure/#linkml-source","text":"name: quantity_measure description: An observation related to the present quantity of a specimen - e.g. its weight, volume, or analyte concentration. comments: - Observations are flexible containers for capturing a specific type of observation/measurement data about an object, along with metadata about how it was generated. The specific type of observation made is captured as data in the Observation object. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: quantity_measure owner: Specimen domain_of: - Specimen range: SpecimenQuantityObservation required: false","title":"LinkML Source"},{"location":"race/","text":"Slot: race An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. URI: bdchm:race Applicable Classes Name Description Modifies Slot Demography Demographics about an individual or animal receiving care or other health-rel... no Properties Range: RaceEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: race owner: Demography domain_of: - Demography range: RaceEnum","title":"Slot: race"},{"location":"race/#slot-race","text":"An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. URI: bdchm:race","title":"Slot: race"},{"location":"race/#applicable-classes","text":"Name Description Modifies Slot Demography Demographics about an individual or animal receiving care or other health-rel... no","title":"Applicable Classes"},{"location":"race/#properties","text":"Range: RaceEnum","title":"Properties"},{"location":"race/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"race/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"race/#linkml-source","text":"name: race description: An arbitrary classification of a taxonomic group that is a division of a species. It usually arises as a consequence of geographical isolation within a species and is characterized by shared heredity, physical attributes and behavior, and in the case of humans, by common history, nationality, or geographic distribution. The provided values are based on the categories defined by the U.S. Office of Management and Business and used by the U.S. Census Bureau. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: race owner: Demography domain_of: - Demography range: RaceEnum","title":"LinkML Source"},{"location":"refills/","text":"Slot: refills Intended refills at time of the prescription. URI: bdchm:refills Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no Properties Range: Integer Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"Slot: refills"},{"location":"refills/#slot-refills","text":"Intended refills at time of the prescription. URI: bdchm:refills","title":"Slot: refills"},{"location":"refills/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"refills/#properties","text":"Range: Integer","title":"Properties"},{"location":"refills/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"refills/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"refills/#linkml-source","text":"name: refills description: Intended refills at time of the prescription. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: refills owner: DrugExposure domain_of: - DrugExposure range: integer required: false","title":"LinkML Source"},{"location":"related_document/","text":"Slot: related_document A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) URI: bdchm:related_document Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: Document Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false","title":"Slot: related_document"},{"location":"related_document/#slot-related_document","text":"A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) URI: bdchm:related_document","title":"Slot: related_document"},{"location":"related_document/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"related_document/#properties","text":"Range: Document Multivalued: True","title":"Properties"},{"location":"related_document/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"related_document/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"related_document/#linkml-source","text":"name: related_document description: A reference to an external document that is about or related to the specimen (e.g. a publication related to the study it is a part of, pathology report containing additional details about it, protocol describing how it was collected) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: related_document owner: Specimen domain_of: - Specimen range: Document required: false","title":"LinkML Source"},{"location":"relationship_to_participant/","text":"Slot: relationship_to_participant A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') URI: bdchm:relationship_to_participant Applicable Classes Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string","title":"Slot: relationship_to_participant"},{"location":"relationship_to_participant/#slot-relationship_to_participant","text":"A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') URI: bdchm:relationship_to_participant","title":"Slot: relationship_to_participant"},{"location":"relationship_to_participant/#applicable-classes","text":"Name Description Modifies Slot Condition Conditions are records of a Person suggesting the presence of a disease or me... no","title":"Applicable Classes"},{"location":"relationship_to_participant/#properties","text":"Range: String","title":"Properties"},{"location":"relationship_to_participant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"relationship_to_participant/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"relationship_to_participant/#linkml-source","text":"name: relationship_to_participant description: A value indicating the relationship between the Participant to which the Condition is attributed and the individual who had the reported Condition. If the Condition is affecting the participant themselves, then 'Self' is the appropriate relationship. If the Condition is affecting a family member (e.g. a parent of the Participant) then an appropriate relationship should be provided (e.g. 'Parent') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: relationship_to_participant owner: Condition domain_of: - Condition range: string","title":"LinkML Source"},{"location":"research_project_type/","text":"Slot: research_project_type The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') URI: bdchm:research_project_type Applicable Classes Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"Slot: research_project_type"},{"location":"research_project_type/#slot-research_project_type","text":"The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') URI: bdchm:research_project_type","title":"Slot: research_project_type"},{"location":"research_project_type/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"research_project_type/#properties","text":"Range: String","title":"Properties"},{"location":"research_project_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"research_project_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"research_project_type/#linkml-source","text":"name: research_project_type description: The 'type' of ResearchStudy represented (e.g. a broad-based Program like 'CPTAC' or a more focused Project like 'CPTAC PDAC Discovery Study') from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: research_project_type owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"LinkML Source"},{"location":"response_value/","text":"Slot: response_value URI: bdchm:response_value Applicable Classes Name Description Modifies Slot QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no Properties Range: QuestionnaireResponseValue Required: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: response_value owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"Slot: response_value"},{"location":"response_value/#slot-response_value","text":"URI: bdchm:response_value","title":"Slot: response_value"},{"location":"response_value/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no","title":"Applicable Classes"},{"location":"response_value/#properties","text":"Range: QuestionnaireResponseValue Required: True","title":"Properties"},{"location":"response_value/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"response_value/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"response_value/#linkml-source","text":"name: response_value from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: response_value owner: QuestionnaireResponseItem domain_of: - QuestionnaireResponseItem range: QuestionnaireResponseValue required: true","title":"LinkML Source"},{"location":"role/","text":"Slot: role A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) URI: bdchm:role Applicable Classes Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no Properties Range: String Multivalued: True Examples Value lysis buffer fixative mounting medium collection media Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false","title":"Slot: role"},{"location":"role/#slot-role","text":"A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) URI: bdchm:role","title":"Slot: role"},{"location":"role/#applicable-classes","text":"Name Description Modifies Slot Substance A type of material substance, or instance thereof, as used in a particular ap... no","title":"Applicable Classes"},{"location":"role/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"role/#examples","text":"Value lysis buffer fixative mounting medium collection media","title":"Examples"},{"location":"role/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"role/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"role/#linkml-source","text":"name: role description: A role played by the substance in a particular application (e.g. the role of a lysis buffer when applied in a specimen creation activity, or the role of fixative when applied in specimen processing) examples: - value: lysis buffer - value: fixative - value: mounting medium - value: collection media from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_role multivalued: true alias: role owner: Substance domain_of: - Substance range: string required: false","title":"LinkML Source"},{"location":"route_concept/","text":"Slot: route_concept Route of drug administration. URI: bdchm:route_concept Applicable Classes Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no Properties Range: DrugRouteEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum","title":"Slot: route_concept"},{"location":"route_concept/#slot-route_concept","text":"Route of drug administration. URI: bdchm:route_concept","title":"Slot: route_concept"},{"location":"route_concept/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"route_concept/#properties","text":"Range: DrugRouteEnum","title":"Properties"},{"location":"route_concept/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"route_concept/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"route_concept/#linkml-source","text":"name: route_concept description: Route of drug administration. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: route_concept owner: DrugExposure domain_of: - DrugExposure range: DrugRouteEnum","title":"LinkML Source"},{"location":"section_location/","text":"Slot: section_location The location in a parent specimen from which a section/portion was excised (e.g. top, middle, bottom) URI: bdchm:section_location Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SectionLocationEnum Examples Value Top Bottom Unknown Comments This attribute applies only to Specimens that are of type 'portion' or 'slide'. 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URI: bdchm:sig","title":"Slot: sig"},{"location":"sig/#applicable-classes","text":"Name Description Modifies Slot DrugExposure DrugExposures are records of a Person suggesting exposure to a medication no","title":"Applicable Classes"},{"location":"sig/#properties","text":"Range: String","title":"Properties"},{"location":"sig/#comments","text":"Put the written out instructions for the drug as it is verbatim in the source, if available.","title":"Comments"},{"location":"sig/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sig/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"sig/#linkml-source","text":"name: sig description: This is the verbatim instruction for the drug as written by the provider. comments: - Put the written out instructions for the drug as it is verbatim in the source, if available. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sig owner: DrugExposure domain_of: - DrugExposure range: string required: false","title":"LinkML Source"},{"location":"site/","text":"Slot: site A term describing any site in the body. URI: bdchm:site Applicable Classes Name Description Modifies Slot BodySite A site in the body of an organism, typically described in terms of an anatomi... no Properties Range: String Required: True Examples Value Adenoid Adipose Adrenal Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: site description: A term describing any site in the body. examples: - value: Adenoid - value: Adipose - value: Adrenal from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_BodySite_site multivalued: false alias: site owner: BodySite domain_of: - BodySite range: string required: true","title":"Slot: site"},{"location":"site/#slot-site","text":"A term describing any site in the body. 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URI: bdchm:source_participant Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: Participant Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false","title":"Slot: source_participant"},{"location":"source_participant/#slot-source_participant","text":"A specific Subject from which the specimen was directly or indirectly derived. URI: bdchm:source_participant","title":"Slot: source_participant"},{"location":"source_participant/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"source_participant/#properties","text":"Range: Participant","title":"Properties"},{"location":"source_participant/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"source_participant/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"source_participant/#linkml-source","text":"name: source_participant description: A specific Subject from which the specimen was directly or indirectly derived. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: source_participant owner: Specimen domain_of: - Specimen range: Participant required: false","title":"LinkML Source"},{"location":"species/","text":"Slot: species The scientific binomial name for the species of the Person (e.g. Homo sapiens, Mus musculus, etc.). 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URI: bdchm:specimen_order","title":"Slot: specimen_order"},{"location":"specimen_order/#applicable-classes","text":"Name Description Modifies Slot SpecimenCreationActivity The process of creating a specimen no","title":"Applicable Classes"},{"location":"specimen_order/#properties","text":"Range: Integer","title":"Properties"},{"location":"specimen_order/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specimen_order/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"specimen_order/#linkml-source","text":"name: specimen_order description: A numeric value that represents the sequential order of this creation activity relative to those producing other specimens from the same source material or parent specimen. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: specimen_order owner: SpecimenCreationActivity domain_of: - SpecimenCreationActivity range: integer required: false","title":"LinkML Source"},{"location":"specimen_type/","text":"Slot: specimen_type The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: bdchm:specimen_type Applicable Classes Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no Properties Range: SpecimenTypeEnum Examples Value Fresh Specimen Portion Aliquot Analyte Slide Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false","title":"Slot: specimen_type"},{"location":"specimen_type/#slot-specimen_type","text":"The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). URI: bdchm:specimen_type","title":"Slot: specimen_type"},{"location":"specimen_type/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"specimen_type/#properties","text":"Range: SpecimenTypeEnum","title":"Properties"},{"location":"specimen_type/#examples","text":"Value Fresh Specimen Portion Aliquot Analyte Slide","title":"Examples"},{"location":"specimen_type/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"specimen_type/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"specimen_type/#linkml-source","text":"name: specimen_type description: The high-level type of the specimen, based on its derivation provenance (i.e. how far removed it is from the original sample extracted from a source). examples: - value: Fresh Specimen - value: Portion - value: Aliquot - value: Analyte - value: Slide from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Specimen_specimen_type multivalued: false alias: specimen_type owner: Specimen domain_of: - Specimen range: SpecimenTypeEnum required: false","title":"LinkML Source"},{"location":"sponsor/","text":"Slot: sponsor An entity that is responsible for the initiation, management, and/or financing of a research project. 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URI: bdchm:sponsor","title":"Slot: sponsor"},{"location":"sponsor/#applicable-classes","text":"Name Description Modifies Slot ResearchStudy A process where a researcher or organization plans and then executes a series... no","title":"Applicable Classes"},{"location":"sponsor/#properties","text":"Range: String","title":"Properties"},{"location":"sponsor/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"sponsor/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"sponsor/#linkml-source","text":"name: sponsor description: An entity that is responsible for the initiation, management, and/or financing of a research project. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: sponsor owner: ResearchStudy domain_of: - ResearchStudy range: string","title":"LinkML Source"},{"location":"storage_activity/","text":"Slot: storage_activity An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. 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URI: bdchm:storage_activity","title":"Slot: storage_activity"},{"location":"storage_activity/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"storage_activity/#properties","text":"Range: SpecimenStorageActivity Multivalued: True","title":"Properties"},{"location":"storage_activity/#comments","text":"The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions","title":"Comments"},{"location":"storage_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"storage_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"storage_activity/#linkml-source","text":"name: storage_activity description: An activity that results in the storage or maintenance of a specimen in a particular location, container, or state. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate periods of storage, in different locations and/or under different conditions from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: storage_activity owner: Specimen domain_of: - Specimen range: SpecimenStorageActivity required: false","title":"LinkML Source"},{"location":"study_arm/","text":"Slot: study_arm The arm(s) of the study on which the Participant is enrolled URI: bdchm:study_arm Applicable Classes Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no Properties Range: String Multivalued: True Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string","title":"Slot: study_arm"},{"location":"study_arm/#slot-study_arm","text":"The arm(s) of the study on which the Participant is enrolled URI: bdchm:study_arm","title":"Slot: study_arm"},{"location":"study_arm/#applicable-classes","text":"Name Description Modifies Slot Participant A Participant is the entity of interest in a research study, typically a huma... no","title":"Applicable Classes"},{"location":"study_arm/#properties","text":"Range: String Multivalued: True","title":"Properties"},{"location":"study_arm/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"study_arm/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"study_arm/#linkml-source","text":"name: study_arm description: The arm(s) of the study on which the Participant is enrolled from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: study_arm owner: Participant domain_of: - Participant range: string","title":"LinkML Source"},{"location":"substance_quantity/","text":"Slot: substance_quantity The quantity of substance this instance stands for. 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May be a specific chemical compound, or the name of a formulation/preparation made up of many compounds. examples: - value: toluene - value: formalin - value: DMEM from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 values_from: - crdch:enum_CRDCH_Substance_substance_type multivalued: false alias: substance_type owner: Substance domain_of: - Substance range: string required: false","title":"LinkML Source"},{"location":"text/","text":"Slot: text URI: bdchm:text Applicable Classes Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no Properties Range: String Identifier and Mapping Information LinkML Source name: text alias: text domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string","title":"Slot: text"},{"location":"text/#slot-text","text":"URI: bdchm:text","title":"Slot: text"},{"location":"text/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireItem QuestionnaireItem defines a question or section within the Questionnaire no QuestionnaireResponseItem QuestionnaireResponseItem provides a complete or partial list of answers to a... no","title":"Applicable Classes"},{"location":"text/#properties","text":"Range: String","title":"Properties"},{"location":"text/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"text/#linkml-source","text":"name: text alias: text domain_of: - QuestionnaireItem - QuestionnaireResponseItem range: string","title":"LinkML Source"},{"location":"title/","text":"Slot: title Name for this Questionnaire (human friendly) URI: bdchm:title Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: title"},{"location":"title/#slot-title","text":"Name for this Questionnaire (human friendly) URI: bdchm:title","title":"Slot: title"},{"location":"title/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"title/#properties","text":"Range: String","title":"Properties"},{"location":"title/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"title/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"title/#linkml-source","text":"name: title description: Name for this Questionnaire (human friendly) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: title owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"transport_activity/","text":"Slot: transport_activity An activity through which the specimen is transported between locations. 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URI: bdchm:transport_activity","title":"Slot: transport_activity"},{"location":"transport_activity/#applicable-classes","text":"Name Description Modifies Slot Specimen Any material taken as a sample from a biological entity (living or dead), or ... no","title":"Applicable Classes"},{"location":"transport_activity/#properties","text":"Range: SpecimenTransportActivity Multivalued: True","title":"Properties"},{"location":"transport_activity/#comments","text":"The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time.","title":"Comments"},{"location":"transport_activity/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"transport_activity/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"transport_activity/#linkml-source","text":"name: transport_activity description: An activity through which the specimen is transported between locations. comments: - The 0..m cardinality of this attribute reflects the fact that a given specimen may undergo many separate transport processes at different periods of time. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: true alias: transport_activity owner: Specimen domain_of: - Specimen range: SpecimenTransportActivity required: false","title":"LinkML Source"},{"location":"transport_destination/","text":"Slot: transport_destination An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. 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URI: bdchm:transport_destination","title":"Slot: transport_destination"},{"location":"transport_destination/#applicable-classes","text":"Name Description Modifies Slot SpecimenTransportActivity An activity through which a specimen is transported between locations or orga... no","title":"Applicable Classes"},{"location":"transport_destination/#properties","text":"Range: Organization","title":"Properties"},{"location":"transport_destination/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"transport_destination/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"transport_destination/#linkml-source","text":"name: transport_destination description: An organization (facility, site, lab, etc) to which the specimen is delivered as a result of the activity. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: transport_destination owner: SpecimenTransportActivity domain_of: - SpecimenTransportActivity range: Organization required: false","title":"LinkML Source"},{"location":"transport_origin/","text":"Slot: transport_origin An organization (facility, site, lab, etc) from which the specimen was transported as a result of the activity. 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URI: bdchm:unit Applicable Classes Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no Properties Range: UnitOfMeasurementEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: unit description: A coded or free text (in the .text field) representation of the unit. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: unit owner: Quantity domain_of: - Quantity range: UnitOfMeasurementEnum required: false","title":"Slot: unit"},{"location":"unit/#slot-unit","text":"A coded or free text (in the .text field) representation of the unit. 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URI: bdchm:valid_from Applicable Classes Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no Properties Range: TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint","title":"Slot: valid_from"},{"location":"valid_from/#slot-valid_from","text":"The point in time from which the consent record is valid. URI: bdchm:valid_from","title":"Slot: valid_from"},{"location":"valid_from/#applicable-classes","text":"Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no","title":"Applicable Classes"},{"location":"valid_from/#properties","text":"Range: TimePoint","title":"Properties"},{"location":"valid_from/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"valid_from/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"valid_from/#linkml-source","text":"name: valid_from description: The point in time from which the consent record is valid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_from owner: Consent domain_of: - Consent range: TimePoint","title":"LinkML Source"},{"location":"valid_to/","text":"Slot: valid_to The point in time after which the consent record is invalid. URI: bdchm:valid_to Applicable Classes Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no Properties Range: TimePoint Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint","title":"Slot: valid_to"},{"location":"valid_to/#slot-valid_to","text":"The point in time after which the consent record is invalid. URI: bdchm:valid_to","title":"Slot: valid_to"},{"location":"valid_to/#applicable-classes","text":"Name Description Modifies Slot Consent An entity that can be used to capture consent code and other relevant data ab... no","title":"Applicable Classes"},{"location":"valid_to/#properties","text":"Range: TimePoint","title":"Properties"},{"location":"valid_to/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"valid_to/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"valid_to/#linkml-source","text":"name: valid_to description: The point in time after which the consent record is invalid. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: valid_to owner: Consent domain_of: - Consent range: TimePoint","title":"LinkML Source"},{"location":"value/","text":"Slot: value A general slot to hold a value. URI: bdchm:value Applicable Classes Name Description Modifies Slot QuestionnaireResponseValue Single-valued answer to the question no ObservationValue Single-valued observation valueholiding slot no QuestionnaireResponseValueDecimal Single-valued decimal answer to the question yes QuestionnaireResponseValueBoolean Single-valued boolean answer to the question yes QuestionnaireResponseValueInteger Single-valued integer answer to the question yes QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question yes QuestionnaireResponseValueString Single-valued string answer to the question yes DimensionalObservation A structured object that describes a single data item about the physical dime... yes SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... yes SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... yes Observation A data structure with key (observation_type) and value (value) attributes tha... no ObservationValueDecimal Single-valued decimal observation yes ObservationValueInteger Single-valued integer observation yes ObservationValueBoolean Single-valued boolean observation yes ObservationValueString Single-valued string observation yes ObservationValueQuantity Single-valued Quantity observation yes Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value domain_of: - QuestionnaireResponseValue - Observation - ObservationValue range: string","title":"Slot: value"},{"location":"value/#slot-value","text":"A general slot to hold a value. URI: bdchm:value","title":"Slot: value"},{"location":"value/#applicable-classes","text":"Name Description Modifies Slot QuestionnaireResponseValue Single-valued answer to the question no ObservationValue Single-valued observation valueholiding slot no QuestionnaireResponseValueDecimal Single-valued decimal answer to the question yes QuestionnaireResponseValueBoolean Single-valued boolean answer to the question yes QuestionnaireResponseValueInteger Single-valued integer answer to the question yes QuestionnaireResponseValueTimePoint Single-valued TimePoint answer to the question yes QuestionnaireResponseValueString Single-valued string answer to the question yes DimensionalObservation A structured object that describes a single data item about the physical dime... yes SpecimenQualityObservation A structured object that describes a characteristic of a specimen indicative ... yes SpecimenQuantityObservation A structured object that describes a single data item about the quantity of a... yes Observation A data structure with key (observation_type) and value (value) attributes tha... no ObservationValueDecimal Single-valued decimal observation yes ObservationValueInteger Single-valued integer observation yes ObservationValueBoolean Single-valued boolean observation yes ObservationValueString Single-valued string observation yes ObservationValueQuantity Single-valued Quantity observation yes","title":"Applicable Classes"},{"location":"value/#properties","text":"Range: String","title":"Properties"},{"location":"value/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"value/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"value/#linkml-source","text":"name: value description: A general slot to hold a value. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: value domain_of: - 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crdch:enum_CRDCH_Quantity_value_codeable_concept multivalued: false alias: value_concept owner: Quantity domain_of: - Quantity range: string required: false","title":"LinkML Source"},{"location":"value_decimal/","text":"Slot: value_decimal An amount, in the given units (if specified) URI: bdchm:value_decimal Applicable Classes Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no Properties Range: Decimal Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false","title":"Slot: value_decimal"},{"location":"value_decimal/#slot-value_decimal","text":"An amount, in the given units (if specified) URI: bdchm:value_decimal","title":"Slot: value_decimal"},{"location":"value_decimal/#applicable-classes","text":"Name Description Modifies Slot Quantity A structured object to represent an amount of something (e no","title":"Applicable Classes"},{"location":"value_decimal/#properties","text":"Range: Decimal","title":"Properties"},{"location":"value_decimal/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"value_decimal/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"value_decimal/#linkml-source","text":"name: value_decimal description: An amount, in the given units (if specified) from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 multivalued: false alias: value_decimal owner: Quantity domain_of: - Quantity range: decimal required: false","title":"LinkML Source"},{"location":"version/","text":"Slot: version The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. URI: bdchm:version Applicable Classes Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no Properties Range: String Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string","title":"Slot: version"},{"location":"version/#slot-version","text":"The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. URI: bdchm:version","title":"Slot: version"},{"location":"version/#applicable-classes","text":"Name Description Modifies Slot Questionnaire A Questionnaire is an organized collection of questions intended to solicit i... no","title":"Applicable Classes"},{"location":"version/#properties","text":"Range: String","title":"Properties"},{"location":"version/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"version/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"version/#linkml-source","text":"name: version description: The identifier that is used to identify this version of the questionnaire when it is referenced in a specification, model, design or instance. This is an arbitrary value managed by the questionnaire author and is not expected to be globally unique. For example, it might be a timestamp (e.g. yyyymmdd) if a managed version is not available. There is also no expectation that versions can be placed in a lexicographical sequence. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: version owner: Questionnaire domain_of: - Questionnaire range: string","title":"LinkML Source"},{"location":"visit_category/","text":"Slot: visit_category A value representing the kind (or category) of visit, like inpatient or outpatient. URI: bdchm:visit_category Applicable Classes Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no Properties Range: VisitCategoryEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum","title":"Slot: visit_category"},{"location":"visit_category/#slot-visit_category","text":"A value representing the kind (or category) of visit, like inpatient or outpatient. URI: bdchm:visit_category","title":"Slot: visit_category"},{"location":"visit_category/#applicable-classes","text":"Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no","title":"Applicable Classes"},{"location":"visit_category/#properties","text":"Range: VisitCategoryEnum","title":"Properties"},{"location":"visit_category/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"visit_category/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"visit_category/#linkml-source","text":"name: visit_category description: A value representing the kind (or category) of visit, like inpatient or outpatient. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_category owner: Visit domain_of: - Visit range: VisitCategoryEnum","title":"LinkML Source"},{"location":"visit_provenance/","text":"Slot: visit_provenance A value representing the provenance of the visit record, or where the record comes from. URI: bdchm:visit_provenance Applicable Classes Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no Properties Range: VisitProvenanceEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum","title":"Slot: visit_provenance"},{"location":"visit_provenance/#slot-visit_provenance","text":"A value representing the provenance of the visit record, or where the record comes from. URI: bdchm:visit_provenance","title":"Slot: visit_provenance"},{"location":"visit_provenance/#applicable-classes","text":"Name Description Modifies Slot Visit Events where Persons engage with the healthcare system for a duration of time no","title":"Applicable Classes"},{"location":"visit_provenance/#properties","text":"Range: VisitProvenanceEnum","title":"Properties"},{"location":"visit_provenance/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"visit_provenance/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"visit_provenance/#linkml-source","text":"name: visit_provenance description: A value representing the provenance of the visit record, or where the record comes from. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: visit_provenance owner: Visit domain_of: - Visit range: VisitProvenanceEnum","title":"LinkML Source"},{"location":"vital_status/","text":"Slot: vital_status Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. URI: bdchm:vital_status Applicable Classes Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no Properties Range: VitalStatusEnum Identifier and Mapping Information Schema Source from schema: https://w3id.org/nhlbidatastage/bdchm LinkML Source name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum","title":"Slot: vital_status"},{"location":"vital_status/#slot-vital_status","text":"Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. URI: bdchm:vital_status","title":"Slot: vital_status"},{"location":"vital_status/#applicable-classes","text":"Name Description Modifies Slot Person Administrative information about an individual or animal receiving care or ot... no","title":"Applicable Classes"},{"location":"vital_status/#properties","text":"Range: VitalStatusEnum","title":"Properties"},{"location":"vital_status/#identifier-and-mapping-information","text":"","title":"Identifier and Mapping Information"},{"location":"vital_status/#schema-source","text":"from schema: https://w3id.org/nhlbidatastage/bdchm","title":"Schema Source"},{"location":"vital_status/#linkml-source","text":"name: vital_status description: Coded value indicating the state or condition of being living or deceased; also includes the case where the vital status is unknown. from_schema: https://w3id.org/nhlbidatastage/bdchm rank: 1000 alias: vital_status owner: Person domain_of: - Person range: VitalStatusEnum","title":"LinkML Source"},{"location":"year_of_birth/","text":"Slot: year_of_birth Numeric value to represent the calendar year in which an individual was born. 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