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
Inheritance
- Entity
- InformationEntity
- EvidenceLine
- InformationEntity
Slots
Direct slots
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
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.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.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.
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.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