Class: Attribute

name: attribute
id_prefixes:
- EDAM-DATA
- EDAM-FORMAT
- EDAM-OPERATION
- EDAM-TOPIC
definition_uri: https://w3id.org/biolink/vocab/Attribute
description: A property or characteristic of an entity. For example, an apple may
  have properties such as color, shape, age, crispiness. An environmental sample may
  have attributes such as depth, lat, long, material.
in_subset:
- samples
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
exact_mappings:
- SIO:000614
is_a: named thing
mixins:
- ontology class
slots:
- id
- category
- type
- description
- has attribute
- deprecated
- provided by
- xref
- full name
- synonym
- attribute_name
- has attribute type
- has quantitative value
- has qualitative value
- iri
slot_usage:
  name:
    name: name
    description: The human-readable 'attribute name' can be set to a string which
      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
      annotation or it can default to the name associated with the 'has attribute
      type' slot ontology term.
    domain_of:
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
class_uri: biolink:Attribute

name: attribute
id_prefixes:
- EDAM-DATA
- EDAM-FORMAT
- EDAM-OPERATION
- EDAM-TOPIC
definition_uri: https://w3id.org/biolink/vocab/Attribute
description: A property or characteristic of an entity. For example, an apple may
  have properties such as color, shape, age, crispiness. An environmental sample may
  have attributes such as depth, lat, long, material.
in_subset:
- samples
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
exact_mappings:
- SIO:000614
is_a: named thing
mixins:
- ontology class
slot_usage:
  name:
    name: name
    description: The human-readable 'attribute name' can be set to a string which
      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
      annotation or it can default to the name associated with the 'has attribute
      type' slot ontology term.
    domain_of:
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
attributes:
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    description: A unique identifier for an entity. Must be either a CURIE shorthand
      for a URI or a complete URI
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: attribute
    domain_of:
    - ontology class
    - entity
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    required: true
  category:
    name: category
    definition_uri: https://w3id.org/biolink/vocab/category
    description: 'Name of the high level ontology class in which this entity is categorized.
      Corresponds to the label for the biolink entity type class. In a neo4j database
      this MAY correspond to the neo4j label tag. In an RDF database it should be
      a biolink model class URI. This field is multi-valued. It should include values
      for ancestors of the biolink class; for example, a protein such as Shh would
      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
      In an RDF database, nodes will typically have an rdf:type triples. This can
      be to the most specific biolink class, or potentially to a class more specific
      than something in biolink. For example, a sequence feature `f` may have a rdf:type
      assertion to a SO class such as TF_binding_site, which is more specific than
      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
      biolink:NamedThing}. NOTE: The category slot was modified to have a curie range
      and a pattern for bican categories.'
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: attribute
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    range: curie
    multivalued: true
    pattern: ^bican:[A-Z][A-Za-z]+$
  type:
    name: type
    definition_uri: https://w3id.org/biolink/vocab/type
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: type
    owner: attribute
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: a human-readable description of an entity
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: attribute
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: narrative text
  has attribute:
    name: has attribute
    definition_uri: https://w3id.org/biolink/vocab/has_attribute
    description: connects any entity to an attribute
    in_subset:
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - SIO:000008
    close_mappings:
    - OBI:0001927
    narrow_mappings:
    - OBAN:association_has_subject_property
    - OBAN:association_has_object_property
    - CPT:has_possibly_included_panel_element
    - DRUGBANK:category
    - EFO:is_executed_in
    - HANCESTRO:0301
    - LOINC:has_action_guidance
    - LOINC:has_adjustment
    - LOINC:has_aggregation_view
    - LOINC:has_approach_guidance
    - LOINC:has_divisor
    - LOINC:has_exam
    - LOINC:has_method
    - LOINC:has_modality_subtype
    - LOINC:has_object_guidance
    - LOINC:has_scale
    - LOINC:has_suffix
    - LOINC:has_time_aspect
    - LOINC:has_time_modifier
    - LOINC:has_timing_of
    - NCIT:R88
    - NCIT:eo_disease_has_property_or_attribute
    - NCIT:has_data_element
    - NCIT:has_pharmaceutical_administration_method
    - NCIT:has_pharmaceutical_basic_dose_form
    - NCIT:has_pharmaceutical_intended_site
    - NCIT:has_pharmaceutical_release_characteristics
    - NCIT:has_pharmaceutical_state_of_matter
    - NCIT:has_pharmaceutical_transformation
    - NCIT:is_qualified_by
    - NCIT:qualifier_applies_to
    - NCIT:role_has_domain
    - NCIT:role_has_range
    - INO:0000154
    - HANCESTRO:0308
    - OMIM:has_inheritance_type
    - orphanet:C016
    - orphanet:C017
    - RO:0000053
    - RO:0000086
    - RO:0000087
    - SNOMED:has_access
    - SNOMED:has_clinical_course
    - SNOMED:has_count_of_base_of_active_ingredient
    - SNOMED:has_dose_form_administration_method
    - SNOMED:has_dose_form_release_characteristic
    - SNOMED:has_dose_form_transformation
    - SNOMED:has_finding_context
    - SNOMED:has_finding_informer
    - SNOMED:has_inherent_attribute
    - SNOMED:has_intent
    - SNOMED:has_interpretation
    - SNOMED:has_laterality
    - SNOMED:has_measurement_method
    - SNOMED:has_method
    - SNOMED:has_priority
    - SNOMED:has_procedure_context
    - SNOMED:has_process_duration
    - SNOMED:has_property
    - SNOMED:has_revision_status
    - SNOMED:has_scale_type
    - SNOMED:has_severity
    - SNOMED:has_specimen
    - SNOMED:has_state_of_matter
    - SNOMED:has_subject_relationship_context
    - SNOMED:has_surgical_approach
    - SNOMED:has_technique
    - SNOMED:has_temporal_context
    - SNOMED:has_time_aspect
    - SNOMED:has_units
    - UMLS:has_structural_class
    - UMLS:has_supported_concept_property
    - UMLS:has_supported_concept_relationship
    - UMLS:may_be_qualified_by
    rank: 1000
    domain: entity
    slot_uri: biolink:has_attribute
    alias: has_attribute
    owner: attribute
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: attribute
    multivalued: true
  deprecated:
    name: deprecated
    definition_uri: https://w3id.org/biolink/vocab/deprecated
    description: A boolean flag indicating that an entity is no longer considered
      current or valid.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: deprecated
    owner: attribute
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: boolean
  provided by:
    name: provided by
    definition_uri: https://w3id.org/biolink/vocab/provided_by
    description: The value in this node property represents the knowledge provider
      that created or assembled the node and all of its attributes.  Used internally
      to represent how a particular node made its way into a knowledge provider or
      graph.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: attribute
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    multivalued: true
  xref:
    name: xref
    definition_uri: https://w3id.org/biolink/vocab/xref
    description: A database cross reference or alternative identifier for a NamedThing
      or edge between two NamedThings.  This property should point to a database record
      or webpage that supports the existence of the edge, or gives more detail about
      the edge. This property can be used on a node or edge to provide multiple URIs
      or CURIE cross references.
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - dbxref
    - Dbxref
    - DbXref
    - record_url
    - source_record_urls
    narrow_mappings:
    - gff3:Dbxref
    - gpi:DB_Xrefs
    rank: 1000
    domain: named thing
    slot_uri: biolink:xref
    alias: xref
    owner: attribute
    domain_of:
    - named thing
    - gene
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - genome
    range: uriorcurie
    multivalued: true
  full name:
    name: full name
    definition_uri: https://w3id.org/biolink/vocab/full_name
    description: a long-form human readable name for a thing
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: attribute
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
  synonym:
    name: synonym
    definition_uri: https://w3id.org/biolink/vocab/synonym
    description: Alternate human-readable names for a thing
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - alias
    narrow_mappings:
    - skos:altLabel
    - gff3:Alias
    - AGRKB:synonyms
    - gpi:DB_Object_Synonyms
    - HANCESTRO:0330
    - IAO:0000136
    - RXNORM:has_tradename
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:synonym
    alias: synonym
    owner: attribute
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
    multivalued: true
  attribute_name:
    name: attribute_name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: The human-readable 'attribute name' can be set to a string which
      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
      annotation or it can default to the name associated with the 'has attribute
      type' slot ontology term.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - label
    - display name
    - title
    mappings:
    - rdfs:label
    exact_mappings:
    - gff3:Name
    - gpi:DB_Object_Name
    narrow_mappings:
    - dct:title
    - WIKIDATA_PROPERTY:P1476
    rank: 1000
    is_a: name
    domain: attribute
    slot_uri: rdfs:label
    alias: name
    owner: attribute
    domain_of:
    - attribute
    is_usage_slot: true
    usage_slot_name: name
    range: label type
  has attribute type:
    name: has attribute type
    definition_uri: https://w3id.org/biolink/vocab/has_attribute_type
    description: connects an attribute to a class that describes it
    in_subset:
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    narrow_mappings:
    - LOINC:has_modality_type
    - LOINC:has_view_type
    rank: 1000
    domain: attribute
    slot_uri: biolink:has_attribute_type
    alias: has_attribute_type
    owner: attribute
    domain_of:
    - attribute
    range: ontology class
    required: true
    multivalued: false
  has quantitative value:
    name: has quantitative value
    definition_uri: https://w3id.org/biolink/vocab/has_quantitative_value
    description: connects an attribute to a value
    in_subset:
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - qud:quantityValue
    narrow_mappings:
    - SNOMED:has_concentration_strength_numerator_value
    - SNOMED:has_presentation_strength_denominator_value
    - SNOMED:has_presentation_strength_numerator_value
    rank: 1000
    domain: attribute
    slot_uri: biolink:has_quantitative_value
    alias: has_quantitative_value
    owner: attribute
    domain_of:
    - attribute
    range: quantity value
    multivalued: true
    inlined: true
  has qualitative value:
    name: has qualitative value
    definition_uri: https://w3id.org/biolink/vocab/has_qualitative_value
    description: connects an attribute to a value
    in_subset:
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    domain: attribute
    slot_uri: biolink:has_qualitative_value
    alias: has_qualitative_value
    owner: attribute
    domain_of:
    - attribute
    range: named thing
    multivalued: false
  iri:
    name: iri
    definition_uri: https://w3id.org/biolink/vocab/iri
    description: An IRI for an entity. This is determined by the id using expansion
      rules.
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: iri
    owner: attribute
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: iri type
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: The human-readable 'attribute name' can be set to a string which
      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
      annotation or it can default to the name associated with the 'has attribute
      type' slot ontology term.
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    domain: entity
    slot_uri: rdfs:label
    alias: name
    owner: attribute
    domain_of:
    - entity
    - named thing
    - organism taxon
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - macromolecular machine mixin
    - gene or gene product
    - gene
    - genome
    range: label type
class_uri: biolink:Attribute