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Class: StudyResult

A collection of data items from a single study that are about a particular subject or experimental unit in the study (along with optional provenance metadata describing how these data items were generated).

URI: vacoreim:StudyResult

classDiagram class StudyResult InformationEntity <|-- StudyResult StudyResult : contributions StudyResult --|> Contribution : contributions StudyResult : dataItems StudyResult --|> DataItem : dataItems StudyResult : dateAuthored StudyResult : derivedFrom StudyResult --|> DataSet : derivedFrom StudyResult : description StudyResult : extensions StudyResult --|> Extension : extensions StudyResult : focus StudyResult --|> Entity : focus StudyResult : id StudyResult : identifiers StudyResult : label StudyResult : recordMetadata StudyResult --|> RecordMetadata : recordMetadata StudyResult : reportedIn StudyResult --|> Document : reportedIn StudyResult : specifiedBy StudyResult --|> Method : specifiedBy StudyResult : subtype StudyResult --|> Coding : subtype StudyResult : type StudyResult : urls StudyResult : xrefs

Inheritance

Slots

Name Cardinality and Range Description Inheritance
subtype 0..1
Coding		 A specific type of result the StudyResult object represents (e.g. an 'Population Allele Frequency Study Result') direct
focus 0..1
Entity		 The specific subject or experimental unit in the Research Study that data in the Result is about, and which guides the selection of data that is included within a single Study Result object. direct
dataItems 0..*
DataItem		 A piece of data from the source Study that is included in the Result, and pertains to the entity that is the 'focus'. Can be data directly about the focus, or metadata relevant to how this data was generated. direct
derivedFrom 0..1
DataSet		 A larger Data Set from which the content of the Result was derived. direct
contributions 0..*
Contribution		 A specific contribution made by some Agent to the creation, modification, or validation of the information represented in the Information Entity. InformationEntity
dateAuthored 0..1
DateTime		 The date the information content expressed in this entity was generated. InformationEntity
specifiedBy 0..*
Method		 A particular plan specification that describes all or part of the process that led to creation of the reported information (e.g. a specific experimental protocol, analysis specification, cohort selection criteria, interpretation guideline, etc.). InformationEntity
reportedIn 0..*
Document		 A document in which the information content carried by the Information Entity is expressed InformationEntity
id 1..1
Identifier		 The logical identifier of the entity in the system of record, e.g. a UUID. This 'id' is unique within a given system. The identified entity may have a different 'id' in a different system. Entity
identifiers 0..*
Identifier		 A business identifier or accession number for the entity, typically as provided by an external system or authority, that is globally unique and persists across implementing systems. Entity
label 0..1
String		 A primary name for the Entity. Entity
urls 0..*
Url		 The URL/web address of a digital resource representing the entity, or providing information about it. Entity
xrefs 0..*
String		 Cross-references to database identifier(s) representing the same (or a closely related) entity or concept as the Entity. Entity
recordMetadata 0..1
RecordMetadata		 A reusable structure that encapsulates provenance metadata about the present record/data object (as opposed to provenance information about the real world entity this record/data object represents). Entity
type 1..1
Class		 The schema class that is instantiated by the data object. Must be the name of a class from the VA schema. Element
description 0..1
String		 A free text description of the Element. Element
extensions 0..*
Extension		 A key-value data structure that allows definition of custom fields to capture information not directly supported by the VA specification. Element

Comments

  • StudyResult objects provide a flexible and useful way to summarize a subset of data items from a larger study that are cited as evidence in curation workflows that generate higher order knowledge about a particular variant or other entity.

For example, a specific subset of allele frequency data items about a particular variant of interest in the gnomAD dataset can be captured in a Study Result object, along with relevant provenance information, and referenced as evidence for a higher-order Statement about the variant's pathogenicity.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: StudyResult
description: A collection of data items from a single study that are about a particular
  subject or experimental unit in the study  (along with optional provenance metadata
  describing how these data items were generated).
title: Study Result
comments:
- "StudyResult objects provide a flexible and useful way to summarize a subset of\
  \ data items from a larger study that are cited as evidence in curation workflows\
  \ that generate higher order knowledge about a particular variant or other entity.\
  \ \n\nFor example, a specific subset of allele frequency data items about a particular\
  \ variant of interest in the gnomAD dataset can be captured in a Study Result object,\
  \ along with relevant provenance information, and referenced as evidence for a higher-order\
  \ Statement about the variant's pathogenicity."
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: InformationEntity
slots:
- subtype
- focus
- dataItems
- derivedFrom
slot_usage:
  subtype:
    name: subtype
    description: A specific type of result the StudyResult object represents (e.g.
      an 'Population Allele Frequency Study Result')
    comments:
    - Implementations can define subtypes based on any features that provide useful
      information about the type of data the Result collects.
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  focus:
    name: focus
    description: The specific subject or experimental unit in the Research Study that
      data in the Result is about, and which guides the selection of data that is
      included within a single Study Result object.
    comments:
    - The value of this field explains why the sleected data as included in the Study
      Result - because it all pertains to the 'focus' of the curator when creating
      it.
    multivalued: false
    domain_of:
    - StudyResult
    range: Entity
    required: false
  dataItems:
    name: dataItems
    description: A piece of data from the source Study that is included in the Result,
      and pertains to the entity that is the 'focus'. Can be data directly about the
      focus, or metadata relevant to how this data was generated.
    multivalued: true
    domain_of:
    - StudyResult
    range: DataItem
    required: false
  derivedFrom:
    name: derivedFrom
    description: A larger Data Set from which the content of the Result was derived.
    comments:
    - Constrains the derivedFrom attribute of the parent InformationEntity class to
      take a DataSet as a value.
    multivalued: false
    domain_of:
    - InformationEntity
    - StudyResult
    - RecordMetadata
    range: DataSet
    required: false

Induced

name: StudyResult
description: A collection of data items from a single study that are about a particular
  subject or experimental unit in the study  (along with optional provenance metadata
  describing how these data items were generated).
title: Study Result
comments:
- "StudyResult objects provide a flexible and useful way to summarize a subset of\
  \ data items from a larger study that are cited as evidence in curation workflows\
  \ that generate higher order knowledge about a particular variant or other entity.\
  \ \n\nFor example, a specific subset of allele frequency data items about a particular\
  \ variant of interest in the gnomAD dataset can be captured in a Study Result object,\
  \ along with relevant provenance information, and referenced as evidence for a higher-order\
  \ Statement about the variant's pathogenicity."
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: InformationEntity
slot_usage:
  subtype:
    name: subtype
    description: A specific type of result the StudyResult object represents (e.g.
      an 'Population Allele Frequency Study Result')
    comments:
    - Implementations can define subtypes based on any features that provide useful
      information about the type of data the Result collects.
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  focus:
    name: focus
    description: The specific subject or experimental unit in the Research Study that
      data in the Result is about, and which guides the selection of data that is
      included within a single Study Result object.
    comments:
    - The value of this field explains why the sleected data as included in the Study
      Result - because it all pertains to the 'focus' of the curator when creating
      it.
    multivalued: false
    domain_of:
    - StudyResult
    range: Entity
    required: false
  dataItems:
    name: dataItems
    description: A piece of data from the source Study that is included in the Result,
      and pertains to the entity that is the 'focus'. Can be data directly about the
      focus, or metadata relevant to how this data was generated.
    multivalued: true
    domain_of:
    - StudyResult
    range: DataItem
    required: false
  derivedFrom:
    name: derivedFrom
    description: A larger Data Set from which the content of the Result was derived.
    comments:
    - Constrains the derivedFrom attribute of the parent InformationEntity class to
      take a DataSet as a value.
    multivalued: false
    domain_of:
    - InformationEntity
    - StudyResult
    - RecordMetadata
    range: DataSet
    required: false
attributes:
  subtype:
    name: subtype
    description: A specific type of result the StudyResult object represents (e.g.
      an 'Population Allele Frequency Study Result')
    comments:
    - Implementations can define subtypes based on any features that provide useful
      information about the type of data the Result collects.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: subtype
    owner: StudyResult
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  focus:
    name: focus
    description: The specific subject or experimental unit in the Research Study that
      data in the Result is about, and which guides the selection of data that is
      included within a single Study Result object.
    comments:
    - The value of this field explains why the sleected data as included in the Study
      Result - because it all pertains to the 'focus' of the curator when creating
      it.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: focus
    owner: StudyResult
    domain_of:
    - StudyResult
    range: Entity
    required: false
  dataItems:
    name: dataItems
    description: A piece of data from the source Study that is included in the Result,
      and pertains to the entity that is the 'focus'. Can be data directly about the
      focus, or metadata relevant to how this data was generated.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: dataItems
    owner: StudyResult
    domain_of:
    - StudyResult
    range: DataItem
    required: false
  derivedFrom:
    name: derivedFrom
    description: A larger Data Set from which the content of the Result was derived.
    comments:
    - Constrains the derivedFrom attribute of the parent InformationEntity class to
      take a DataSet as a value.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: derivedFrom
    owner: StudyResult
    domain_of:
    - InformationEntity
    - StudyResult
    - RecordMetadata
    range: DataSet
    required: false
  contributions:
    name: contributions
    description: A specific contribution made by some Agent to the creation, modification,
      or validation of the information represented in the Information Entity.
    comments:
    - This attribute points to a Contribution object, which holds a structured description
      of the actions taken by a particular agent in contributing to an Information
      Entity.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: contributions
    owner: StudyResult
    domain_of:
    - InformationEntity
    - RecordMetadata
    range: Contribution
    required: false
  dateAuthored:
    name: dateAuthored
    description: The date the information content expressed in this entity was generated.
    comments:
    - We use the term 'authored' to refer to the generation of information in the
      abstract - i.e. the information content expressed in a Statement, not a concrete
      encoding of it in a specific language or format.  The 'dateAuthored' attribute
      captures when this abstract information content was first created.  Information
      about when a particular concrete encoding of this information was created (e.g.
      as a VA-based json object) would live in a RecordMetadata object attached to
      the Information Entity).
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: dateAuthored
    owner: StudyResult
    domain_of:
    - InformationEntity
    range: DateTime
    required: false
  specifiedBy:
    name: specifiedBy
    description: A particular plan specification that describes all or part of the
      process that led to creation of the reported information (e.g. a specific experimental
      protocol, analysis specification, cohort selection criteria, interpretation
      guideline, etc.).
    comments:
    - 'This field captures specific instances of specifications / methods (vs the
      ''methodTypes'' attribute which captures types of methods applied).

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