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Concept Attribute Tables
This page defines SEPIO core concepts and presents key attributes used to describe them in SEPIO data models. More in depth description of each concept and their scope and use in SEPIO models can be found in the individual Core Concept Pages to the right.
To Do: Add concept diagram of full model.
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
An Information Content Entity (ICE) is an entity that is about something. ICEs are abstract (non-physical) entities that represent the information encoded in physical artifacts such as photographs, books, or digital storage medium (as opposed to the physical medium itself).
The attributes below apply generally to any type of ICE, and are inherited by all ICE subtypes defined in SEPIO, including the core concepts of an Assertion, Evidence Line, and Evidence Item.
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| description | xsd:string | 0..m | A free-text description of an entity. |
| date | xsd:dateTime | 1..1 | A date associated with an event in the life-cycle of an entity (from Dublin Core). SEPIO defines sub-properties for specific evnets, e.g. creation date, modification date. |
| is_about | Entity | 1..m | An entity that the ICE is about (describes, denotes, mentions, specifies, etc). |
| has_contributor | Agent | 1..m | An Agent that contributes to the creation, modification, or evaluation of an entity. SEPIO defines sub-properties for these and other specific forms of contribution. |
| is_output_of | Activity | 1..1 | An activity that generated an entity. |
| is_specified_by | Directive Information Entity | 0..m | A method (e.g. protocol, recipe, guideline) that specifies how an ICE such as an Assertion or Data Item is generated. |
| source | Information Content Entity | 0..m | An information resource from which an entity is derived, in whole or in part (from Dublin Core). |
| qualified_contribution | Contribution | 0..m | This property reifies the has_contributor relation to allow recording of additional context (e.g. a role played by the Agent making the contribution). It is analogous to a qualifiedAttribution in PROV-O. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
A statement of purported truth, as made by a particular agent on a particular occasion. Also known as a 'Claim'. Assertions put forth a proposition that the Agent purports to be true. SEPIO describes 'scientific' Assertions in particular, which are the result of some inference or conclusion drawn from a critical evaluation of evidence.
Assertion inherits from Information Content Entity, and adds the following attributes or constraints:
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| asserted_by | Agent | 1..1 | The Agent who made the Assertion. If more than one Agent is involved, consider them collectively as a group or organization. |
| date_asserted | xsd:dateTime | 1..1 | The date and time on which the Assertion was originally made. |
| is_specified_by | Assertion Method | 0..m | The method (e.g. a protocol, guideline, rule set) that specifies how the Assertion was generated by some Agent (e.g. what types of data may be used as evidence, how to weight and combine Evidence Lines to make a final Assertion. |
| has_evidence_line | Evidence Line | 1..m | An Evidence Line that is used to evaluate the validity of the Proposition put forth by the Assertion. IAll scientific claims have at least one Evidence Line supporting them. |
| assertion_validated_by | Agent | 0..m | An Agent who validates the quality of an Assertion. Validation is common practice in many assertion pipelines, e.g. clinical variant interpretation performed by ClinGen or CIViC. |
| date_validated | xsd:dateTime | 0..m | The date and time at which the Assertion is validated as meeting a defined standard of quality or rigor. |
| assertion_confidence_level | Value Set | 0..1 | A qualitative value assigned to an Assertion that indicates the degree of confidence that the Proposition it puts forth is true. e.g. CIViC 'trust ratings' [4] assign confidence levels based on a 5-star scale. |
| assertion_confidence_score | integer or float | 0..1 | A quantitative value that is calculated as an indicator of the degree of confidence that the Proposition put forth by an Assertion is true. |
| has_evidence_from_source | Publication | 0..m | A shortcut relation used to directly link an Assertion to a resource (e.g. a Publication) that describes evidence used to evaluate its validity. |
| asserts | Proposition | 1..1 | The Proposition that is put forth as true by the Assertion. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
An Evidence Item is any Information that is used to evaluate the validity of a Proposition put forth by an Assertion. Evidence Item is a 'defined class' in SEPIO, representing any piece of Information that plays an evidence role.
Evidence Item inherits all attributes of Information Content Entity, and additionally holds an 'Evidence Role'.
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| has_role | Evidence Role | 1..1 | Any ICE that qualifies as an Evidence Item bears an Evidence Role. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
An Evidence Line is an independent, evidence-based argument used to evaluate the validity of a particular proposition.
Evidence Line inherits from Information Content Entity, and adds the following attributes or constraints:
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| has_evidence_item | Evidence Item | 1..m | The individual information entities (Evidence Items) that support the argument the Evidence Line represents. |
| evidence_strength | Value Set | 0..1 | An quality reflecting how strongly an Evidence Line supports or refutes a Proposition. Different resources often create their own value sets to capture this attribute (e.g. 'very strong', 'strong', 'moderate'). |
| evidence_has_strength_ assessed_by | Agent | 0..1 | An Agent who determines the asserted strength of the Evidence Line. |
| date_evidence_ strength_assessed | xsd:dateTime | 0..1 | The data and time on which the asserted strength of the Evidence Line was assessed. |
| has_supporting_ activity | Activity | 0..m | A shortcut relation that links directly to activities (studies, assays, computation, curation) that generated Evidence Items contributing to the Evidence Line. |
| has_supporting_ reference | Document | 0..m | A shortcut relation that links directly to citable documents or reports that describe Evidence Items contributing to the Evidence Line. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
An Activity is a process occurring over time that acts upon or with entities. Activities can generate, modify, evaluate, or destroy entities, including Assertions, Evidence Lines, and Evidence Items.
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| has_agent | Agent | 1..m | An Agent or Agents that perform the Activity. |
| date_of_activity | xsd:dateTime | 1..1 | The date the activity was performed. If Activity spanned multiple days, it is common to record the end date, or use date_ended and date_started properties. |
| has_input | Material Entity or Information Content Entity | 1..m | An entity that is present as input at the beginning of an Activity. |
| has_output | Material Entity or Information Content Entity | 1..m | An entity output from the activity - given scope of SEPIO this will always be an ICE. |
| has_part | Activity | 0..m | A smaller task or process that is part of some larger Activity, e.g. a particular technique, assay or data processing task performed in a Research Study. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
An Agent is something that bears some form of responsibility for an activity taking place, for the existence of an entity, or for another agent's activity. Agents typically persons, organization, or software agents who perform tasks, including making Assertions, and generating information used as evidence.
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| contributed_to | Entity | 0..m | An entity whose creation, modification, or assessment an Agent has contributed. |
| member_of | Organization | 0..m | An Organization in which the Agent is a member. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
The part played by a particular Agent in the creation, modification, assessment, or destruction of an artifact. The scope of a particular Contribution is constrained to include only the actions of a particular Agent toward the creation, modification, or evaluation of an entity. This may span a single period of time, or multiple sessions of work.
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| has_agent | Agent | 1..1 | The Agent making the Contribution. |
| date_of_contribution | xsd:dateTime | 1..1 | The date the Contribution was made. |
| realizes | Agent Role | 1..m | A role realized in the act of contributing, indicating a specific type of contribution made (e.g. Creator, Validator, Curator). |
| performed_on_behalf_of | Agent | 0..m | A separate Agent, typically an organization, on whose behalf an Agent makes a Contribution. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition
Definition: Propositions are abstract entities representing the sharable meaning expressed in a particular Assertion. Propositions express the core fact or meaning that is put forth as true in an Assertion. They are 'sharable' in that the same Proposition can be expressed in separate Assertions made by different Agents, on different occasions.
| Property | Value Type | Cardinality | Description |
|---|---|---|---|
| asserted_in | Assertion | 1..m | An Assertion that puts forth the Proposition as true. |
| has_evidence_line | Evidence Line | 1..m | An Evidence Line that is used to evaluate the validity of the Proposition. |
Jump to: Information Content Entity | Assertion | Evidence Item | Evidence Line | Agent | Activity | Contribution | Proposition