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Class: EvidenceLine

A discrete, independent argument relevant to the validity of the Proposition put forth as true in the Statement, that is based on the interpretation of one or more pieces of information as evidence.

URI: vacoreim:EvidenceLine

classDiagram class EvidenceLine InformationEntity <|-- EvidenceLine EvidenceLine : contributions EvidenceLine --|> Contribution : contributions EvidenceLine : dateAuthored EvidenceLine : derivedFrom EvidenceLine --|> InformationEntity : derivedFrom EvidenceLine : description EvidenceLine : directionOfEvidenceProvided EvidenceLine --|> Coding : directionOfEvidenceProvided EvidenceLine : evidenceItems EvidenceLine --|> InformationEntity : evidenceItems EvidenceLine : extensions EvidenceLine --|> Extension : extensions EvidenceLine : id EvidenceLine : identifiers EvidenceLine : label EvidenceLine : recordMetadata EvidenceLine --|> RecordMetadata : recordMetadata EvidenceLine : reportedIn EvidenceLine --|> Document : reportedIn EvidenceLine : specifiedBy EvidenceLine --|> Method : specifiedBy EvidenceLine : strengthOfEvidenceProvided EvidenceLine --|> Coding : strengthOfEvidenceProvided EvidenceLine : subtype EvidenceLine --|> Coding : subtype EvidenceLine : targetProposition EvidenceLine --|> Proposition : targetProposition EvidenceLine : type EvidenceLine : urls EvidenceLine : xrefs

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subtype 0..1
Coding		 A specific type of evidence the EvidenceLine object represents (e.g. 'mutant phenotype evidence', 'evidence from manual interpretation', 'ACMG PM2 evidence') direct
targetProposition 0..1
Proposition		 The proposition against which the evidence items were evaluated, in determining the overall strength and direction of evidence they provide (as captured in the Evidence Line) direct
evidenceItems 0..*
InformationEntity		 An Information Entity that was evaluated in making the argument represented by the Evidence Lines. direct
directionOfEvidenceProvided 0..1
Coding		 The direction of support that the Evidence Line is determined to provide for its target Proposition (can be supporting, disputing, or neutral) direct
strengthOfEvidenceProvided 0..1
Coding		 The strength of support that an Evidence Line is determined to provide for or against its target Proposition. direct
contributions 0..*
Contribution		 A specific contribution made by some Agent to the creation, modification, or validation of the information represented in the Information Entity. InformationEntity
dateAuthored 0..1
DateTime		 The date the information content expressed in this entity was generated. InformationEntity
specifiedBy 0..*
Method		 A particular plan specification that describes all or part of the process that led to creation of the reported information (e.g. a specific experimental protocol, analysis specification, cohort selection criteria, interpretation guideline, etc.). InformationEntity
derivedFrom 0..*
InformationEntity		 An information resource from which the Information Entity is derived, in whole or in part InformationEntity
reportedIn 0..*
Document		 A document in which the information content carried by the Information Entity is expressed InformationEntity
id 1..1
Identifier		 The logical identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system. Entity
identifiers 0..*
Identifier		 A business identifier or accession number for the entity, typically as provided by an external system or authority, that is globally unique and persists across implementing systems. Entity
label 0..1
String		 A primary name for the Entity. Entity
urls 0..*
Url		 The URL/web address of a digital resource representing the entity, or providing information about it. Entity
xrefs 0..*
String		 Cross-references to database identifier(s) representing the same (or a closely related) entity or concept as the Entity. Entity
recordMetadata 0..1
RecordMetadata		 A reusable structure that encapsulates provenance metadata about the present record/data object (as opposed to provenance information about the real world entity this record/data object represents). Entity
type 1..1
Class		 The schema class that is instantiated by the data object. Must be the name of a class from the VA schema. Element
description 0..1
String		 A free text description of the Element. Element
extensions 0..*
Extension		 A key-value data structure that allows definition of custom fields to capture information not directly supported by the VA specification. Element

Usages

used by used in type used
Statement hasEvidenceLines range EvidenceLine

Comments

  • Evidence Lines result from the interpretation of one or more pieces of information (Evidence Items) to build an argument for or against a particular Proposition (possible fact). The Evidence Line that results can be considered a special kind of Statement that asserts the direction and strength such an argument provides for some target Proposition.

For example, the various allele counts and frequency calculations for the BRCA2 c.8023A>G variant found in the ExAC database are Evidence Items that might be collectively assessed by a ClinGen curator to build an Evidence Line that is deemed to 'support' with 'moderate' strength a target proposition that the variant is pathogenic for Breast Cancer.

The narrative form of the Statement represented by this Evidence Line is roughly: "ExAC allele frequency data for BRCA2 c.8023A>G {0.0000021, 0.0000034, ...} provides evidence of moderate strength supporting the proposition that BRCA2 c.8023A>G is pathogenic for Breast Cancer".

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/ga4gh-va-core-im

Mappings

Mapping Type Mapped Value
self vacoreim:EvidenceLine
native vacoreim:EvidenceLine

LinkML Source

Direct

name: EvidenceLine
description: A discrete, independent argument relevant to the validity of the Proposition
  put forth as true in the Statement,  that is based on the interpretation of one
  or more pieces of information as evidence.
title: Evidence Line
comments:
- "Evidence Lines result from the interpretation of one or more pieces of information\
  \ (Evidence Items) to build an argument for or against a particular Proposition\
  \ (possible fact). The Evidence Line that results can be considered a special kind\
  \ of Statement that asserts the direction and strength such an argument provides\
  \ for some target Proposition. \n\nFor example, the various allele counts and frequency\
  \ calculations for the BRCA2 c.8023A>G variant found in the ExAC database are Evidence\
  \ Items  that might be collectively assessed by a ClinGen curator to build an Evidence\
  \ Line that is deemed to 'support' with 'moderate' strength a target proposition\
  \ that the variant is pathogenic for Breast Cancer.  \n\nThe narrative form of the\
  \ Statement represented by this Evidence Line is roughly: \"ExAC allele frequency\
  \ data for BRCA2 c.8023A>G {0.0000021, 0.0000034, ...} provides evidence of moderate\
  \ strength supporting the proposition that BRCA2 c.8023A>G is pathogenic for Breast\
  \ Cancer\"."
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: InformationEntity
slots:
- subtype
- targetProposition
- evidenceItems
- directionOfEvidenceProvided
- strengthOfEvidenceProvided
slot_usage:
  subtype:
    name: subtype
    description: A specific type of evidence the EvidenceLine object represents (e.g.
      'mutant phenotype evidence', 'evidence from manual interpretation', 'ACMG PM2
      evidence')
    comments:
    - Data creators may choose to define specific types of evidence lines relevant
      for their domain/use case, based on the type of evidence items that comprise
      it, the methodology that guided evidence interpretation, or the type of statement
      the evidence line supports.  Terms from ontologies like the Evidence and Conclusion
      Ontology (ECO) can be used as values here.
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  targetProposition:
    name: targetProposition
    description: The proposition against which the evidence items were evaluated,
      in determining the overall strength and direction of evidence they provide (as
      captured in the Evidence Line)
    comments:
    - 'An example based on the ACMG Guidelines for germline variant pathogenicity
      interpretation: consider a curator assessing the evidence provided by population
      frequency data for a specific variant based on the ACMG criteria.  In order
      to assign a strength (e.g. moderate, strong) and direction (PM2 or  BS1) to
      this data as evidence, there must be some ''target proposition'' toward which
      the evidence is assessed. If the PM2 criteria is deemed ''met'', this indicates
      that the population frequency evidence supports with moderate strength the target
      proposition that the variant is pathogenic for the disease of interest.'
    multivalued: false
    domain_of:
    - EvidenceLine
    range: Proposition
    required: false
  evidenceItems:
    name: evidenceItems
    description: An Information Entity that was evaluated in making the argument represented
      by the Evidence Lines.
    comments:
    - A given Evidence Line might be suported by one or many individual pieces of
      evidence. Different types or scales of information entity can serve as evidence
      - but only when it realizes this role do we call it an 'Evidence Item'. For
      example, a piece of population frequency data about BRCA2 c.8023A>G  becomes
      an Evidence Item when it is assessed as evidence (e.g. for the variant’s pathogenicity
      - and thus contributes to an argument for (or against) this target proposition.
    multivalued: true
    domain_of:
    - EvidenceLine
    range: InformationEntity
    required: false
  directionOfEvidenceProvided:
    name: directionOfEvidenceProvided
    description: The direction of support that the Evidence Line is determined to
      provide for its target Proposition (can be supporting, disputing, or neutral)
    multivalued: false
    domain_of:
    - EvidenceLine
    range: Coding
    required: false
  strengthOfEvidenceProvided:
    name: strengthOfEvidenceProvided
    description: The strength of support that an Evidence Line is determined to provide
      for or against its target Proposition.
    multivalued: false
    domain_of:
    - EvidenceLine
    range: Coding
    required: false

Induced

name: EvidenceLine
description: A discrete, independent argument relevant to the validity of the Proposition
  put forth as true in the Statement,  that is based on the interpretation of one
  or more pieces of information as evidence.
title: Evidence Line
comments:
- "Evidence Lines result from the interpretation of one or more pieces of information\
  \ (Evidence Items) to build an argument for or against a particular Proposition\
  \ (possible fact). The Evidence Line that results can be considered a special kind\
  \ of Statement that asserts the direction and strength such an argument provides\
  \ for some target Proposition. \n\nFor example, the various allele counts and frequency\
  \ calculations for the BRCA2 c.8023A>G variant found in the ExAC database are Evidence\
  \ Items  that might be collectively assessed by a ClinGen curator to build an Evidence\
  \ Line that is deemed to 'support' with 'moderate' strength a target proposition\
  \ that the variant is pathogenic for Breast Cancer.  \n\nThe narrative form of the\
  \ Statement represented by this Evidence Line is roughly: \"ExAC allele frequency\
  \ data for BRCA2 c.8023A>G {0.0000021, 0.0000034, ...} provides evidence of moderate\
  \ strength supporting the proposition that BRCA2 c.8023A>G is pathogenic for Breast\
  \ Cancer\"."
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: InformationEntity
slot_usage:
  subtype:
    name: subtype
    description: A specific type of evidence the EvidenceLine object represents (e.g.
      'mutant phenotype evidence', 'evidence from manual interpretation', 'ACMG PM2
      evidence')
    comments:
    - Data creators may choose to define specific types of evidence lines relevant
      for their domain/use case, based on the type of evidence items that comprise
      it, the methodology that guided evidence interpretation, or the type of statement
      the evidence line supports.  Terms from ontologies like the Evidence and Conclusion
      Ontology (ECO) can be used as values here.
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  targetProposition:
    name: targetProposition
    description: The proposition against which the evidence items were evaluated,
      in determining the overall strength and direction of evidence they provide (as
      captured in the Evidence Line)
    comments:
    - 'An example based on the ACMG Guidelines for germline variant pathogenicity
      interpretation: consider a curator assessing the evidence provided by population
      frequency data for a specific variant based on the ACMG criteria.  In order
      to assign a strength (e.g. moderate, strong) and direction (PM2 or  BS1) to
      this data as evidence, there must be some ''target proposition'' toward which
      the evidence is assessed. If the PM2 criteria is deemed ''met'', this indicates
      that the population frequency evidence supports with moderate strength the target
      proposition that the variant is pathogenic for the disease of interest.'
    multivalued: false
    domain_of:
    - EvidenceLine
    range: Proposition
    required: false
  evidenceItems:
    name: evidenceItems
    description: An Information Entity that was evaluated in making the argument represented
      by the Evidence Lines.
    comments:
    - A given Evidence Line might be suported by one or many individual pieces of
      evidence. Different types or scales of information entity can serve as evidence
      - but only when it realizes this role do we call it an 'Evidence Item'. For
      example, a piece of population frequency data about BRCA2 c.8023A>G  becomes
      an Evidence Item when it is assessed as evidence (e.g. for the variant’s pathogenicity
      - and thus contributes to an argument for (or against) this target proposition.
    multivalued: true
    domain_of:
    - EvidenceLine
    range: InformationEntity
    required: false
  directionOfEvidenceProvided:
    name: directionOfEvidenceProvided
    description: The direction of support that the Evidence Line is determined to
      provide for its target Proposition (can be supporting, disputing, or neutral)
    multivalued: false
    domain_of:
    - EvidenceLine
    range: Coding
    required: false
  strengthOfEvidenceProvided:
    name: strengthOfEvidenceProvided
    description: The strength of support that an Evidence Line is determined to provide
      for or against its target Proposition.
    multivalued: false
    domain_of:
    - EvidenceLine
    range: Coding
    required: false
attributes:
  subtype:
    name: subtype
    description: A specific type of evidence the EvidenceLine object represents (e.g.
      'mutant phenotype evidence', 'evidence from manual interpretation', 'ACMG PM2
      evidence')
    comments:
    - Data creators may choose to define specific types of evidence lines relevant
      for their domain/use case, based on the type of evidence items that comprise
      it, the methodology that guided evidence interpretation, or the type of statement
      the evidence line supports.  Terms from ontologies like the Evidence and Conclusion
      Ontology (ECO) can be used as values here.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: subtype
    owner: EvidenceLine
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  targetProposition:
    name: targetProposition
    description: The proposition against which the evidence items were evaluated,
      in determining the overall strength and direction of evidence they provide (as
      captured in the Evidence Line)
    comments:
    - 'An example based on the ACMG Guidelines for germline variant pathogenicity
      interpretation: consider a curator assessing the evidence provided by population
      frequency data for a specific variant based on the ACMG criteria.  In order
      to assign a strength (e.g. moderate, strong) and direction (PM2 or  BS1) to
      this data as evidence, there must be some ''target proposition'' toward which
      the evidence is assessed. If the PM2 criteria is deemed ''met'', this indicates
      that the population frequency evidence supports with moderate strength the target
      proposition that the variant is pathogenic for the disease of interest.'
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: targetProposition
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: Proposition
    required: false
  evidenceItems:
    name: evidenceItems
    description: An Information Entity that was evaluated in making the argument represented
      by the Evidence Lines.
    comments:
    - A given Evidence Line might be suported by one or many individual pieces of
      evidence. Different types or scales of information entity can serve as evidence
      - but only when it realizes this role do we call it an 'Evidence Item'. For
      example, a piece of population frequency data about BRCA2 c.8023A>G  becomes
      an Evidence Item when it is assessed as evidence (e.g. for the variant’s pathogenicity
      - and thus contributes to an argument for (or against) this target proposition.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: evidenceItems
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: InformationEntity
    required: false
  directionOfEvidenceProvided:
    name: directionOfEvidenceProvided
    description: The direction of support that the Evidence Line is determined to
      provide for its target Proposition (can be supporting, disputing, or neutral)
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: directionOfEvidenceProvided
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: Coding
    required: false
  strengthOfEvidenceProvided:
    name: strengthOfEvidenceProvided
    description: The strength of support that an Evidence Line is determined to provide
      for or against its target Proposition.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: strengthOfEvidenceProvided
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: Coding
    required: false
  contributions:
    name: contributions
    description: A specific contribution made by some Agent to the creation, modification,
      or validation of the information represented in the Information Entity.
    comments:
    - This attribute points to a Contribution object, which holds a structured description
      of the actions taken by a particular agent in contributing to an Information
      Entity.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: contributions
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    - RecordMetadata
    range: Contribution
    required: false
  dateAuthored:
    name: dateAuthored
    description: The date the information content expressed in this entity was generated.
    comments:
    - We use the term 'authored' to refer to the generation of information in the
      abstract - i.e. the information content expressed in a Statement, not a concrete
      encoding of it in a specific language or format.  The 'dateAuthored' attribute
      captures when this abstract information content was first created.  Information
      about when a particular concrete encoding of this information was created (e.g.
      as a VA-based json object) would live in a RecordMetadata object attached to
      the Information Entity).
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: dateAuthored
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: DateTime
    required: false
  specifiedBy:
    name: specifiedBy
    description: A particular plan specification that describes all or part of the
      process that led to creation of the reported information (e.g. a specific experimental
      protocol, analysis specification, cohort selection criteria, interpretation
      guideline, etc.).
    comments:
    - 'This field captures specific instances of specifications / methods (vs the
      ''methodTypes'' attribute which captures types of methods applied).

      In various domains and communities, such specifications may be called ''protocols'',
      ''guidelines'', ''methods'', ''rule sets'', etc.'
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: specifiedBy
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    - Activity
    range: Method
    required: false
  derivedFrom:
    name: derivedFrom
    description: An information resource from which the Information Entity is derived,
      in whole or in part
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: derivedFrom
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    - StudyResult
    - RecordMetadata
    range: InformationEntity
    required: false
  reportedIn:
    name: reportedIn
    description: A document in which the information content carried by the Information
      Entity is expressed
    comments:
    - "This attribute is used specifically to reference documents/publications where\
      \ the Information Entity is expressed or reported.  For a Statement, this might\
      \ be a publication where the authors express the statement in text.  For a Data\
      \ Item, this might be a publication with a table or figure that reports the\
      \ value of the  data.  \nNote that the VA-Spec provide separate attributes for\
      \ describing different types of 'references' from an Information Entity to a\
      \ Document (e.g. hasEvidenceFromSource is used by a Statement to reference a\
      \ Document that provided evidence for the knowldege the Statement expresses."
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: reportedIn
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: Document
    required: false
  id:
    name: id
    description: The logical identifier of the entity in the system of record, e.g.
      a UUID.  This 'id' is unique within a given system. The identified entity may
      have a different 'id' in a different system.
    comments:
    - FHIR naming conventions are followed here, where an 'id' field holds logical
      identifiers which are unique only within a given system, and an 'identifier'
      field holds business identifiers, which are globally unique and used to connect
      entities and share content across systems.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: id
    owner: EvidenceLine
    domain_of:
    - Entity
    range: Identifier
    required: true
  identifiers:
    name: identifiers
    description: A business identifier or accession number for the entity, typically
      as provided by an external system or authority, that is globally unique and
      persists across implementing systems.
    comments:
    - FHIR naming conventions are followed here, where an 'id' field holds logical
      identifiers which are unique only within a given system, and an 'identifier'
      field holds business identifiers, which are globally unique and used to connect
      entities and share content across systems.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: identifiers
    owner: EvidenceLine
    domain_of:
    - Entity
    range: Identifier
    required: false
  label:
    name: label
    description: A primary name for the Entity.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: label
    owner: EvidenceLine
    domain_of:
    - Entity
    - Coding
    range: string
    required: false
  urls:
    name: urls
    description: The URL/web address of a digital resource representing the entity,
      or providing information about it.
    comments:
    - This attribute is meant to point directly to locations on the web where more
      information about the Entity can be found.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: urls
    owner: EvidenceLine
    domain_of:
    - Entity
    range: Url
    required: false
  xrefs:
    name: xrefs
    description: Cross-references to database identifier(s) representing the same
      (or a closely related) entity or concept as the Entity.
    comments:
    - Preferred values for this field are CURIEs or URLs for database records - so
      the system that provisioned the identifier is clear.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: xrefs
    owner: EvidenceLine
    domain_of:
    - Entity
    range: string
    required: false
  recordMetadata:
    name: recordMetadata
    description: A reusable structure that encapsulates provenance metadata about
      the present record/data object  (as opposed to provenance information about
      the real world entity this record/data object represents).
    comments:
    - Record-level metadata applies to a specific concrete encoding/serialization
      of information (e.g as a record in a specific knowlegebase, or an online digital
      resource). A RecordMetadata object can capture when, how, and by whom a specific
      record was generated or modified; what upstream resources it was derived/retrieved
      from; and record-level administrative information such as versioning and system
      / lifecycle status.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: recordMetadata
    owner: EvidenceLine
    domain_of:
    - Entity
    range: RecordMetadata
    required: false
  type:
    name: type
    description: The schema class that is instantiated by the data object.  Must be
      the name of a class from the VA schema.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: type
    owner: EvidenceLine
    domain_of:
    - Element
    range: Class
    required: true
  description:
    name: description
    description: A free text description of the Element.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: description
    owner: EvidenceLine
    domain_of:
    - Element
    - Extension
    range: string
    required: false
  extensions:
    name: extensions
    description: A key-value data structure that allows definition of custom fields
      to capture information not directly supported by the VA specification.
    comments:
    - The VA-Spec provides  implementers the ability to extend any model elements
      with new attributes using this flexible Extension element.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: extensions
    owner: EvidenceLine
    domain_of:
    - Element
    range: Extension
    required: false