Class: CellTypeTaxonomy

A systematic classification of cell types and their hierarchical relationships in the mammalian brain, including annotation levels and their corresponding cell type nodes.

URI: [bican:CellTypeTaxonomy](https://identifiers.org/brain-bican/vocab/CellTypeTaxonomy)

classDiagram class CellTypeTaxonomy click CellTypeTaxonomy href "../CellTypeTaxonomy/" ProvEntity <|-- CellTypeTaxonomy click ProvEntity href "../ProvEntity/" NamedThing <|-- CellTypeTaxonomy click NamedThing href "../NamedThing/" CellTypeTaxonomy : accession_id CellTypeTaxonomy : batch_condition CellTypeTaxonomy : category CellTypeTaxonomy : cellannotation_schema CellTypeTaxonomy : cluster_algorithm CellTypeTaxonomy : cluster_info CellTypeTaxonomy : content_url CellTypeTaxonomy : default_embedding CellTypeTaxonomy : dendrogram CellTypeTaxonomy : deprecated CellTypeTaxonomy : description CellTypeTaxonomy : equivalent_identifiers CellTypeTaxonomy : filter CellTypeTaxonomy : full_name CellTypeTaxonomy : has_attribute CellTypeTaxonomy --> "*" Attribute : has_attribute click Attribute href "../Attribute/" CellTypeTaxonomy : has_embedding CellTypeTaxonomy --> "*" Embedding : has_embedding click Embedding href "../Embedding/" CellTypeTaxonomy : has_expression_matrix CellTypeTaxonomy --> "*" ExpressionMatrix : has_expression_matrix click ExpressionMatrix href "../ExpressionMatrix/" CellTypeTaxonomy : hierarchy CellTypeTaxonomy : id CellTypeTaxonomy : information_content CellTypeTaxonomy : iri CellTypeTaxonomy : mode CellTypeTaxonomy : name CellTypeTaxonomy : named_thing_category CellTypeTaxonomy : provided_by CellTypeTaxonomy : quality_control_markers CellTypeTaxonomy : schema_version CellTypeTaxonomy : synonym CellTypeTaxonomy : title CellTypeTaxonomy : type CellTypeTaxonomy : was_derived_from CellTypeTaxonomy --> "*" ClusterSet : was_derived_from click ClusterSet href "../ClusterSet/" CellTypeTaxonomy : was_generated_by CellTypeTaxonomy --> "0..1" ProvActivity : was_generated_by click ProvActivity href "../ProvActivity/" CellTypeTaxonomy : xref

## Inheritance * [Entity](Entity.md) * [NamedThing](NamedThing.md) * **CellTypeTaxonomy** [ [ProvEntity](ProvEntity.md)] ## Slots | Name | Cardinality and Range | Description | Inheritance | | --- | --- | --- | --- | | [was_derived_from](was_derived_from.md) | *
[ClusterSet](ClusterSet.md) | One or more cluster sets from which this taxonomy was derived | direct | | [id](id.md) | 1
[String](String.md) | Unique identifier for this taxonomy | direct | | [accession_id](accession_id.md) | 0..1
[String](String.md) | Provider-assigned accession identifier for this taxonomy (e | direct | | [content_url](content_url.md) | *
[Uri](Uri.md) | Permanent URL to molecular data if the expression matrix is not embedded in t... | direct | | [has_embedding](has_embedding.md) | *
[Embedding](Embedding.md) | One or more dimensionality reductions associated with this taxonomy | direct | | [has_expression_matrix](has_expression_matrix.md) | *
[ExpressionMatrix](ExpressionMatrix.md) | One or more cell-by-gene matrices associated with this taxonomy (normalized a... | direct | | [title](title.md) | 0..1
[String](String.md) | Description differentiating this taxonomy from others in the same collection;... | direct | | [schema_version](schema_version.md) | 0..1
[String](String.md) | Version of the AIT schema used to produce this file (e | direct | | [batch_condition](batch_condition.md) | 0..1
[String](String.md) | Cell metadata key(s) in obs that define batches for normalization or integrat... | direct | | [dendrogram](dendrogram.md) | 0..1
[String](String.md) | JSON-formatted hierarchical clustering dendrogram encoding the taxonomy hiera... | direct | | [hierarchy](hierarchy.md) | 0..1
[String](String.md) | Ordered mapping of annotation level names to integer ranks; lower rank means ... | direct | | [mode](mode.md) | 0..1
[String](String.md) | Active taxonomy mode controlling which subset of cells and analysis component... | direct | | [filter](filter.md) | 0..1
[Boolean](Boolean.md) | Per-mode boolean flags indicating cells to exclude (True means exclude) | direct | | [cluster_algorithm](cluster_algorithm.md) | 0..1
[String](String.md) | Full description of clustering algorithm and parameters used to produce clust... | direct | | [cluster_info](cluster_info.md) | 0..1
[String](String.md) | Summary table of cluster-level metadata including cluster sizes and represent... | direct | | [default_embedding](default_embedding.md) | 0..1
[String](String.md) | Key in obsm of the embedding to display by default; must match an X_-prefixed... | direct | | [cellannotation_schema](cellannotation_schema.md) | 0..1
[String](String.md) | CAS annotation schema stored as JSON encoding labelset and annotation metadat... | direct | | [quality_control_markers](quality_control_markers.md) | 0..1
[String](String.md) | Marker gene expression data for patchseq quality control analysis | direct | | [was_generated_by](was_generated_by.md) | 0..1
[ProvActivity](ProvActivity.md) | Generation is the completion of production of a new entity by an activity | [ProvEntity](ProvEntity.md) | | [iri](iri.md) | 0..1
[IriType](IriType.md) | An IRI for an entity | [NamedThing](NamedThing.md), [Entity](Entity.md) | | [type](type.md) | *
[String](String.md) | | [NamedThing](NamedThing.md), [Entity](Entity.md) | | [name](name.md) | 0..1
[LabelType](LabelType.md) | A human-readable name for an attribute or entity | [NamedThing](NamedThing.md), [Entity](Entity.md) | | [description](description.md) | 0..1
[NarrativeText](NarrativeText.md) | a human-readable description of an entity | [NamedThing](NamedThing.md), [Entity](Entity.md) | | [has_attribute](has_attribute.md) | *
[Attribute](Attribute.md) | connects any entity to an attribute | [NamedThing](NamedThing.md), [Entity](Entity.md) | | [deprecated](deprecated.md) | 0..1
[Boolean](Boolean.md) | A boolean flag indicating that an entity is no longer considered current or v... | [NamedThing](NamedThing.md), [Entity](Entity.md) | | [provided_by](provided_by.md) | *
[String](String.md) | The value in this node property represents the knowledge provider that create... | [NamedThing](NamedThing.md) | | [xref](xref.md) | *
[Uriorcurie](Uriorcurie.md) | A database cross reference or alternative identifier for a NamedThing or edge... | [NamedThing](NamedThing.md) | | [full_name](full_name.md) | 0..1
[LabelType](LabelType.md) | a long-form human readable name for a thing | [NamedThing](NamedThing.md) | | [synonym](synonym.md) | *
[LabelType](LabelType.md) | Alternate human-readable names for a thing | [NamedThing](NamedThing.md) | | [information_content](information_content.md) | 0..1
[Float](Float.md) | Information content (IC) value for a term, primarily from Automats | [NamedThing](NamedThing.md) | | [equivalent_identifiers](equivalent_identifiers.md) | *
[Uriorcurie](Uriorcurie.md) | A set of identifiers that are considered equivalent to the primary identifier... | [NamedThing](NamedThing.md) | | [named_thing_category](named_thing_category.md) | 1..*
[Uriorcurie](Uriorcurie.md) | Name of the high level ontology class in which this entity is categorized | [NamedThing](NamedThing.md) | | [category](category.md) | 1..*
[Uriorcurie](Uriorcurie.md) | Name of the high level ontology class in which this entity is categorized | [Entity](Entity.md) | ## Usages | used by | used in | type | used | | --- | --- | --- | --- | | [CellTypeSet](CellTypeSet.md) | [part_of_taxonomy](part_of_taxonomy.md) | range | [CellTypeTaxonomy](CellTypeTaxonomy.md) | ## Identifier and Mapping Information ### Schema Source * from schema: https://w3id.org/brain-bican/cell-taxonomy ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | bican:CellTypeTaxonomy | | native | bican:CellTypeTaxonomy | ## LinkML Source ### Direct

name: CellTypeTaxonomy
description: A systematic classification of cell types and their hierarchical relationships
  in the mammalian brain, including annotation levels and their corresponding cell
  type nodes.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
is_a: named thing
mixins:
- ProvEntity
slots:
- was_derived_from
- id
- accession_id
- content_url
slot_usage:
  was_derived_from:
    name: was_derived_from
    description: One or more cluster sets from which this taxonomy was derived.
    range: ClusterSet
    multivalued: true
  id:
    name: id
    description: Unique identifier for this taxonomy.
    from_schema: bican_biolink
    range: string
  accession_id:
    name: accession_id
    description: Provider-assigned accession identifier for this taxonomy (e.g. CCN20230722).
    in_subset:
    - uns
    - tooling
    range: string
  content_url:
    name: content_url
    description: Permanent URL to molecular data if the expression matrix is not embedded
      in the file.
    in_subset:
    - uns
    - data
    from_schema: bican_core
    range: uri
attributes:
  has_embedding:
    name: has_embedding
    description: One or more dimensionality reductions associated with this taxonomy.
    in_subset:
    - obsm
    - analysis
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: Embedding
    multivalued: true
  has_expression_matrix:
    name: has_expression_matrix
    description: One or more cell-by-gene matrices associated with this taxonomy (normalized
      and/or raw counts).
    in_subset:
    - X
    - raw
    - data
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: ExpressionMatrix
    multivalued: true
  title:
    name: title
    description: Description differentiating this taxonomy from others in the same
      collection; should be unique within a collection.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  schema_version:
    name: schema_version
    description: Version of the AIT schema used to produce this file (e.g. 1.0.0).
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  batch_condition:
    name: batch_condition
    description: Cell metadata key(s) in obs that define batches for normalization
      or integration.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  dendrogram:
    name: dendrogram
    description: JSON-formatted hierarchical clustering dendrogram encoding the taxonomy
      hierarchy.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  hierarchy:
    name: hierarchy
    description: Ordered mapping of annotation level names to integer ranks; lower
      rank means broader type.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  mode:
    name: mode
    description: Active taxonomy mode controlling which subset of cells and analysis
      components to use.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  filter:
    name: filter
    description: Per-mode boolean flags indicating cells to exclude (True means exclude).
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: boolean
  cluster_algorithm:
    name: cluster_algorithm
    description: Full description of clustering algorithm and parameters used to produce
      cluster assignments.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  cluster_info:
    name: cluster_info
    description: Summary table of cluster-level metadata including cluster sizes and
      representative metadata.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  default_embedding:
    name: default_embedding
    description: Key in obsm of the embedding to display by default; must match an
      X_-prefixed entry.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  cellannotation_schema:
    name: cellannotation_schema
    description: CAS annotation schema stored as JSON encoding labelset and annotation
      metadata.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string
  quality_control_markers:
    name: quality_control_markers
    description: Marker gene expression data for patchseq quality control analysis.
    in_subset:
    - uns
    - analysis
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    domain_of:
    - CellTypeTaxonomy
    range: string

### Induced

name: CellTypeTaxonomy
description: A systematic classification of cell types and their hierarchical relationships
  in the mammalian brain, including annotation levels and their corresponding cell
  type nodes.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
is_a: named thing
mixins:
- ProvEntity
slot_usage:
  was_derived_from:
    name: was_derived_from
    description: One or more cluster sets from which this taxonomy was derived.
    range: ClusterSet
    multivalued: true
  id:
    name: id
    description: Unique identifier for this taxonomy.
    from_schema: bican_biolink
    range: string
  accession_id:
    name: accession_id
    description: Provider-assigned accession identifier for this taxonomy (e.g. CCN20230722).
    in_subset:
    - uns
    - tooling
    range: string
  content_url:
    name: content_url
    description: Permanent URL to molecular data if the expression matrix is not embedded
      in the file.
    in_subset:
    - uns
    - data
    from_schema: bican_core
    range: uri
attributes:
  has_embedding:
    name: has_embedding
    description: One or more dimensionality reductions associated with this taxonomy.
    in_subset:
    - obsm
    - analysis
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: Embedding
    multivalued: true
  has_expression_matrix:
    name: has_expression_matrix
    description: One or more cell-by-gene matrices associated with this taxonomy (normalized
      and/or raw counts).
    in_subset:
    - X
    - raw
    - data
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: ExpressionMatrix
    multivalued: true
  title:
    name: title
    description: Description differentiating this taxonomy from others in the same
      collection; should be unique within a collection.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  schema_version:
    name: schema_version
    description: Version of the AIT schema used to produce this file (e.g. 1.0.0).
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  batch_condition:
    name: batch_condition
    description: Cell metadata key(s) in obs that define batches for normalization
      or integration.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  dendrogram:
    name: dendrogram
    description: JSON-formatted hierarchical clustering dendrogram encoding the taxonomy
      hierarchy.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  hierarchy:
    name: hierarchy
    description: Ordered mapping of annotation level names to integer ranks; lower
      rank means broader type.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  mode:
    name: mode
    description: Active taxonomy mode controlling which subset of cells and analysis
      components to use.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  filter:
    name: filter
    description: Per-mode boolean flags indicating cells to exclude (True means exclude).
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: boolean
  cluster_algorithm:
    name: cluster_algorithm
    description: Full description of clustering algorithm and parameters used to produce
      cluster assignments.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  cluster_info:
    name: cluster_info
    description: Summary table of cluster-level metadata including cluster sizes and
      representative metadata.
    in_subset:
    - uns
    - annotations
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  default_embedding:
    name: default_embedding
    description: Key in obsm of the embedding to display by default; must match an
      X_-prefixed entry.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  cellannotation_schema:
    name: cellannotation_schema
    description: CAS annotation schema stored as JSON encoding labelset and annotation
      metadata.
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  quality_control_markers:
    name: quality_control_markers
    description: Marker gene expression data for patchseq quality control analysis.
    in_subset:
    - uns
    - analysis
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    range: string
  was_derived_from:
    name: was_derived_from
    description: One or more cluster sets from which this taxonomy was derived.
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    - ProvEntity
    range: ClusterSet
    multivalued: true
  id:
    name: id
    definition_uri: https://w3id.org/biolink/vocab/id
    description: Unique identifier for this taxonomy.
    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
    owner: CellTypeTaxonomy
    domain_of:
    - ontology class
    - entity
    - Cell
    - CellTypeSet
    - CellTypeTaxon
    - CellTypeTaxonomy
    - ClusterSet
    - Cluster
    - ExpressionMatrix
    - Embedding
    - 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: Provider-assigned accession identifier for this taxonomy (e.g. CCN20230722).
    in_subset:
    - uns
    - tooling
    from_schema: https://w3id.org/brain-bican/cell-taxonomy
    rank: 1000
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxon
    - CellTypeTaxonomy
    range: string
  content_url:
    name: content_url
    description: Permanent URL to molecular data if the expression matrix is not embedded
      in the file.
    in_subset:
    - uns
    - data
    from_schema: bican_core
    rank: 1000
    slot_uri: schema:url
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    - ExpressionMatrix
    - GenomeAnnotation
    range: uri
    multivalued: true
  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: CellTypeTaxonomy
    domain_of:
    - 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/cell-taxonomy
    exact_mappings:
    - WIKIDATA_PROPERTY:P854
    rank: 1000
    slot_uri: biolink:iri
    owner: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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
  name:
    name: name
    definition_uri: https://w3id.org/biolink/vocab/name
    description: A human-readable name for an attribute or entity.
    in_subset:
    - translator_minimal
    - samples
    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: CellTypeTaxonomy
    domain_of:
    - attribute
    - entity
    - macromolecular machine mixin
    - CellTypeSet
    - CellTypeTaxon
    - ClusterSet
    - Cluster
    - 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: label type
  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: CellTypeTaxonomy
    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: 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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    domain_of:
    - entity
    is_class_field: true
    range: uriorcurie
    required: true
    multivalued: true