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Class: Evidence Line (EvidenceLine)

An independent, evidence-based argument that may support or refute the validity of a specific proposition. The strength and direction of this argument is based on an interpretation of one or more pieces of information as evidence for or against the target proposition.

Comments

  • Evidence Lines are used to capture various pieces of information (i.e. 'evidence items') that are assessed together as an argument for or against some 'target proposition' - and to report the direction (supports or disputes) and strength (e.g. strong, moderate, weak) that the argument is determined to make. For example, the various allele counts and population frequency calculations for the BRCA2 c.8023A>G variant in the ExAC database are evidence items that may be collectively assessed to build an EvidenceLine making argument of 'moderate' strength that 'supports' a target proposition that the variant is pathogenic for Breast Cancer.
  • Evidence Lines are flexible with respect to the granularity of arguments they support, and the scope of evidence items they can collectively assess. Narrow scoping will bucket available evidence into many, fine-grained Evidence Lines that make the most atomic independently meaningful arguments possible. The ACMG Variant Pathogenicity Interpretation Guidelines are an example of a fairly fine-grained evidence interpretation framework. Broader scoping approaches may organize the same available evidence into fewer Evidence Lines that build and assess less atomic arguments based on a wider and more diverse set of evidence items. For example, CIViC curators assess the strength and direction of evidence items at the level of all information reported in a publication for a specific study - which can encompass many different results and evidence types that under more fine-grained interpretation approaches might be split apart and assessed as separate lines of evidence.
  • This CIViC EID5682 record (https://civicdb.org/evidence/5682/summary) is a clear example of this - illustrating how ACMG-curated evidence assessed at a finer-grained level would lend itself to SEPIO representations that creates a larger number of more atomic Evidence Lines, as compared to how CIViC-curated evidence from the same source or publication would be represented. We see here that CIViC evidence assessments are performed at the level of all results reported in PMID:23143947 - which SEPIO would capture as a single Evidence Line that assigns a strength (level C) and direction (supports) to the collective argument made by this evidence. However, as detailed in the free-text summary of this EID, the more fine-grained ACMG framework breaks out and separately assess two arguments here - one based on criterion PP1 (disease co-segregation evidence), and one based on criterion PP4 (highly specific gene-phenotype information) - which SEPIO woudl capture as two distinct Evidence Lines.

URI: sepio_linkml:EvidenceLine

classDiagram class EvidenceLine click EvidenceLine href "../EvidenceLine" InformationEntity <|-- EvidenceLine click InformationEntity href "../InformationEntity" EvidenceLine : alternativeLabels EvidenceLine : contributions EvidenceLine --> "*" Contribution : contributions click Contribution href "../Contribution" EvidenceLine : dateAuthored EvidenceLine : derivedFrom EvidenceLine --> "*" InformationEntity : derivedFrom click InformationEntity href "../InformationEntity" EvidenceLine : description EvidenceLine : directionOfEvidenceProvided EvidenceLine : evidenceItemSources EvidenceLine : extensions EvidenceLine --> "*" Extension : extensions click Extension href "../Extension" EvidenceLine : hasEvidenceItems EvidenceLine --> "*" InformationEntity : hasEvidenceItems click InformationEntity href "../InformationEntity" EvidenceLine : id EvidenceLine : identifiers EvidenceLine : informationQuality EvidenceLine --> "0..1" Coding : informationQuality click Coding href "../Coding" EvidenceLine : isAbout EvidenceLine : label EvidenceLine : recordMetadata EvidenceLine --> "0..1" RecordMetadata : recordMetadata click RecordMetadata href "../RecordMetadata" EvidenceLine : reportedIn EvidenceLine : scoreOfEvidenceProvided EvidenceLine : sources EvidenceLine : specifiedBy EvidenceLine : strengthOfEvidenceProvided EvidenceLine : subtype EvidenceLine --> "0..1" Coding : subtype click Coding href "../Coding" EvidenceLine : supportingMethods EvidenceLine : supportingMethodTypes EvidenceLine --> "*" Coding : supportingMethodTypes click Coding href "../Coding" EvidenceLine : targetProposition EvidenceLine --> "0..1" Proposition : targetProposition click Proposition href "../Proposition" EvidenceLine : type

Inheritance

Slots

Direct slots

subtype --> Coding [0..1]

A specific type of evidence the EvidenceLine instance represents (e.g. 'mutant phenotype evidence', 'evidence from manual interpretation', 'ACMG PM2 evidence')

Implementation Guidance * 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), or categories from evidence interpretation frameworks like the ACMG Variant Interpretation Guidelines, can be used as values here.

targetProposition --> Proposition [0..1]

The possible fact against which evidence items contained in an Evidence Line were collectively evaluated, in determining the overall strength and direction of support they provide. For example, in an ACMG Guideline-based assessment of variant pathogenicity, the support provided by distinct lines of evidence are assessed against a target proposition that some variant is pathogenic for a specific disease.

Implementation Guidance * 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 vs strong) and direction (supports vs disputes) to this data as evidence, there must be some 'target proposition' toward which the evidence is assessed - which in this cases is the proposition that the variant is pathogenic for the disease of interest. If the PM2 criteria is deemed 'met', this indicates that the population frequency evidence provides 'moderate' (strength) 'support' (direction) for this target proposition.

hasEvidenceItems --> InformationEntity [*]

An individual piece of information that was evaluated as evidence in building the argument represented by an Evidence Line.

Implementation Guidance * A given Evidence Line may be supported by one or many individual evidence items. What matters is that all evidence items in a given Evidence Line get collectively assessed and assigned direction and strength as a single argument for or against a target proposition.
* Different types and scales of information entity can serve as evidence (experimental measurements or observations, data tables or figures, images, prior assertions, etc.) Only when assessed as evidence do we consider the information to be an 'Evidence Item'. For example, a piece of population frequency data about BRCA2 c.8023A>G becomes an Evidence Item when it is assessed for the support it may offer for a target proposition (e.g. the prospect of the variant’s pathogenicity).


directionOfEvidenceProvided --> String [0..1]

The direction of support that the Evidence Line is determined to provide toward its target Proposition (supports, disputes, neutral).


strengthOfEvidenceProvided --> String [0..1]

The strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided.

Implementation Guidance * Values of this attribute can be defined by for a given profile based on domain/application needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate', 'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative assessments of evidence provided.

scoreOfEvidenceProvided --> Float [0..1]

A quantitative score indicating the strength of support that an Evidence Line is determined to provide for or against its target Proposition, evaluated relative to the direction indicated by the directionOfEvidenceProvided value.

Implementation Guidance * A given profile or implementation can define a scoring scale and rules that meet the needs of their domain or application.

evidenceItemSources --> String [*]

An information resource (e.g. document, dataset, digital resource such as a database or knowledgebase) that provides information interpreted as evidence in building an Evidence Line.

Implementation Guidance * This is a 'shortcut relation' that can be used to directly link an Evidence Line to sources of its supporting Evidence Items, without having to represent those Evidence Items directly. Populate with the name or uri or curie of a source of information. Future work will define a more formal framework for referencing information sources.

Inherited slots

isAbout --> String [*]

An entity or concept in the world that the information entity describes/is about.

Inherited from: InformationEntity

Implementation Guidance * e.g. In the context of a Statement object, this attribute may be used to indicate entities/concepts it is about, in lieu of providing a more precise description of what the Statement asserts to be true using subject, predicate, object, and qualifier properties. e.g. the Statement that "BRCA2 c.8023A>G is pathogenic for Breast Cancer" might be annotated to be about the variant 'BRCA2 c.8023A>G', and the disease 'Breast Cancer'.

contributions --> Contribution [*]

Specific actions taken by an Agent toward the creation, modification, validation, or deprecation of an Information Entity.

Inherited from: InformationEntity

Implementation Guidance * This attribute holds one or more Contribution objects, which provide structured descriptions of a contribution made to the Information Entity by a particular agent.

dateAuthored --> String [0..1]

Indicates when the information content expressed in the Information Entity was generated.

Inherited from: InformationEntity

Implementation Guidance * The term 'authored' as used in the model refers to the generation of 'information content' in the abstract sense, as opposed to a concrete encoding of this information in a specific language or format. e.g. for a Statement, this attribute captures when the information content expressed in the Statement was first generated by an agent. Information about when a particular concrete encoding of this information was created (e.g. as row in a table, or object in a json document) would live in a RecordMetadata object attached to the Information Entity).

specifiedBy --> String [*]

A specification that describes all or part of the process that led to creation of the Information Entity.

Inherited from: InformationEntity

Implementation Guidance * Examples - an experimental protocol or data analysis specification that describe how data were generated, or an evidence interpretation guideline that describes steps taken to interpret data in making a variant pathogenicity classification.
* Note that this attribute captures specific *instances* of specifications/methods (e.g. the specific electron microscopy method described in https://doi.org/10.1002/ cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. "Transmission Electron Microscopy").

supportingMethods --> String [*]

Specific methods that were executed to directly or indirectly support creation of the Information Entity.

Inherited from: InformationEntity

Implementation Guidance * These may include methods that directly produced the Information Entity, or upstream/accessory methods that indirectly support creation of the Information Entity - e.g. methods used to produce data that was interpreted as evidence to generate a Statement of knowledge.
* This field captures terms representing specific INSTANCES of methods applied, vs the 'supportingMethodTypes' attribute which captures TYPES of methods used.

supportingMethodTypes --> Coding [*]

Types of methodological approaches that were executed to directly or indirectly support creation of the Information Entity.

Inherited from: InformationEntity

Implementation Guidance * This field captures terms representing TYPES of methods applied, vs the 'specifiedBy' or'supportingMethods' attributes which capture specific INSTANCES of methods used. These may include types of methods that directly produced the Information Entity, or upstream/accessory methods that indirectly support creation of the Information Entity
* Implementers should define a relevant source or set of method type codes/terms to use here, based on the needs of the domain or application.'

derivedFrom --> InformationEntity [*]

Another Information Entity from which this Information Entity is derived, in whole or in part.

Inherited from: InformationEntity

reportedIn --> String [*]

A document in which the Information Entity is reported.

Inherited from: InformationEntity

Implementation Guidance * 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.

sources --> String [*]

A document or other informtion resource in which the information entity, or evidence supporting it, is reported.

Inherited from: InformationEntity

Implementation Guidance * This attribute is more general than InformationEntity.reportedIn (which is used to references a Docuement that directly reports the infrormation), and Statement.hasEvidenceFromSources (which is used to reference resources that provided evidence used to generate the knowledge expressed in a Statement). It can be used to cover both cases, in situations where a data provider does not know which is the case, or does not wish to make the distinction.

informationQuality --> Coding [0..1]

A qualitative term indicating the scientific rigor or reliability with which the information was generated/collected.

Inherited from: InformationEntity

Implementation Guidance * This is typically based on the quality of design and execution of the study or curation activity that generated it (e.g. were relevant controls assessed to show instruments were working, were all samples taken care of and handled identically, are methods sound and well documented, etc.).
* The quality of information is intrinsic to the information itself, and not to a particular application of the information (e.g. as evidence for making an Assertion)
* The quality of information is one factor that goes into the confidence we have in the information''s veracity (i.e. that it is an accurate reflection of reality it intends to measure or describe). Other factors informing confidence may include who did it (we may just not trust some Agents), when (if data created 500 years ago, we may have less confidence in it), and for Assertions, the relevance and abundance of supporting evidence.
* Implementers should define a relevant source of codes or terms to use here, based on the needs of the domain or application.'

recordMetadata --> RecordMetadata [0..1]

Provenance metadata about a specific concrete record of information as encoded/serialized in a particular data set or object (as opposed to provenance about the abstract information content the encoding carries).

Inherited from: InformationEntity

Implementation Guidance * This attribute holds a structured RecordMetadata objects, which can be used to capture when, how, and by whom a record serialization was generated or modified; what upstream resources it was derived or retrieved from; and record-level administrative information such as versioning and lifecycle status.

id --> String [1]

The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference one object from another.

Inherited from: Entity

Implementation Guidance * Note that it is common for implementers to create their own internal logical ids - typically a serially or randomly generated value like a UUID that is assigned to the data object as it is created in a system. But an implementer may choose to reuse an existing, globally unique id from an external system or authority for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique within the implementing system, and can be used to reference the identified object in this context.

identifiers --> String [*]

A globally-unique 'business' identifier or accession number for the real-world entity represented by a data object. These are typically assigned by an external system or authority, and used to connect entities and share content across different systems.

Inherited from: Entity

Implementation Guidance * Preferred values for this attribute are CURIEs or URIs - so the system that provisioned the identifier is clear.
* A given real world entity - e.g. a genetic variant - may have many business identifiers defined by different systems, which can be captured in the "identifiers" property to indicate that they represent the same thing.

type --> String [1]

The name of the class that is instantiated by a data object representing the Entity.

Inherited from: Entity

Implementation Guidance * MUST be the label of a concrete class from the data model.

label --> String [0..1]

A primary name for the Entity.

Inherited from: Entity

alternativeLabels --> String [*]

Alternative name(s) for the Entity.

Inherited from: Entity

description --> String [0..1]

A free text description of the Entity.

Inherited from: Entity

extensions --> Extension [*]

A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.

Inherited from: Entity

Implementation Guidance * Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems.

Usages

used by used in type used
Statement hasEvidenceLines range EvidenceLine

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/sepio-framework/sepio-linkml

Mappings

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

LinkML Source

Direct

name: EvidenceLine
description: An independent, evidence-based argument that may support or refute the
  validity of a specific proposition. The strength and direction of this argument
  is based on an interpretation of one or more pieces of information as evidence for
  or against the target proposition.
title: Evidence Line
comments:
- Evidence Lines are used to capture various pieces of information (i.e. 'evidence
  items') that are assessed together as an argument for or against some 'target proposition'
  - and to report the direction (supports or disputes) and strength (e.g. strong,
  moderate, weak) that the argument is determined to make. For example, the various
  allele counts and population frequency calculations for the BRCA2 c.8023A>G variant
  in the ExAC database are evidence items that may be collectively assessed to build
  an EvidenceLine making argument of 'moderate' strength that 'supports' a target
  proposition that the variant is pathogenic for Breast Cancer.
- Evidence Lines are flexible with respect to the granularity of arguments they support,
  and the scope of evidence items they can collectively assess. Narrow scoping will
  bucket available evidence into many, fine-grained Evidence Lines that make the most
  atomic independently meaningful arguments possible. The ACMG Variant Pathogenicity
  Interpretation Guidelines are an example of a fairly fine-grained evidence interpretation
  framework. Broader scoping approaches may organize the same available evidence into
  fewer Evidence Lines that build and assess less atomic arguments based on a wider
  and more diverse set of evidence items.  For example, CIViC curators assess the
  strength and direction of evidence items at the level of *all information reported
  in a publication for a specific study* - which can encompass many different results
  and evidence types that under more fine-grained interpretation approaches might
  be split apart and assessed as separate lines of evidence.
- This CIViC EID5682 record (https://civicdb.org/evidence/5682/summary) is a clear
  example of this - illustrating how ACMG-curated evidence assessed at a finer-grained
  level would lend itself to SEPIO representations that creates a larger number of
  more atomic Evidence Lines, as compared to how CIViC-curated evidence from the same
  source or publication would be represented. We see here that CIViC evidence assessments
  are performed at the level of all results reported in PMID:23143947 - which SEPIO
  would capture as a single Evidence Line that assigns a strength (level C) and direction
  (supports) to the collective argument made by this evidence. However, as detailed
  in the free-text summary of this EID, the more fine-grained ACMG framework breaks
  out and separately assess two arguments here - one based on criterion PP1 (disease
  co-segregation evidence), and one based on criterion PP4 (highly specific gene-phenotype
  information) - which SEPIO woudl capture as two distinct Evidence Lines.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Draft
is_a: InformationEntity
attributes:
  subtype:
    name: subtype
    description: A specific type of evidence the EvidenceLine instance 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), or categories from evidence interpretation frameworks like the
      ACMG Variant Interpretation Guidelines, can be used as values here.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  targetProposition:
    name: targetProposition
    description: The possible fact against which evidence items contained in an Evidence
      Line were collectively evaluated, in determining the overall strength and direction
      of support they provide. For example, in an ACMG Guideline-based assessment
      of variant pathogenicity, the support provided by distinct lines of evidence
      are assessed against a target proposition that some variant is pathogenic for
      a specific disease.
    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 vs strong) and direction (supports vs disputes)
      to this data as evidence, there must be some ''target proposition'' toward which
      the evidence is assessed - which in this cases is the proposition that the variant
      is pathogenic for the disease of interest. If the PM2 criteria is deemed ''met'',
      this indicates that the population frequency evidence provides ''moderate''
      (strength) ''support'' (direction) for this target proposition.'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - EvidenceLine
    range: Proposition
    required: false
    multivalued: false
  hasEvidenceItems:
    name: hasEvidenceItems
    description: An individual piece of information that was evaluated as evidence
      in building the argument represented by an Evidence Line.
    comments:
    - A given Evidence Line may be supported by one or many individual evidence items.
      What matters is that all evidence items in a given Evidence Line get collectively
      assessed and assigned direction and strength  as a single argument for or against
      a target proposition.
    - Different types and scales of information entity can serve as evidence (experimental
      measurements or observations, data tables or figures, images, prior assertions,
      etc.) Only when assessed as evidence do we consider the information to be an
      'Evidence Item'.  For example, a piece of population frequency data about BRCA2
      c.8023A>G  becomes an Evidence Item when it is assessed for the support it may
      offer for a target proposition (e.g. the prospect of the variant’s pathogenicity).
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - EvidenceLine
    range: InformationEntity
    required: false
    multivalued: true
  directionOfEvidenceProvided:
    name: directionOfEvidenceProvided
    description: The direction of support that the Evidence Line is determined to
      provide toward its target Proposition (supports, disputes, neutral).
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - EvidenceLine
    range: string
    required: false
    multivalued: false
  strengthOfEvidenceProvided:
    name: strengthOfEvidenceProvided
    description: The strength of support that an Evidence Line is determined to provide
      for or against its target Proposition, evaluated relative to the direction indicated
      by the directionOfEvidenceProvided.
    comments:
    - Values of this attribute can be defined by for a given profile based on domain/application
      needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate',
      'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative
      assessments of evidence provided.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - EvidenceLine
    range: string
    required: false
    multivalued: false
  scoreOfEvidenceProvided:
    name: scoreOfEvidenceProvided
    description: A quantitative score indicating the strength of support that an Evidence
      Line is determined to provide for or against its target Proposition, evaluated
      relative to the direction indicated by the directionOfEvidenceProvided value.
    comments:
    - A given profile or implementation can define a scoring scale and rules that
      meet the needs of their domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    domain_of:
    - EvidenceLine
    range: float
    required: false
    multivalued: false
  evidenceItemSources:
    name: evidenceItemSources
    description: An information resource (e.g. document, dataset, digital resource
      such as a database or  knowledgebase) that provides information interpreted
      as evidence in building an Evidence Line.
    comments:
    - This is a 'shortcut relation' that can be used to directly link an Evidence
      Line to sources of its supporting Evidence Items, without having to represent
      those Evidence Items directly. Populate with the name or uri or curie of a source
      of information. Future work will define a more formal framework for referencing
      information sources.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - EvidenceLine
    range: string
    required: false
    multivalued: true

Induced

name: EvidenceLine
description: An independent, evidence-based argument that may support or refute the
  validity of a specific proposition. The strength and direction of this argument
  is based on an interpretation of one or more pieces of information as evidence for
  or against the target proposition.
title: Evidence Line
comments:
- Evidence Lines are used to capture various pieces of information (i.e. 'evidence
  items') that are assessed together as an argument for or against some 'target proposition'
  - and to report the direction (supports or disputes) and strength (e.g. strong,
  moderate, weak) that the argument is determined to make. For example, the various
  allele counts and population frequency calculations for the BRCA2 c.8023A>G variant
  in the ExAC database are evidence items that may be collectively assessed to build
  an EvidenceLine making argument of 'moderate' strength that 'supports' a target
  proposition that the variant is pathogenic for Breast Cancer.
- Evidence Lines are flexible with respect to the granularity of arguments they support,
  and the scope of evidence items they can collectively assess. Narrow scoping will
  bucket available evidence into many, fine-grained Evidence Lines that make the most
  atomic independently meaningful arguments possible. The ACMG Variant Pathogenicity
  Interpretation Guidelines are an example of a fairly fine-grained evidence interpretation
  framework. Broader scoping approaches may organize the same available evidence into
  fewer Evidence Lines that build and assess less atomic arguments based on a wider
  and more diverse set of evidence items.  For example, CIViC curators assess the
  strength and direction of evidence items at the level of *all information reported
  in a publication for a specific study* - which can encompass many different results
  and evidence types that under more fine-grained interpretation approaches might
  be split apart and assessed as separate lines of evidence.
- This CIViC EID5682 record (https://civicdb.org/evidence/5682/summary) is a clear
  example of this - illustrating how ACMG-curated evidence assessed at a finer-grained
  level would lend itself to SEPIO representations that creates a larger number of
  more atomic Evidence Lines, as compared to how CIViC-curated evidence from the same
  source or publication would be represented. We see here that CIViC evidence assessments
  are performed at the level of all results reported in PMID:23143947 - which SEPIO
  would capture as a single Evidence Line that assigns a strength (level C) and direction
  (supports) to the collective argument made by this evidence. However, as detailed
  in the free-text summary of this EID, the more fine-grained ACMG framework breaks
  out and separately assess two arguments here - one based on criterion PP1 (disease
  co-segregation evidence), and one based on criterion PP4 (highly specific gene-phenotype
  information) - which SEPIO woudl capture as two distinct Evidence Lines.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Draft
is_a: InformationEntity
attributes:
  subtype:
    name: subtype
    description: A specific type of evidence the EvidenceLine instance 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), or categories from evidence interpretation frameworks like the
      ACMG Variant Interpretation Guidelines, can be used as values here.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: subtype
    owner: EvidenceLine
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  targetProposition:
    name: targetProposition
    description: The possible fact against which evidence items contained in an Evidence
      Line were collectively evaluated, in determining the overall strength and direction
      of support they provide. For example, in an ACMG Guideline-based assessment
      of variant pathogenicity, the support provided by distinct lines of evidence
      are assessed against a target proposition that some variant is pathogenic for
      a specific disease.
    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 vs strong) and direction (supports vs disputes)
      to this data as evidence, there must be some ''target proposition'' toward which
      the evidence is assessed - which in this cases is the proposition that the variant
      is pathogenic for the disease of interest. If the PM2 criteria is deemed ''met'',
      this indicates that the population frequency evidence provides ''moderate''
      (strength) ''support'' (direction) for this target proposition.'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: targetProposition
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: Proposition
    required: false
    multivalued: false
  hasEvidenceItems:
    name: hasEvidenceItems
    description: An individual piece of information that was evaluated as evidence
      in building the argument represented by an Evidence Line.
    comments:
    - A given Evidence Line may be supported by one or many individual evidence items.
      What matters is that all evidence items in a given Evidence Line get collectively
      assessed and assigned direction and strength  as a single argument for or against
      a target proposition.
    - Different types and scales of information entity can serve as evidence (experimental
      measurements or observations, data tables or figures, images, prior assertions,
      etc.) Only when assessed as evidence do we consider the information to be an
      'Evidence Item'.  For example, a piece of population frequency data about BRCA2
      c.8023A>G  becomes an Evidence Item when it is assessed for the support it may
      offer for a target proposition (e.g. the prospect of the variant’s pathogenicity).
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: hasEvidenceItems
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: InformationEntity
    required: false
    multivalued: true
  directionOfEvidenceProvided:
    name: directionOfEvidenceProvided
    description: The direction of support that the Evidence Line is determined to
      provide toward its target Proposition (supports, disputes, neutral).
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: directionOfEvidenceProvided
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: string
    required: false
    multivalued: false
  strengthOfEvidenceProvided:
    name: strengthOfEvidenceProvided
    description: The strength of support that an Evidence Line is determined to provide
      for or against its target Proposition, evaluated relative to the direction indicated
      by the directionOfEvidenceProvided.
    comments:
    - Values of this attribute can be defined by for a given profile based on domain/application
      needs, but should be framed in qualitative terms (e.g. 'strong', 'moderate',
      'weak'). The 'scoreOfEvidenceProvided' attribute can be used to report quantitative
      assessments of evidence provided.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: strengthOfEvidenceProvided
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: string
    required: false
    multivalued: false
  scoreOfEvidenceProvided:
    name: scoreOfEvidenceProvided
    description: A quantitative score indicating the strength of support that an Evidence
      Line is determined to provide for or against its target Proposition, evaluated
      relative to the direction indicated by the directionOfEvidenceProvided value.
    comments:
    - A given profile or implementation can define a scoring scale and rules that
      meet the needs of their domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: scoreOfEvidenceProvided
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: float
    required: false
    multivalued: false
  evidenceItemSources:
    name: evidenceItemSources
    description: An information resource (e.g. document, dataset, digital resource
      such as a database or  knowledgebase) that provides information interpreted
      as evidence in building an Evidence Line.
    comments:
    - This is a 'shortcut relation' that can be used to directly link an Evidence
      Line to sources of its supporting Evidence Items, without having to represent
      those Evidence Items directly. Populate with the name or uri or curie of a source
      of information. Future work will define a more formal framework for referencing
      information sources.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: evidenceItemSources
    owner: EvidenceLine
    domain_of:
    - EvidenceLine
    range: string
    required: false
    multivalued: true
  isAbout:
    name: isAbout
    description: An entity or concept in the world that the information entity describes/is
      about.
    comments:
    - e.g. In the context of a Statement object, this attribute may be used to indicate
      entities/concepts it is about, in lieu of providing a more precise description
      of what the Statement asserts to be true using subject, predicate, object, and
      qualifier properties. e.g. the Statement that "BRCA2 c.8023A>G is pathogenic
      for Breast Cancer" might be annotated to be about the variant 'BRCA2 c.8023A>G',
      and the disease 'Breast Cancer'.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: isAbout
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  contributions:
    name: contributions
    description: Specific actions taken by an Agent toward the creation, modification,
      validation, or deprecation of an Information Entity.
    comments:
    - This attribute holds one or more Contribution objects, which provide structured
      descriptions of a contribution made to the Information Entity by a particular
      agent.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: contributions
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    - RecordMetadata
    range: Contribution
    required: false
    multivalued: true
  dateAuthored:
    name: dateAuthored
    description: Indicates when the information content expressed in the Information
      Entity was generated.
    comments:
    - The term 'authored' as used in the model refers to the generation of 'information
      content' in the abstract  sense, as opposed to a concrete encoding of this information
      in a specific language or format. e.g. for a Statement, this attribute captures
      when the information content expressed in the Statement was first generated
      by an agent.  Information about when a particular concrete encoding of this
      information was created (e.g. as row in a table, or object in a json document)
      would live in a RecordMetadata object attached to the Information Entity).
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: dateAuthored
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: false
  specifiedBy:
    name: specifiedBy
    description: A specification that describes all or part of the process that led
      to creation of the Information Entity.
    comments:
    - Examples - an experimental protocol or data analysis specification that describe
      how data were generated, or an evidence interpretation guideline that describes
      steps taken to interpret data in making a variant pathogenicity classification.
    - Note that this attribute captures specific *instances* of specifications/methods
      (e.g. the specific electron microscopy method described in https://doi.org/10.1002/
      cpz1.1045) - as opposed to reporting a *type* of method applied (e.g. "Transmission
      Electron Microscopy").
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: specifiedBy
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    - Activity
    range: string
    required: false
    multivalued: true
  supportingMethods:
    name: supportingMethods
    description: Specific methods that were executed to directly or indirectly support
      creation of the Information Entity.
    comments:
    - These may include methods that directly produced the Information Entity, or
      upstream/accessory methods that indirectly support creation of the Information
      Entity - e.g. methods used to produce data that was interpreted as evidence
      to generate a Statement of knowledge.
    - This field captures terms representing specific INSTANCES of methods applied,
      vs the 'supportingMethodTypes' attribute which captures TYPES of methods used.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: supportingMethods
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  supportingMethodTypes:
    name: supportingMethodTypes
    description: Types of methodological approaches that were executed to directly
      or indirectly support creation of the Information Entity.
    comments:
    - This field captures terms representing TYPES of methods applied, vs the 'specifiedBy'
      or'supportingMethods' attributes which capture specific INSTANCES of methods
      used. These may include types of methods that directly produced the Information
      Entity, or upstream/accessory methods that indirectly support creation of the
      Information Entity
    - Implementers should define a relevant source or set of method type codes/terms
      to use here, based on the needs of the domain or application.'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: supportingMethodTypes
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: Coding
    required: false
    multivalued: true
  derivedFrom:
    name: derivedFrom
    description: Another Information Entity from which this Information Entity is
      derived, in whole or in part.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: derivedFrom
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: InformationEntity
    required: false
    multivalued: true
  reportedIn:
    name: reportedIn
    description: A document in which the Information Entity is reported.
    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.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: reportedIn
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  sources:
    name: sources
    description: A document or other informtion resource in which the information
      entity, or evidence supporting it, is reported.
    comments:
    - This attribute is more general than InformationEntity.reportedIn (which is used
      to references a Docuement that directly reports the infrormation), and Statement.hasEvidenceFromSources
      (which is used to reference resources that provided evidence used to generate
      the knowledge expressed in a Statement). It can be used to cover both cases,
      in situations where a data provider does not know which is the case, or does
      not wish to make the distinction.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: sources
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: string
    required: false
    multivalued: true
  informationQuality:
    name: informationQuality
    description: A qualitative term indicating the scientific rigor or reliability
      with which the information was generated/collected.
    comments:
    - This is typically based on the quality of design and execution of the study
      or curation activity that generated it (e.g. were relevant controls assessed
      to show instruments were working, were all samples taken care of and handled
      identically, are methods sound and well documented, etc.).
    - The quality of information is intrinsic to the information itself, and not to
      a particular application of the information (e.g. as evidence for making an
      Assertion)
    - The quality of information is one factor that goes into the confidence we have
      in the information''s veracity (i.e. that it is an accurate reflection of reality
      it intends to measure or describe). Other factors informing confidence may include
      who did it (we may just not trust some Agents), when (if data created 500 years
      ago, we may have less confidence in it), and for Assertions, the relevance and
      abundance of supporting evidence.
    - Implementers should define a relevant source of codes or terms to use here,
      based on the needs of the domain or application.'
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: informationQuality
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: Coding
    required: false
    multivalued: false
  recordMetadata:
    name: recordMetadata
    description: Provenance metadata about a specific concrete record of information
      as encoded/serialized in a particular data set or object (as opposed to provenance
      about the abstract information content the encoding carries).
    comments:
    - This attribute holds a structured RecordMetadata objects, which can be used
      to capture when, how, and by whom a record serialization was generated or modified;
      what upstream resources it was derived or retrieved from; and record-level administrative
      information such as versioning and lifecycle status.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: recordMetadata
    owner: EvidenceLine
    domain_of:
    - InformationEntity
    range: RecordMetadata
    required: false
    multivalued: 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, but may or may not be globally
      unique outside the system. It is used within a system to reference one object
      from another.
    comments:
    - Note that it is common for implementers to create their own internal logical
      ids - typically a serially or randomly generated value like a UUID that is assigned
      to the data object as it is created in a system. But an implementer may choose
      to reuse an existing, globally unique id from an external system or authority
      for this purpose (e.g. an HGNC id for a Gene object) - as long as it is unique
      within the implementing system, and can be used to reference the identified
      object in this context.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: id
    owner: EvidenceLine
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  identifiers:
    name: identifiers
    description: A globally-unique 'business' identifier or accession number for the
      real-world entity represented by a data object. These are typically assigned
      by an external system or authority, and used to connect entities and share content
      across different systems.
    comments:
    - Preferred values for this attribute are CURIEs or URIs - so the system that
      provisioned the identifier is clear.
    - A given real world entity - e.g. a genetic variant - may have many business
      identifiers defined by different systems, which can be captured in the "identifiers"
      property to indicate that they represent the same thing.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: identifiers
    owner: EvidenceLine
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  type:
    name: type
    description: The name of the class that is instantiated by a data object representing
      the Entity.
    comments:
    - MUST be the label of a concrete class from the data model.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: type
    owner: EvidenceLine
    domain_of:
    - Entity
    range: string
    required: true
    multivalued: false
  label:
    name: label
    description: A primary name for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: label
    owner: EvidenceLine
    domain_of:
    - Entity
    - Coding
    range: string
    required: false
    multivalued: false
  alternativeLabels:
    name: alternativeLabels
    description: Alternative name(s) for the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: alternativeLabels
    owner: EvidenceLine
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: true
  description:
    name: description
    description: A free text description of the Entity.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: description
    owner: EvidenceLine
    domain_of:
    - Entity
    range: string
    required: false
    multivalued: false
  extensions:
    name: extensions
    description: A list of extensions to the Entity, that allow for capture of information
      not directly supported by elements defined in the model.
    comments:
    - Extension objects have a key-value data structure that allows definition of
      custom fields in the data itself. Extensions are not expected to be natively
      understood, but may be used for pre-negotiated exchange of message attributes
      between systems.
    from_schema: https://w3id.org/sepio-model
    status: Draft
    rank: 1000
    alias: extensions
    owner: EvidenceLine
    domain_of:
    - Entity
    range: Extension
    required: false
    multivalued: true