Class: Method

A set of instructions that specify how to achieve some objective (e.g. study/experimental protocols, curation guidelines, rule sets, etc.)

URI: vacoreim:Method

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

Inheritance

Element
- Entity
  - InformationEntity
    - Method

Slots

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

Usages

used by	used in	type	used
InformationEntity	specifiedBy	range	Method
DataItem	specifiedBy	range	Method
DataSet	specifiedBy	range	Method
Document	specifiedBy	range	Method
Statement	specifiedBy	range	Method
StudyResult	specifiedBy	range	Method
EvidenceLine	specifiedBy	range	Method
Method	specifiedBy	range	Method
Activity	specifiedBy	range	Method
Contribution	specifiedBy	range	Method

Comments

Methods guide human or computational agents by specifying what actions to perform and how to do so. Examples include research protocols specifying how to execute studies or experiments to generate data, and guidelines for data curation or interpretation that specify how information can be organized, evaluated, and interpreted to generate evidence-based assertions.

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Method
description: A set of instructions that specify how to achieve some objective (e.g.
  study/experimental protocols, curation guidelines, rule sets, etc.)
title: Method
comments:
- Methods guide human or computational agents by specifying what actions to perform
  and how to do so.  Examples include research protocols specifying how to execute
  studies or experiments to generate data, and guidelines for data curation or interpretation
  that specify how information can be organized, evaluated, and interpreted to generate
  evidence-based assertions.
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: InformationEntity
slots:
- subtype
- license
slot_usage:
  subtype:
    name: subtype
    description: A specific type of method that the Method object represents (e.g.
      'Variant Interpretation Guideline', 'Experimental Protocol')
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  license:
    name: license
    description: The type of license that dictates legal permissions for how a published
      method (e.g. an experimental protocol, workflow specification, curation guideline)
      can be used - typically referenced by its URL.
    multivalued: false
    domain_of:
    - DataSet
    - Document
    - Method
    range: string
    required: false

Induced

name: Method
description: A set of instructions that specify how to achieve some objective (e.g.
  study/experimental protocols, curation guidelines, rule sets, etc.)
title: Method
comments:
- Methods guide human or computational agents by specifying what actions to perform
  and how to do so.  Examples include research protocols specifying how to execute
  studies or experiments to generate data, and guidelines for data curation or interpretation
  that specify how information can be organized, evaluated, and interpreted to generate
  evidence-based assertions.
from_schema: https://w3id.org/ga4gh-va-core-im
is_a: InformationEntity
slot_usage:
  subtype:
    name: subtype
    description: A specific type of method that the Method object represents (e.g.
      'Variant Interpretation Guideline', 'Experimental Protocol')
    multivalued: false
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  license:
    name: license
    description: The type of license that dictates legal permissions for how a published
      method (e.g. an experimental protocol, workflow specification, curation guideline)
      can be used - typically referenced by its URL.
    multivalued: false
    domain_of:
    - DataSet
    - Document
    - Method
    range: string
    required: false
attributes:
  subtype:
    name: subtype
    description: A specific type of method that the Method object represents (e.g.
      'Variant Interpretation Guideline', 'Experimental Protocol')
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: subtype
    owner: Method
    domain_of:
    - DataItem
    - DataSet
    - Document
    - Statement
    - StudyResult
    - EvidenceLine
    - Method
    - Activity
    - Agent
    - Proposition
    range: Coding
    required: false
  license:
    name: license
    description: The type of license that dictates legal permissions for how a published
      method (e.g. an experimental protocol, workflow specification, curation guideline)
      can be used - typically referenced by its URL.
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: false
    alias: license
    owner: Method
    domain_of:
    - DataSet
    - Document
    - Method
    range: string
    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: Method
    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: Method
    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: Method
    domain_of:
    - InformationEntity
    - Activity
    range: Method
    required: false
  derivedFrom:
    name: derivedFrom
    description: An information resource from which the Information Entity is derived,
      in whole or in part
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: derivedFrom
    owner: Method
    domain_of:
    - InformationEntity
    - StudyResult
    - RecordMetadata
    range: InformationEntity
    required: false
  reportedIn:
    name: reportedIn
    description: A document in which the information content carried by the Information
      Entity is expressed
    comments:
    - "This attribute is used specifically to reference documents/publications where\
      \ the Information Entity is expressed or reported.  For a Statement, this might\
      \ be a publication where the authors express the statement in text.  For a Data\
      \ Item, this might be a publication with a table or figure that reports the\
      \ value of the  data.  \nNote that the VA-Spec provide separate attributes for\
      \ describing different types of 'references' from an Information Entity to a\
      \ Document (e.g. hasEvidenceFromSource is used by a Statement to reference a\
      \ Document that provided evidence for the knowldege the Statement expresses."
    from_schema: https://w3id.org/ga4gh-va-core-im
    rank: 1000
    multivalued: true
    alias: reportedIn
    owner: Method
    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: Method
    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: Method
    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: Method
    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: Method
    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: Method
    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: Method
    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: Method
    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: Method
    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: Method
    domain_of:
    - Element
    range: Extension
    required: false