gen3.config.yaml

#
# deprecated use iceberg instead
#



# Gen3 entity category: defaults to Clinical
categories:
  DocumentReference: data_file
  Location: Administrative
  Organization: Administrative
  Patient: Administrative
  Practitioner: Administrative
  PractitionerRole: Administrative
  ResearchStudy: Administrative
  ResearchSubject: Administrative
  Specimen: Biospecimen
  Task: Analysis

ignored_properties:
  - contained
  - meta
  - implicitRules
  - language
  - contained
  - modifierExtension
  - assigner
  - fhir_comments
  - text


dependency_order:
  # gen3 scaffolding
  - _definitions.yaml
  - _terms.yaml
  # gen3 required objects
  - Program
  - Project
  # FHIR - "in scope"
#  - Organization
#  - Location
#  - Practitioner
#  - PractitionerRole
  - ResearchStudy
  - Patient
  - ResearchSubject
  - Substance
  - Specimen
  - Encounter
  - Observation
  - DiagnosticReport
  - Condition
  - Medication
  - MedicationAdministration
#  - ImagingStudy
#  - Procedure
  - DocumentReference
  - Task
  - FamilyMemberHistory
  - BodyStructure

# edges that we manually curate, _not_ generated
# the context variables are substituted [$base_uri]
manually_curated_edges:

  EdgeConfig:
    type: object
    title: EdgeConfig
    id: EdgeConfig
    description: Information about the edge between two nodes.
    properties:
      resourceType:
        description: The title of the resource
        type: string
      source:
        description: A pointer to the source resource, encapsulates type & id.
        "$ref": Reference
      target:
        description: A pointer to the target resource, encapsulates type & id.
        "$ref": Reference
    required:
    - resourceType
    - source
    - target

  Task_owner_Patient:
    id: Task_owner_Patient
    allOf:
    - $ref: EdgeConfig.yaml
    description: Responsible individual.
    destination_multiplicity: many
    destination_property_name: owner_task
    destination_type: Patient
    is_primary: false
    label: Task_owner_Patient
    source_multiplicity: many
    source_property_name: owner
    source_type: Task
    title: Task_owner_Patient
    type: object


  Task_for_fhir_Patient:
    id: Task_for_fhir_Patient
    allOf:
    - $ref: EdgeConfig.yaml
    description: Beneficiary of the Task.
    destination_multiplicity: many
    destination_property_name: for_fhir_task
    destination_type: Patient
    is_primary: true
    label: Task_for_Patient
    source_multiplicity: many
    source_property_name: for_fhir
    source_type: Task
    title: Task_for_fhir_Patient
    type: object


  Task_output_DocumentReference:
    id: Task_output_DocumentReference
    allOf:
    - $ref: EdgeConfig.yaml
    description: Information produced as part of task.
    destination_multiplicity: many
    destination_property_name: owner_task
    destination_type: DocumentReference
    is_primary: true
    label: Task_output_DocumentReference
    source_multiplicity: one
#    source_property_name: 'output[*].valueReference'
    source_property_name: output_valueReference
    source_type: Task
    title: Task_output_DocumentReference
    type: object


  Observation_hasMember_Observation:
    id: Observation_hasMember_Observation
    allOf:
    - $ref: EdgeConfig.yaml
    description: Related resource that belongs to the Observation group.
    destination_multiplicity: many
    destination_property_name: hasMember_observation
    destination_type: Observation
    is_primary: true
    label: Observation_hasMember_Observation
    source_multiplicity: many
    source_property_name: hasMember
    source_type: Observation
    title: Observation_hasMember_Observation
    type: object


  Task_focus_Specimen:
    id: Task_focus_Specimen
    allOf:
    - $ref: EdgeConfig.yaml
    description: What task is acting on.
    destination_multiplicity: many
    destination_property_name: focus_task
    destination_type: Specimen
    is_primary: true
    label: Task_focus_Specimen
    source_multiplicity: many
    source_property_name: focus
    source_type: Task
    title: Task_focus_Specimen
    type: object

  Medication_ingredient_Substance:
    id: Medication_ingredient_Substance
    allOf:
    - $ref: EdgeConfig.yaml
    description: Active or inactive ingredient.
    destination_multiplicity: many
    destination_property_name: ingredient_medication
    destination_type: Substance
    is_primary: true
    label: Medication_ingredient_Substance
    source_multiplicity: one
#    source_property_name: 'ingredient[*].itemReference'
    source_property_name: 'ingredient_itemReference'
    source_type: Medication
    title: Medication_ingredient_Substance
    type: object

  Observation_partOf_MedicationAdministration:
    id: Observation_partOf_MedicationAdministration
    allOf:
    - $ref: EdgeConfig.yaml
    description: Part of referenced event.
    destination_multiplicity: many
    destination_property_name: observation
    destination_type: MedicationAdministration
    # set to false, so it is __not__ included in gen3 schema (psqlgraph problems for unknown reasons)
    is_primary: false
    label: Observation_partOf_MedicationAdministration
    source_multiplicity: many
    source_property_name: partOf
    source_type: Observation
    title: Observation_partOf_MedicationAdministration
    type: object

  ResearchStudy_project_project:
    id: ResearchStudy_project_project
    allOf:
    - $ref: EdgeConfig.yaml
    description: Link to required Gen3 project.
    destination_multiplicity: many
    destination_property_name: research_studies
    destination_type: project
    is_primary: true
    label: ResearchStudy_project_project
    source_multiplicity: many
    source_property_name: project
    source_type: ResearchStudy
    title: ResearchStudy_project_project
    type: object

  Observation_focus_ResearchStudy:
    id: Observation_focus_ResearchStudy
    allOf:
    - $ref: EdgeConfig.yaml
    description: Part of referenced event.
    destination_multiplicity: many
    destination_property_name: observation
    destination_type: ResearchStudy
    is_primary: true
    label: Observation_focus_ResearchStudy
    source_multiplicity: many
    source_property_name: focus_ResearchStudy
    source_type: Observation
    title: Observation_focus_ResearchStudy
    type: object


  # qualify source_property_name
  MedicationAdministration_reasonReference_Condition:
    id: MedicationAdministration_reasonReference_Condition
    allOf:
    - $ref: EdgeConfig.yaml
    description: Condition or observation that supports why the medication was administered. (Generated Edge)
    destination_multiplicity: many
    destination_property_name: medication_administration
    destination_type: Condition
    is_primary: true
    label: MedicationAdministration_reasonReference_Condition
    source_multiplicity: many
    source_property_name: reasonReference_Condition
    source_type: MedicationAdministration
    title: MedicationAdministration_reasonReference_Condition
    type: object

  Signature_who_Patient:
    id: Signature_who_Patient
    allOf:
    - $ref: EdgeConfig.yaml
    description: Who signed. (Generated Edge)
    destination_multiplicity: many
    destination_property_name: who_signature
    destination_type: Patient
    is_primary: true
    label: Signature_who_Patient
    source_multiplicity: many
    source_property_name: who
    source_type: Signature
    title: Signature_who_Patient
    type: object


extra_properties:

  # add gen3 file scaffolding
  DocumentReference:
    $ref: "_definitions.yaml#/data_file_properties"
    data_category:
      term:
        $ref: "_terms.yaml#/data_category"
      type: string
    data_type:
      term:
        $ref: "_terms.yaml#/data_type"
      type: string
    data_format:
      term:
        $ref: "_terms.yaml#/data_format"
      type: string
    auth_resource_path:
        type: string
        description: Gen3 scaffolding
    category_coding:
        type: array
        items:
          type: string
    category_coding_display:
        type: string
    content_url:
        type: string
    patient_id:
        type: string

#    type_coding:
#        type: string
#    type_coding_1:
#        type: string
#    type_coding_display:
#        type: string
#    type_coding_display_1:
#        type: string

  # add us-core-race, us-core-ethnicity and synthea extensions
  Patient:

    us_core_race_coding:
        type: string
        description: "The 5 race category codes according to the [OMB Standards for Maintaining, Collecting, and Presenting Federal Data on Race and Ethnicity, Statistical Policy Directive No. 15, as revised, October 30, 1997](https://www.govinfo.gov/content/pkg/FR-1997-10-30/pdf/97-28653.pdf)."
        termDef:
            cde_id: http://hl7.org/fhir/us/core/ValueSet/omb-race-category
            term: http://hl7.org/fhir/us/core/ValueSet/omb-race-category
            term_url: http://hl7.org/fhir/us/core/ValueSet/omb-race-category
            cde_version:
            source: fhir
            strength: required
    us_core_race:
        type: string
        description: Coding's text value
    us_core_ethnicity_coding:
        type: string
        description: "The 2 ethnicity category codes according to the [OMB Standards for Maintaining, Collecting, and Presenting Federal Data on Race and Ethnicity, Statistical Policy Directive No. 15, as revised, October 30, 1997](https://www.govinfo.gov/content/pkg/FR-1997-10-30/pdf/97-28653.pdf)."
        termDef:
            cde_id: http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity-category
            term: http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity-category
            term_url: http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity-category
            cde_version:
            source: fhir
            strength: required
    us_core_ethnicity:
        type: string
        description: Coding's text value
    patient_mothersMaidenName:
        type: string
        description: "Mother's maiden (unmarried) name, commonly collected to help verify patient identity."
        termDef:
            cde_id: http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName
            term: http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName
            term_url: http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName
            cde_version:
            source: fhir
            strength: required
    us_core_birthsex_code:
        type: string
        description: "A code classifying the person’s sex assigned at birth as specified by the Office of the National Coordinator for Health IT (ONC). This extension aligns with the C-CDA Birth Sex Observation (LOINC 76689-9)."
        termDef:
            cde_id: http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex
            term: http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex
            term_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex
            cde_version:
            source: fhir
            strength: required
    patient_birthPlace_valueAddress:
        type: string
        description: "The registered place of birth of the patient. A sytem may use the address.text if they don't store the birthPlace address in discrete elements."
        termDef:
            cde_id: http://hl7.org/fhir/StructureDefinition/patient-birthPlace
            term: http://hl7.org/fhir/StructureDefinition/patient-birthPlace
            term_url: http://hl7.org/fhir/StructureDefinition/patient-birthPlace
            cde_version:
            source: fhir
            strength: required
    disability_adjusted_life_years_valueDecimal:
        type: number
        description: "Disability Adjusted Life Years as defined in the literature and summarized at https://en.wikipedia.org/wiki/Disability-adjusted_life_year http://synthetichealth.github.io/synthea/StructureDefinition/disability-adjusted-life-years"
    quality_adjusted_life_years_valueDecimal:
        type: number
        description: "Quality Adjusted Life Years as defined in the literature and summarized at https://en.wikipedia.org/wiki/Quality-adjusted_life_year   http://synthetichealth.github.io/synthea/StructureDefinition/quality-adjusted-life-years."
    maritalStatus_coding:
        type: string
        description: This field contains a patient's most recent marital (civil) status. See http://hl7.org/fhir/ValueSet/marital-status

    auth_resource_path:
        type: string
        description: Gen3 scaffolding


  # add genomic observation
  Observation:

    auth_resource_path:
        type: string
        description: Gen3 scaffolding

#    gene_studied_id:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    gene_studied_id_coding:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    genomic_reference_sequence_id:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    genomic_reference_sequence_id_coding:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    conclusion_string:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    evidence_level:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    evidence_level_coding:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_1:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding_1:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_2:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding_2:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_3:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding_3:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_4:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding_4:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_5:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding_5:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_6:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    predicted_phenotype_coding_6:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    valueCodeableConcept_coding_1:
#        type: string
#    valueCodeableConcept_1:
#        type: string
#    observation_interpretation:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    observation_interpretation_coding:
#        type: string
#        description: See http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-risk-assessment
#    systolic_blood_pressure:
#        type: string
#    systolic_blood_pressure_unit:
#        type: string
#    systolic_blood_pressure_value:
#        type: number
#    diastolic_blood_pressure:
#        type: string
#    diastolic_blood_pressure_unit:
#        type: string
#    diastolic_blood_pressure_value:
#        type: number
#    identifier_1:
#        type: string
#        description: A string, typically numeric or alphanumeric, that is associated with a single object or entity within a given system. See https://build.fhir.org/datatypes.html#Identifier
#    identifier_2:
#        type: string
#        description: A string, typically numeric or alphanumeric, that is associated with a single object or entity within a given system. See https://build.fhir.org/datatypes.html#Identifier
#    identifier_3:
#        type: string
#        description: A string, typically numeric or alphanumeric, that is associated with a single object or entity within a given system. See https://build.fhir.org/datatypes.html#Identifier
#    identifier_4:
#        type: string
#        description: A string, typically numeric or alphanumeric, that is associated with a single object or entity within a given system. See https://build.fhir.org/datatypes.html#Identifier
#    identifier_5:
#        type: string
#        description: A string, typically numeric or alphanumeric, that is associated with a single object or entity within a given system. See https://build.fhir.org/datatypes.html#Identifier
#    identifier_6:
#        type: string
#        description: A string, typically numeric or alphanumeric, that is associated with a single object or entity within a given system. See https://build.fhir.org/datatypes.html#Identifier
#    category_coding:
#        type: string
#    category_1:
#        type: string
#    category_coding_1:
#        type: string
#    category_coding_display:
#        type: string
#    category_coding_display_1:
#        type: string
#    code_coding:
#        type: string
#    code_coding_1:
#        type: string
#    code_1:
#        type: string

  # inputs and outputs
  Task:
    input_type:
      type: string
    input_type_coding:
      type: string
    input_valueReference:
      type: string
    output_type:
      type: string
    output_type_coding:
      type: string
    output_valueReference:
      type: string


# TODO
#      targets:
#        - $ref: $base_url/Medication
#          backref: observation
#        - $ref: $base_url/Patient
#          backref: subject_observation
#        - $ref: $base_url/Substance
#          backref: observation