Class: CellTypeTaxon

name: CellTypeTaxon
description: A node in the cell type taxonomy representing a unit of cell type classification
  at a specific annotation level. Taxons may be organized into a hierarchy and grouped
  into neighborhoods.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
is_a: named thing
mixins:
- ProvEntity
- OntologyMappable
slots:
- id
- name
- accession_id
- order
- has_parent
- part_of_set
- has_abbreviation
slot_usage:
  id:
    name: id
    annotations:
      ait_location:
        tag: ait_location
        value: (synthesized)
    description: Unique identifier for this cell type taxon.
    range: string
  name:
    name: name
    annotations:
      ait_location:
        tag: ait_location
        value: obs.<annotation_level>
    description: Human-readable label for this cell type taxon at the given annotation
      level (e.g. Glutamatergic).
    in_subset:
    - obs
    - annotations
    range: string
  accession_id:
    name: accession_id
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.accession_<level> (data only)
    description: Stable cross-version identifier for this cell type taxon (e.g. CS20230722_CLAS_11).
    in_subset:
    - uns
    - annotations
    range: string
  order:
    name: order
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.display_order_<level> (data only)
    description: The priority or display order of this taxon among all taxons in the
      taxonomy.
    in_subset:
    - uns
    - annotations
    range: integer
  has_parent:
    name: has_parent
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: the taxon at the preceding uns.hierarchy level, same uns.cluster_info
          row)'
    description: Reference to the parent taxon at the next broader annotation level.
    in_subset:
    - uns
    - annotations
    range: CellTypeTaxon
  part_of_set:
    name: part_of_set
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: the uns.hierarchy level whose uns.cluster_info column this
          taxon came from)'
    description: The annotation level (CellTypeSet) for which this taxon is a member.
    in_subset:
    - uns
    - annotations
    range: CellTypeSet
  has_abbreviation:
    name: has_abbreviation
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.tokens_<level> (data only)
      ait_separator:
        tag: ait_separator
        value: '|'
    description: One of potentially many abbreviations that are part of the cell type
      taxon name.
    in_subset:
    - uns
    - annotations
    range: Abbreviation
    multivalued: true
attributes:
  cell_type_ontology_term:
    name: cell_type_ontology_term
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.CL:ID_<level> (data only)
    description: CL ontology term for this cell type; use CL:0000003 for native cell
      if unknown.
    in_subset:
    - obs
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    aliases:
    - cell_type_ontology_term_id
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: string
    pattern: ^CL:\d{7}$
  number_of_cells:
    name: number_of_cells
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: count obs rows grouped by obs.<annotation_level>)'
    description: The aggregated number of cells that defines this cell type taxon.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: integer
  literature_support:
    name: literature_support
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.literature_support
      ait_separator:
        tag: ait_separator
        value: '|'
    description: Published study in which this cell type was previously described.
      The value "Novel" indicates no prior published description.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: string
    multivalued: true
  literature_name_short:
    name: literature_name_short
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.literature_name_short
      ait_separator:
        tag: ait_separator
        value: '|'
    description: Short name used for this cell type in the supporting literature.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: string
    multivalued: true
  literature_name_long:
    name: literature_name_long
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.literature_name_long
      ait_separator:
        tag: ait_separator
        value: '|'
    description: Full name used for this cell type in the supporting literature.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: string
    multivalued: true
  curated_markers:
    name: curated_markers
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.curated_markers
      ait_separator:
        tag: ait_separator
        value: ','
    description: Marker genes curated as characteristic of this cell type. One set
      per taxon; the AIT consensus taxonomy does not split these by species.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: GeneAnnotation
    multivalued: true

name: CellTypeTaxon
description: A node in the cell type taxonomy representing a unit of cell type classification
  at a specific annotation level. Taxons may be organized into a hierarchy and grouped
  into neighborhoods.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
is_a: named thing
mixins:
- ProvEntity
- OntologyMappable
slot_usage:
  id:
    name: id
    annotations:
      ait_location:
        tag: ait_location
        value: (synthesized)
    description: Unique identifier for this cell type taxon.
    range: string
  name:
    name: name
    annotations:
      ait_location:
        tag: ait_location
        value: obs.<annotation_level>
    description: Human-readable label for this cell type taxon at the given annotation
      level (e.g. Glutamatergic).
    in_subset:
    - obs
    - annotations
    range: string
  accession_id:
    name: accession_id
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.accession_<level> (data only)
    description: Stable cross-version identifier for this cell type taxon (e.g. CS20230722_CLAS_11).
    in_subset:
    - uns
    - annotations
    range: string
  order:
    name: order
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.display_order_<level> (data only)
    description: The priority or display order of this taxon among all taxons in the
      taxonomy.
    in_subset:
    - uns
    - annotations
    range: integer
  has_parent:
    name: has_parent
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: the taxon at the preceding uns.hierarchy level, same uns.cluster_info
          row)'
    description: Reference to the parent taxon at the next broader annotation level.
    in_subset:
    - uns
    - annotations
    range: CellTypeTaxon
  part_of_set:
    name: part_of_set
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: the uns.hierarchy level whose uns.cluster_info column this
          taxon came from)'
    description: The annotation level (CellTypeSet) for which this taxon is a member.
    in_subset:
    - uns
    - annotations
    range: CellTypeSet
  has_abbreviation:
    name: has_abbreviation
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.tokens_<level> (data only)
      ait_separator:
        tag: ait_separator
        value: '|'
    description: One of potentially many abbreviations that are part of the cell type
      taxon name.
    in_subset:
    - uns
    - annotations
    range: Abbreviation
    multivalued: true
attributes:
  cell_type_ontology_term:
    name: cell_type_ontology_term
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.CL:ID_<level> (data only)
    description: CL ontology term for this cell type; use CL:0000003 for native cell
      if unknown.
    in_subset:
    - obs
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    aliases:
    - cell_type_ontology_term_id
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: string
    pattern: ^CL:\d{7}$
  number_of_cells:
    name: number_of_cells
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: count obs rows grouped by obs.<annotation_level>)'
    description: The aggregated number of cells that defines this cell type taxon.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: integer
  literature_support:
    name: literature_support
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.literature_support
      ait_separator:
        tag: ait_separator
        value: '|'
    description: Published study in which this cell type was previously described.
      The value "Novel" indicates no prior published description.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: string
    multivalued: true
  literature_name_short:
    name: literature_name_short
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.literature_name_short
      ait_separator:
        tag: ait_separator
        value: '|'
    description: Short name used for this cell type in the supporting literature.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: string
    multivalued: true
  literature_name_long:
    name: literature_name_long
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.literature_name_long
      ait_separator:
        tag: ait_separator
        value: '|'
    description: Full name used for this cell type in the supporting literature.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: string
    multivalued: true
  curated_markers:
    name: curated_markers
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.curated_markers
      ait_separator:
        tag: ait_separator
        value: ','
    description: Marker genes curated as characteristic of this cell type. One set
      per taxon; the AIT consensus taxonomy does not split these by species.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: GeneAnnotation
    multivalued: true
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    annotations:
      ait_location:
        tag: ait_location
        value: (synthesized)
    description: Unique identifier for this cell type taxon.
    in_subset:
    - translator_minimal
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    owner: CellTypeTaxon
    domain_of:
    - ontology class
    - entity
    - Cell
    - CellTypeSet
    - CellTypeTaxon
    - CellTypeTaxonomy
    - ClusterSet
    - Cluster
    - ExpressionMatrix
    - Embedding
    - Abbreviation
    - ColorPalette
    - DisplayColor
    - attribute
    - named thing
    - taxonomic rank
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
    required: true
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    annotations:
      ait_location:
        tag: ait_location
        value: obs.<annotation_level>
    description: Human-readable label for this cell type taxon at the given annotation
      level (e.g. Glutamatergic).
    in_subset:
    - obs
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    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
    domain: entity
    slot_uri: rdfs:label
    owner: CellTypeTaxon
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - ColorPalette
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: string
  accession_id:
    name: accession_id
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.accession_<level> (data only)
    description: Stable cross-version identifier for this cell type taxon (e.g. CS20230722_CLAS_11).
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    - CellTypeTaxonomy
    range: string
  order:
    name: order
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.display_order_<level> (data only)
    description: The priority or display order of this taxon among all taxons in the
      taxonomy.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    range: integer
  has_parent:
    name: has_parent
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: the taxon at the preceding uns.hierarchy level, same uns.cluster_info
          row)'
    description: Reference to the parent taxon at the next broader annotation level.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    - Cluster
    range: CellTypeTaxon
  part_of_set:
    name: part_of_set
    annotations:
      ait_location:
        tag: ait_location
        value: '(derived: the uns.hierarchy level whose uns.cluster_info column this
          taxon came from)'
    description: The annotation level (CellTypeSet) for which this taxon is a member.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    - Cluster
    range: CellTypeSet
  has_abbreviation:
    name: has_abbreviation
    annotations:
      ait_location:
        tag: ait_location
        value: uns.cluster_info.tokens_<level> (data only)
      ait_separator:
        tag: ait_separator
        value: '|'
    description: One of potentially many abbreviations that are part of the cell type
      taxon name.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    range: Abbreviation
    multivalued: true
  was_derived_from:
    name: was_derived_from
    description: A derivation is a transformation of an entity into another, an update
      of an entity resulting in a new one, or the construction of a new entity based
      on a pre-existing entity.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    - ProvEntity
    range: ProvEntity
  was_generated_by:
    name: was_generated_by
    description: Generation is the completion of production of a new entity by an
      activity. This entity did not exist before generation and becomes available
      for usage after this generation.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    owner: CellTypeTaxon
    domain_of:
    - ProvEntity
    range: ProvActivity
  mapping_relation:
    name: mapping_relation
    description: 'A mapping of unspecified kind. The honest choice when the relationship
      is not established: it entails nothing, being neither symmetric nor transitive
      and carrying no direction.'
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: skos:mappingRelation
    owner: CellTypeTaxon
    domain_of:
    - OntologyMappable
    range: ontology class
    multivalued: true
  exact_match:
    name: exact_match
    description: 'The external concept is interchangeable with this entity. Symmetric
      AND transitive, so it chains through third-party mappings. Do not use where
      several of our entities map to one external concept: the entailment would then
      assert that those entities are equivalent to each other.'
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: skos:exactMatch
    owner: CellTypeTaxon
    domain_of:
    - OntologyMappable
    range: ontology class
    multivalued: true
  close_match:
    name: close_match
    description: Close enough to be used interchangeably in some applications. Symmetric
      but not transitive. Asserts similarity at the same level, so it is not a substitute
      for broad_match where a hierarchy exists.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: skos:closeMatch
    owner: CellTypeTaxon
    domain_of:
    - OntologyMappable
    range: ontology class
    multivalued: true
  broad_match:
    name: broad_match
    description: The external concept is broader than this entity. Use where several
      of our entities map to a single external concept.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: skos:broadMatch
    owner: CellTypeTaxon
    domain_of:
    - OntologyMappable
    range: ontology class
    multivalued: true
  narrow_match:
    name: narrow_match
    description: The external concept is narrower than this entity.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: skos:narrowMatch
    owner: CellTypeTaxon
    domain_of:
    - OntologyMappable
    range: ontology class
    multivalued: true
  related_match:
    name: related_match
    description: Associatively related. Note that this positively asserts that the
      concepts are NOT equivalent and NOT hierarchically related, so it is a claim
      in its own right rather than a neutral fallback.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: skos:relatedMatch
    owner: CellTypeTaxon
    domain_of:
    - OntologyMappable
    range: ontology class
    multivalued: true
  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://w3id.org/brain-bican/cell-taxonomy
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    owner: CellTypeTaxon
    domain_of:
    - attribute
    - entity
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: iri type
  type:
    name: type
    definition_uri: https://w3id.org/biolink/vocab/type
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    owner: CellTypeTaxon
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    owner: CellTypeTaxon
    domain_of:
    - entity
    - ColorPalette
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    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
    - 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: CellTypeTaxon
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    owner: CellTypeTaxon
    domain_of:
    - entity
    - attribute
    - named thing
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    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
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - gene
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - 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://w3id.org/brain-bican/cell-taxonomy
    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
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: label type
    multivalued: true
  information content:
    name: information content
    definition_uri: https://w3id.org/biolink/vocab/information_content
    description: Information content (IC) value for a term, primarily from Automats.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:information_content
    alias: information_content
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: float
  equivalent identifiers:
    name: equivalent identifiers
    definition_uri: https://w3id.org/biolink/vocab/equivalent_identifiers
    description: A set of identifiers that are considered equivalent to the primary
      identifier of the entity. This attribute is used to represent a collection of
      identifiers that are considered equivalent to the primary identifier of an entity.
      These equivalent identifiers may come from different databases, ontologies,
      or naming conventions, but they all refer to the same underlying concept or
      entity. This attribute is particularly useful in data integration and interoperability
      scenarios, where it is important to recognize and link different representations
      of the same entity across various sources.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    see_also:
    - biolink:xref
    - biolink:synonyms
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:equivalent_identifiers
    alias: equivalent_identifiers
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    range: uriorcurie
    multivalued: true
  named thing_category:
    name: named thing_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}
    in_subset:
    - translator_minimal
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    is_a: category
    domain: named thing
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: CellTypeTaxon
    domain_of:
    - named thing
    - attribute
    - organism taxon
    - study result
    - relative frequency analysis result
    - information content entity
    - dataset
    - physical entity
    - activity
    - procedure
    - material sample
    - biological entity
    - gene
    - genome
    is_class_field: true
    is_usage_slot: true
    usage_slot_name: category
    range: uriorcurie
    required: true
    multivalued: 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}
    in_subset:
    - translator_minimal
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    owner: CellTypeTaxon
    domain_of:
    - entity
    is_class_field: true
    range: uriorcurie
    required: true
    multivalued: true