Class: CellTypeTaxonomy

name: CellTypeTaxonomy
description: A cell type taxonomy is a systematic classification of cell types and
  their heirarchical relationships and groupings. A taxonomy may include concepts
  such as heirarchical taxonomic levels or (potentially overlapping) neighborhoods.
from_schema: https://w3id.org/brain-bican/bke-taxonomy
is_a: named thing
mixins:
- ProvEntity
slots:
- was_generated_by
- was_derived_from
- is_revision_of
- id
- creation date
- accession_id
- name
- description
- xref
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The analysis process from which the cell types taxonomy was generated
      by.
    from_schema: bican_prov
    range: CellTypeTaxonomyCreationProcess
  was_derived_from:
    name: was_derived_from
    description: One of potentially many input clusters set from which the cell type
      taxonomy is derived.
    from_schema: bican_prov
    range: ClusterSet
    multivalued: true
  is_revision_of:
    name: is_revision_of
    description: The previous version for which this cell type taxonomy is a revision
      of.
    range: CellTypeTaxonomy
  id:
    name: id
    description: ( database GUID)
    from_schema: bican_biolink
    range: string
  creation date:
    name: creation date
    description: The creation date of the cell type taxonomy.
    from_schema: bican_biolink
  accession_id:
    name: accession_id
    description: A provider assigned accession identifier for the taxonomy.
    examples:
    - value: CCN20230722
    range: string
  name:
    name: name
    description: Name of the cell type taxonomy.
    examples:
    - value: AIT21.0
    from_schema: bican_biolink
    range: string
  description:
    name: description
    description: Description of the cell type taxonomy.
    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

name: CellTypeTaxonomy
description: A cell type taxonomy is a systematic classification of cell types and
  their heirarchical relationships and groupings. A taxonomy may include concepts
  such as heirarchical taxonomic levels or (potentially overlapping) neighborhoods.
from_schema: https://w3id.org/brain-bican/bke-taxonomy
is_a: named thing
mixins:
- ProvEntity
slot_usage:
  was_generated_by:
    name: was_generated_by
    description: The analysis process from which the cell types taxonomy was generated
      by.
    from_schema: bican_prov
    range: CellTypeTaxonomyCreationProcess
  was_derived_from:
    name: was_derived_from
    description: One of potentially many input clusters set from which the cell type
      taxonomy is derived.
    from_schema: bican_prov
    range: ClusterSet
    multivalued: true
  is_revision_of:
    name: is_revision_of
    description: The previous version for which this cell type taxonomy is a revision
      of.
    range: CellTypeTaxonomy
  id:
    name: id
    description: ( database GUID)
    from_schema: bican_biolink
    range: string
  creation date:
    name: creation date
    description: The creation date of the cell type taxonomy.
    from_schema: bican_biolink
  accession_id:
    name: accession_id
    description: A provider assigned accession identifier for the taxonomy.
    examples:
    - value: CCN20230722
    range: string
  name:
    name: name
    description: Name of the cell type taxonomy.
    examples:
    - value: AIT21.0
    from_schema: bican_biolink
    range: string
  description:
    name: description
    description: Description of the cell type taxonomy.
    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:
  was_generated_by:
    name: was_generated_by
    description: The analysis process from which the cell types taxonomy was generated
      by.
    from_schema: bican_prov
    rank: 1000
    slot_uri: prov:wasGeneratedBy
    alias: was_generated_by
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    - ObservationMatrix
    - ProvEntity
    range: CellTypeTaxonomyCreationProcess
  was_derived_from:
    name: was_derived_from
    description: One of potentially many input clusters set from which the cell type
      taxonomy is derived.
    from_schema: bican_prov
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    alias: was_derived_from
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    - ObservationMatrix
    - ObservationRow
    - ProvEntity
    range: ClusterSet
    multivalued: true
  is_revision_of:
    name: is_revision_of
    description: The previous version for which this cell type taxonomy is a revision
      of.
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: is_revision_of
    owner: CellTypeTaxonomy
    domain_of:
    - CellTypeTaxonomy
    - ClusterSet
    range: CellTypeTaxonomy
  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: CellTypeTaxonomy
    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
  creation date:
    name: creation date
    definition_uri: https://w3id.org/biolink/vocab/creation_date
    description: The creation date of the cell type taxonomy.
    from_schema: bican_biolink
    aliases:
    - publication date
    - date started
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:creation_date
    alias: creation_date
    owner: CellTypeTaxonomy
    domain_of:
    - information content entity
    - CellTypeTaxonomy
    - ClusterSet
    - study result
    - relative frequency analysis result
    - dataset
    range: date
  accession_id:
    name: accession_id
    description: A provider assigned accession identifier for the taxonomy.
    examples:
    - value: CCN20230722
    from_schema: https://w3id.org/brain-bican/bke-taxonomy
    rank: 1000
    alias: accession_id
    owner: CellTypeTaxonomy
    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 taxonomy.
    examples:
    - value: AIT21.0
    in_subset:
    - translator_minimal
    - samples
    from_schema: bican_biolink
    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: CellTypeTaxonomy
    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
  description:
    name: description
    definition_uri: https://w3id.org/biolink/vocab/description
    description: Description of the cell type taxonomy.
    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: CellTypeTaxonomy
    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: CellTypeTaxonomy
    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
  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: 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/bke-taxonomy
    mappings:
    - rdf:type
    exact_mappings:
    - gff3:type
    - gpi:DB_Object_Type
    rank: 1000
    domain: entity
    slot_uri: rdf:type
    alias: 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
  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: 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/bke-taxonomy
    exact_mappings:
    - oboInOwl:ObsoleteClass
    rank: 1000
    slot_uri: biolink:deprecated
    alias: 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/bke-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
  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: 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/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: 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/bke-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/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: 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/bke-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/bke-taxonomy
    rank: 1000
    is_a: type
    domain: entity
    slot_uri: biolink:category
    designates_type: true
    alias: category
    owner: CellTypeTaxonomy
    domain_of:
    - entity
    is_class_field: true
    range: uriorcurie
    required: true
    multivalued: true