Class: Data Set (DataSet)

name: DataSet
description: A collection of related data items or records that are organized together
  in a common format or structure, to enable their computational manipulation as a
  unit.
title: Data Set
comments:
- Instances of this class represent a *specific version* of a given dataset. Examples
  include the  gnomAD version 3.1.2 dataset carrying allele population frequencies,
  or a specific version of a VCF file that describes variations observed in a particular
  patient and various annotations made on them, or a SIFT dataset of computational
  predictions functional impact for a set of variants.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Draft
is_a: InformationEntity
attributes:
  subtype:
    name: subtype
    description: A specific type of data set the DataSet instance represents (e.g.
      a 'clinical data set', a 'sequencing data set', a 'gene expression data set',
      a 'genome annotation data set').
    comments:
    - This attribute can be used to report a specific type for the DataSet, in cases
      where a model does not define DataSet subclasses for this purpose.  Implementers
      can define their own set of data set type codes/terms, to match the needs of
      the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  releaseDate:
    name: releaseDate
    description: Indicates when a version of a DataSet was formally released.
    comments:
    - This attribute may apply to version and distribution-level DataSet representations.
      It refers to when the data set was released, which may be different than the
      data set was generated.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataSet
    range: string
    required: false
    multivalued: false
  version:
    name: version
    description: The version of the DataSet, as assigned by its creator.
    comments:
    - This property can capture version information for resources such as data sets
      and documents that get published and released as a unit for community use. These
      may go through rounds of revisions that add or modify content, but don't change
      the identity of the resource. Use this attribute in cases where version is not
      reflected in an identifier associated with the data set
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    domain_of:
    - DataSet
    range: string
    required: false
    multivalued: false
  license:
    name: license
    description: A specific license that dictates legal permissions for how a data
      set can be used (by whom, where, for what purposes, with what additional requirements,
      etc.).
    comments:
    - Where possible, provide a URL pointing to the license or a description of it
      (e.g. "https://creativecommons.org/licenses/by/4.0/"). Otherwise, provide a
      free-text name or description of the license (e.g. "CC-BY").
    from_schema: https://w3id.org/sepio-model
    status: Informative
    domain_of:
    - Document
    - DataSet
    range: string
    required: false
    multivalued: false

name: DataSet
description: A collection of related data items or records that are organized together
  in a common format or structure, to enable their computational manipulation as a
  unit.
title: Data Set
comments:
- Instances of this class represent a *specific version* of a given dataset. Examples
  include the  gnomAD version 3.1.2 dataset carrying allele population frequencies,
  or a specific version of a VCF file that describes variations observed in a particular
  patient and various annotations made on them, or a SIFT dataset of computational
  predictions functional impact for a set of variants.
from_schema: https://w3id.org/sepio-framework/sepio-linkml
status: Draft
is_a: InformationEntity
attributes:
  subtype:
    name: subtype
    description: A specific type of data set the DataSet instance represents (e.g.
      a 'clinical data set', a 'sequencing data set', a 'gene expression data set',
      a 'genome annotation data set').
    comments:
    - This attribute can be used to report a specific type for the DataSet, in cases
      where a model does not define DataSet subclasses for this purpose.  Implementers
      can define their own set of data set type codes/terms, to match the needs of
      the domain or application.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: subtype
    owner: DataSet
    domain_of:
    - Method
    - Document
    - DataItem
    - DataSet
    - Activity
    - Agent
    - EvidenceLine
    range: Coding
    required: false
    multivalued: false
  releaseDate:
    name: releaseDate
    description: Indicates when a version of a DataSet was formally released.
    comments:
    - This attribute may apply to version and distribution-level DataSet representations.
      It refers to when the data set was released, which may be different than the
      data set was generated.
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: releaseDate
    owner: DataSet
    domain_of:
    - DataSet
    range: string
    required: false
    multivalued: false
  version:
    name: version
    description: The version of the DataSet, as assigned by its creator.
    comments:
    - This property can capture version information for resources such as data sets
      and documents that get published and released as a unit for community use. These
      may go through rounds of revisions that add or modify content, but don't change
      the identity of the resource. Use this attribute in cases where version is not
      reflected in an identifier associated with the data set
    from_schema: https://w3id.org/sepio-model
    status: Informative
    rank: 1000
    alias: version
    owner: DataSet
    domain_of:
    - DataSet
    range: string
    required: false
    multivalued: false
  license:
    name: license
    description: A specific license that dictates legal permissions for how a data
      set can be used (by whom, where, for what purposes, with what additional requirements,
      etc.).
    comments:
    - Where possible, provide a URL pointing to the license or a description of it
      (e.g. "https://creativecommons.org/licenses/by/4.0/"). Otherwise, provide a
      free-text name or description of the license (e.g. "CC-BY").
    from_schema: https://w3id.org/sepio-model
    status: Informative
    alias: license
    owner: DataSet
    domain_of:
    - Document
    - DataSet
    range: string
    required: false
    multivalued: false
  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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    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: DataSet
    domain_of:
    - Entity
    range: Extension
    required: false
    multivalued: true