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Class: CellTypeTaxon

A cell type taxon is a node in a taxonomy. Taxons represents a unit of cell type classification and is defined by a set of clusters. Taxons may be organized into a heirarchy and levels. Taxons at higher levels represents broader cell type classes and partitioned into more specific types at lower levels. Additionally, taxons may be organized into neighborhoods or related groups.

URI: bican:CellTypeTaxon

classDiagram class CellTypeTaxon click CellTypeTaxon href "../CellTypeTaxon" ProvEntity <|-- CellTypeTaxon click ProvEntity href "../ProvEntity" NamedThing <|-- CellTypeTaxon click NamedThing href "../NamedThing" CellTypeTaxon : accession_id CellTypeTaxon : category CellTypeTaxon : contains_cluster CellTypeTaxon --> "*" Cluster : contains_cluster click Cluster href "../Cluster" CellTypeTaxon : curated_markers_to_mouse CellTypeTaxon --> "*" GeneAnnotation : curated_markers_to_mouse click GeneAnnotation href "../GeneAnnotation" CellTypeTaxon : curated_markers_to_primates CellTypeTaxon --> "*" GeneAnnotation : curated_markers_to_primates click GeneAnnotation href "../GeneAnnotation" CellTypeTaxon : deprecated CellTypeTaxon : description CellTypeTaxon : equivalent_identifiers CellTypeTaxon : full_name CellTypeTaxon : has_attribute CellTypeTaxon --> "*" Attribute : has_attribute click Attribute href "../Attribute" CellTypeTaxon : has_abbreviation CellTypeTaxon --> "*" Abbreviation : has_abbreviation click Abbreviation href "../Abbreviation" CellTypeTaxon : has_parent CellTypeTaxon --> "0..1" CellTypeTaxon : has_parent click CellTypeTaxon href "../CellTypeTaxon" CellTypeTaxon : id CellTypeTaxon : information_content CellTypeTaxon : iri CellTypeTaxon : name CellTypeTaxon : named_thing_category CellTypeTaxon : number_of_cells CellTypeTaxon : order CellTypeTaxon : part_of_taxonomy CellTypeTaxon --> "0..1" CellTypeTaxonomy : part_of_taxonomy click CellTypeTaxonomy href "../CellTypeTaxonomy" CellTypeTaxon : provided_by CellTypeTaxon : spatial_proportions_human CellTypeTaxon --> "0..1" SpatialProportions : spatial_proportions_human click SpatialProportions href "../SpatialProportions" CellTypeTaxon : spatial_proportions_macaque CellTypeTaxon --> "0..1" SpatialProportions : spatial_proportions_macaque click SpatialProportions href "../SpatialProportions" CellTypeTaxon : spatial_proportions_marmoset CellTypeTaxon --> "0..1" SpatialProportions : spatial_proportions_marmoset click SpatialProportions href "../SpatialProportions" CellTypeTaxon : spatial_regional_proportions CellTypeTaxon --> "0..1" SpatialProportions : spatial_regional_proportions click SpatialProportions href "../SpatialProportions" CellTypeTaxon : synonym CellTypeTaxon : type CellTypeTaxon : was_derived_from CellTypeTaxon --> "0..1" ProvEntity : was_derived_from click ProvEntity href "../ProvEntity" CellTypeTaxon : was_generated_by CellTypeTaxon --> "0..1" ProvActivity : was_generated_by click ProvActivity href "../ProvActivity" CellTypeTaxon : xref

Inheritance

Slots

Name Cardinality and Range Description Inheritance
part_of_taxonomy 0..1
CellTypeTaxonomy		 The cell types taxonomy for which the cell type taxon is part of direct
has_parent 0..1
CellTypeTaxon		 When the taxonomy is a single inheritance tree, the parent represents the sup... direct
has_abbreviation *
Abbreviation		 One of many abbreviation that are part of the cell type taxon name direct
id 1
String		 ( database GUID) direct
accession_id 0..1
String		 A provider assigned accession identifier for the cell type taxon direct
name 0..1
String		 Name of the cell type taxon direct
order 0..1
Integer		 The priority or display order of the cell type taxon among all other taxons i... direct
description 0..1
String		 Description of the cell type taxon (optional) direct
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... direct
contains_cluster *
Cluster		 One of potentially cell clusters which together defines the cell type taxon direct
spatial_regional_proportions 0..1
SpatialProportions		 Species-independent quantification of regional composition (how much of somet... direct
spatial_proportions_marmoset 0..1
SpatialProportions		 Quantification of regional composition (how much of something is found in eac... direct
spatial_proportions_macaque 0..1
SpatialProportions		 Quantification of regional composition (how much of something is found in eac... direct
spatial_proportions_human 0..1
SpatialProportions		 Quantification of regional composition (how much of something is found in eac... direct
curated_markers_to_primates *
GeneAnnotation		 Marker genes in the primate species that are related to the respective cell t... direct
curated_markers_to_mouse *
GeneAnnotation		 Marker genes in the mouse species that are related to the respective cell typ... direct
number_of_cells 0..1
Integer		 The aggregated number of cells that defines the cell type taxon direct
was_derived_from 0..1
ProvEntity		 A derivation is a transformation of an entity into another, an update of an e... ProvEntity
was_generated_by 0..1
ProvActivity		 Generation is the completion of production of a new entity by an activity ProvEntity
iri 0..1
IriType		 An IRI for an entity NamedThing, Entity
type *
String		 NamedThing, Entity
has_attribute *
Attribute		 connects any entity to an attribute NamedThing, Entity
deprecated 0..1
Boolean		 A boolean flag indicating that an entity is no longer considered current or v... NamedThing, Entity
provided_by *
String		 The value in this node property represents the knowledge provider that create... NamedThing
full_name 0..1
LabelType		 a long-form human readable name for a thing NamedThing
synonym *
LabelType		 Alternate human-readable names for a thing NamedThing
information_content 0..1
Float		 Information content (IC) value for a term, primarily from Automats NamedThing
equivalent_identifiers *
Uriorcurie		 A set of identifiers that are considered equivalent to the primary identifier... NamedThing
named_thing_category 1..*
Uriorcurie		 Name of the high level ontology class in which this entity is categorized NamedThing
category 1..*
Uriorcurie		 Name of the high level ontology class in which this entity is categorized Entity

Usages

used by used in type used
CellTypeSet contains_taxon range CellTypeTaxon
CellTypeTaxon has_parent range CellTypeTaxon
Abbreviation denotes_cell_type range CellTypeTaxon
DisplayColor is_color_for_taxon range CellTypeTaxon

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/brain-bican/bke-taxonomy

Mappings

Mapping Type Mapped Value
self bican:CellTypeTaxon
native bican:CellTypeTaxon

LinkML Source

Direct

name: CellTypeTaxon
description: A cell type taxon is a node in a taxonomy. Taxons represents a unit of
  cell type classification and is defined by a set of clusters. Taxons may be organized
  into a heirarchy and levels. Taxons at higher levels represents broader cell type
  classes and partitioned into more specific types at lower levels. Additionally,
  taxons may be organized into neighborhoods or related groups.
from_schema: https://w3id.org/brain-bican/bke-taxonomy
is_a: named thing
mixins:
- ProvEntity
slots:
- part_of_taxonomy
- has_parent
- has_abbreviation
- id
- accession_id
- name
- order
- description
- xref
slot_usage:
  part_of_taxonomy:
    name: part_of_taxonomy
    description: The cell types taxonomy for which the cell type taxon is part of.
    range: CellTypeTaxonomy
  has_parent:
    name: has_parent
    description: When the taxonomy is a single inheritance tree, the parent represents
      the superclass for which the cell type taxon is a member of.
    range: CellTypeTaxon
  has_abbreviation:
    name: has_abbreviation
    description: One of many abbreviation that are part of the cell type taxon name.
    range: Abbreviation
    multivalued: true
  id:
    name: id
    description: ( database GUID)
    from_schema: bican_biolink
    range: string
  accession_id:
    name: accession_id
    description: A provider assigned accession identifier for the cell type taxon.
    examples:
    - value: CS20230722_CLAS_11
    range: string
  name:
    name: name
    description: Name of the cell type taxon.
    examples:
    - value: 11 CNU-HYa GABA
    range: string
  order:
    name: order
    local_names:
      allen:
        local_name_source: allen
        local_name_value: order_idx
    description: The priority or display order of the cell type taxon among all other
      taxons in the taxonomy.
    examples:
    - value: '11'
    range: integer
    minimum_value: '0.0'
  description:
    name: description
    description: Description of the cell type taxon (optional).
    from_schema: bican_biolink
    range: string
  xref:
    name: xref
    local_names:
      allen:
        local_name_source: allen
        local_name_value: unique_id
    from_schema: bican_biolink
attributes:
  contains_cluster:
    name: contains_cluster
    description: One of potentially cell clusters which together defines the cell
      type taxon.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: Cluster
    multivalued: true
  spatial_regional_proportions:
    name: spatial_regional_proportions
    description: Species-independent quantification of regional composition (how much
      of something is found in each named brain region),
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  spatial_proportions_marmoset:
    name: spatial_proportions_marmoset
    description: Quantification of regional composition (how much of something is
      found in each named brain region) in Marmoset species.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  spatial_proportions_macaque:
    name: spatial_proportions_macaque
    description: Quantification of regional composition (how much of something is
      found in each named brain region) in Macaque species.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  spatial_proportions_human:
    name: spatial_proportions_human
    description: Quantification of regional composition (how much of something is
      found in each named brain region) in Human species.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  curated_markers_to_primates:
    name: curated_markers_to_primates
    description: Marker genes in the primate species that are related to the respective
      cell type.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: GeneAnnotation
    multivalued: true
  curated_markers_to_mouse:
    name: curated_markers_to_mouse
    description: Marker genes in the mouse species that are related to the respective
      cell type.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: GeneAnnotation
    multivalued: true
  number_of_cells:
    name: number_of_cells
    description: The aggregated number of cells that defines the cell type taxon.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxon
    range: integer
    minimum_value: '0.0'

Induced

name: CellTypeTaxon
description: A cell type taxon is a node in a taxonomy. Taxons represents a unit of
  cell type classification and is defined by a set of clusters. Taxons may be organized
  into a heirarchy and levels. Taxons at higher levels represents broader cell type
  classes and partitioned into more specific types at lower levels. Additionally,
  taxons may be organized into neighborhoods or related groups.
from_schema: https://w3id.org/brain-bican/bke-taxonomy
is_a: named thing
mixins:
- ProvEntity
slot_usage:
  part_of_taxonomy:
    name: part_of_taxonomy
    description: The cell types taxonomy for which the cell type taxon is part of.
    range: CellTypeTaxonomy
  has_parent:
    name: has_parent
    description: When the taxonomy is a single inheritance tree, the parent represents
      the superclass for which the cell type taxon is a member of.
    range: CellTypeTaxon
  has_abbreviation:
    name: has_abbreviation
    description: One of many abbreviation that are part of the cell type taxon name.
    range: Abbreviation
    multivalued: true
  id:
    name: id
    description: ( database GUID)
    from_schema: bican_biolink
    range: string
  accession_id:
    name: accession_id
    description: A provider assigned accession identifier for the cell type taxon.
    examples:
    - value: CS20230722_CLAS_11
    range: string
  name:
    name: name
    description: Name of the cell type taxon.
    examples:
    - value: 11 CNU-HYa GABA
    range: string
  order:
    name: order
    local_names:
      allen:
        local_name_source: allen
        local_name_value: order_idx
    description: The priority or display order of the cell type taxon among all other
      taxons in the taxonomy.
    examples:
    - value: '11'
    range: integer
    minimum_value: '0.0'
  description:
    name: description
    description: Description of the cell type taxon (optional).
    from_schema: bican_biolink
    range: string
  xref:
    name: xref
    local_names:
      allen:
        local_name_source: allen
        local_name_value: unique_id
    from_schema: bican_biolink
attributes:
  contains_cluster:
    name: contains_cluster
    description: One of potentially cell clusters which together defines the cell
      type taxon.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: contains_cluster
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: Cluster
    multivalued: true
  spatial_regional_proportions:
    name: spatial_regional_proportions
    description: Species-independent quantification of regional composition (how much
      of something is found in each named brain region),
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: spatial_regional_proportions
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  spatial_proportions_marmoset:
    name: spatial_proportions_marmoset
    description: Quantification of regional composition (how much of something is
      found in each named brain region) in Marmoset species.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: spatial_proportions_marmoset
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  spatial_proportions_macaque:
    name: spatial_proportions_macaque
    description: Quantification of regional composition (how much of something is
      found in each named brain region) in Macaque species.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: spatial_proportions_macaque
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  spatial_proportions_human:
    name: spatial_proportions_human
    description: Quantification of regional composition (how much of something is
      found in each named brain region) in Human species.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: spatial_proportions_human
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: SpatialProportions
  curated_markers_to_primates:
    name: curated_markers_to_primates
    description: Marker genes in the primate species that are related to the respective
      cell type.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: curated_markers_to_primates
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: GeneAnnotation
    multivalued: true
  curated_markers_to_mouse:
    name: curated_markers_to_mouse
    description: Marker genes in the mouse species that are related to the respective
      cell type.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: curated_markers_to_mouse
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: GeneAnnotation
    multivalued: true
  number_of_cells:
    name: number_of_cells
    description: The aggregated number of cells that defines the cell type taxon.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: number_of_cells
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxon
    range: integer
    minimum_value: '0.0'
  part_of_taxonomy:
    name: part_of_taxonomy
    description: The cell types taxonomy for which the cell type taxon is part of.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: part_of_taxonomy
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    range: CellTypeTaxonomy
  has_parent:
    name: has_parent
    description: When the taxonomy is a single inheritance tree, the parent represents
      the superclass for which the cell type taxon is a member of.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: has_parent
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    range: CellTypeTaxon
  has_abbreviation:
    name: has_abbreviation
    description: One of many abbreviation that are part of the cell type taxon name.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: has_abbreviation
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    range: Abbreviation
    multivalued: true
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    description: ( database GUID)
    in_subset:
    - translator_minimal
    from_schema: bican_biolink
    exact_mappings:
    - AGRKB:primaryId
    - gff3:ID
    - gpi:DB_Object_ID
    rank: 1000
    domain: entity
    slot_uri: biolink:id
    identifier: true
    alias: id
    owner: CellTypeTaxon
    domain_of:
    - ontology class
    - entity
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - 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
  accession_id:
    name: accession_id
    description: A provider assigned accession identifier for the cell type taxon.
    examples:
    - value: CS20230722_CLAS_11
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: accession_id
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    range: string
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: Name of the cell type taxon.
    examples:
    - value: 11 CNU-HYa GABA
    in_subset:
    - translator_minimal
    - samples
    from_schema: https://w3id.org/brain-bican/bke-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
    alias: name
    owner: CellTypeTaxon
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - CellTypeTaxonomy
    - 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
  order:
    name: order
    local_names:
      allen:
        local_name_source: allen
        local_name_value: order_idx
    description: The priority or display order of the cell type taxon among all other
      taxons in the taxonomy.
    examples:
    - value: '11'
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: order
    owner: CellTypeTaxon
    domain_of:
    - CellTypeSet
    - CellTypeTaxon
    range: integer
    minimum_value: '0.0'
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: Description of the cell type taxon (optional).
    in_subset:
    - translator_minimal
    from_schema: bican_biolink
    aliases:
    - definition
    mappings:
    - dct:description
    exact_mappings:
    - IAO:0000115
    - skos:definitions
    narrow_mappings:
    - gff3:Description
    rank: 1000
    slot_uri: dct:description
    alias: description
    owner: CellTypeTaxon
    domain_of:
    - entity
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - 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: string
  xref:
    name: xref
    definition_uri: https://w3id.org/biolink/vocab/xref
    local_names:
      allen:
        local_name_source: allen
        local_name_value: unique_id
    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: bican_biolink
    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: CellTypeTaxon
    domain_of:
    - named thing
    - gene
    - CellTypeTaxonomy
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - ObservationMatrix
    - ObservationRow
    - Abbreviation
    - MatrixFile
    - ColorPalette
    - DisplayColor
    - 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
  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/bke-taxonomy
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    alias: was_derived_from
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    - ObservationMatrix
    - ObservationRow
    - 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/bke-taxonomy
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: CellTypeTaxon
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    - ObservationMatrix
    - ProvEntity
    range: ProvActivity
  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/bke-taxonomy
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    alias: 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/bke-taxonomy
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: 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
  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/bke-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/bke-taxonomy
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: 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/bke-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
  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/bke-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/bke-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
    alias: 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/bke-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/bke-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/bke-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/bke-taxonomy
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: CellTypeTaxon
    domain_of:
    - entity
    is_class_field: true
    range: uriorcurie
    required: true
    multivalued: true