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 : deprecated
CellTypeTaxon : description
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 : iri
CellTypeTaxon : name
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 : 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
- Entity
- NamedThing
- CellTypeTaxon [ ProvEntity]
- NamedThing
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 |
contains_cluster | * Cluster |
One of potentially cell clusters which together defines the cell type taxon | 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 |
number_of_cells | 0..1 Integer |
The aggregated number of cells that defines the cell type taxon | direct |
xref | * Uriorcurie |
A database cross reference or alternative identifier for a NamedThing or edge... | 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 |
category | * Curie |
Name of the high level ontology class in which this entity is categorized | 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 |
Usages
used by | used in | type | used |
---|---|---|---|
CellTypeSet | contains_taxon | range | CellTypeTaxon |
CellTypeTaxon | has_parent | 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
- contains_cluster
- has_parent
- has_abbreviation
- id
- accession_id
- name
- order
- description
- number_of_cells
- 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
contains_cluster:
name: contains_cluster
description: One of potentially cell clusters which together defines the cell
type taxon.
range: Cluster
multivalued: true
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)
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).
range: string
number_of_cells:
name: number_of_cells
description: The aggregated number of cells that defines the cell type taxon.
range: integer
minimum_value: '0.0'
xref:
name: xref
local_names:
allen:
local_name_source: allen
local_name_value: unique_id
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
contains_cluster:
name: contains_cluster
description: One of potentially cell clusters which together defines the cell
type taxon.
range: Cluster
multivalued: true
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)
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).
range: string
number_of_cells:
name: number_of_cells
description: The aggregated number of cells that defines the cell type taxon.
range: integer
minimum_value: '0.0'
xref:
name: xref
local_names:
allen:
local_name_source: allen
local_name_value: unique_id
attributes:
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
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
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: https:/w3id.org/brain-bican/bke-taxonomy
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
- 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
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene or gene product
- 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: https:/w3id.org/brain-bican/bke-taxonomy
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
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: string
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'
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: https:/w3id.org/brain-bican/bke-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
alias: xref
owner: CellTypeTaxon
domain_of:
- named thing
- gene
- CellTypeTaxonomy
- CellTypeSet
- CellTypeTaxon
- ClusterSet
- Cluster
- Abbreviation
- ColorPalette
- DisplayColor
- attribute
- organism taxon
- 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
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: iri type
category:
name: category
definition_uri: https://w3id.org/biolink/vocab/category
description: 'Name of the high level ontology class in which this entity is categorized.
Corresponds to the label for the biolink entity type class. In a neo4j database
this MAY correspond to the neo4j label tag. In an RDF database it should be
a biolink model class URI. This field is multi-valued. It should include values
for ancestors of the biolink class; for example, a protein such as Shh would
have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
In an RDF database, nodes will typically have an rdf:type triples. This can
be to the most specific biolink class, or potentially to a class more specific
than something in biolink. For example, a sequence feature `f` may have a rdf:type
assertion to a SO class such as TF_binding_site, which is more specific than
anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
biolink:NamedThing}. NOTE: The category slot was modified to have a curie range
and a pattern for bican categories.'
in_subset:
- translator_minimal
from_schema: https:/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
- attribute
- named thing
- organism taxon
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
is_class_field: true
range: curie
multivalued: true
pattern: ^bican:[A-Z][A-Za-z]+$
type:
name: type
definition_uri: https://w3id.org/biolink/vocab/type
from_schema: https:/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
- 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
- OMIM:has_inheritance_type
- orphanet:C016
- orphanet:C017
- RO:0000053
- RO:0000086
- RO:0000087
- SNOMED:has_access
- SNOMED:has_clinical_course
- SNOMED:has_count_of_base_of_active_ingredient
- SNOMED:has_dose_form_administration_method
- SNOMED:has_dose_form_release_characteristic
- SNOMED:has_dose_form_transformation
- SNOMED:has_finding_context
- SNOMED:has_finding_informer
- SNOMED:has_inherent_attribute
- SNOMED:has_intent
- SNOMED:has_interpretation
- SNOMED:has_laterality
- SNOMED:has_measurement_method
- SNOMED:has_method
- SNOMED:has_priority
- SNOMED:has_procedure_context
- SNOMED:has_process_duration
- SNOMED:has_property
- SNOMED:has_revision_status
- SNOMED:has_scale_type
- SNOMED:has_severity
- SNOMED:has_specimen
- SNOMED:has_state_of_matter
- SNOMED:has_subject_relationship_context
- SNOMED:has_surgical_approach
- SNOMED:has_technique
- SNOMED:has_temporal_context
- SNOMED:has_time_aspect
- SNOMED:has_units
- UMLS:has_structural_class
- UMLS:has_supported_concept_property
- UMLS:has_supported_concept_relationship
- UMLS:may_be_qualified_by
rank: 1000
domain: entity
slot_uri: biolink:has_attribute
alias: has_attribute
owner: CellTypeTaxon
domain_of:
- entity
- attribute
- named thing
- organism taxon
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: attribute
multivalued: true
deprecated:
name: deprecated
definition_uri: https://w3id.org/biolink/vocab/deprecated
description: A boolean flag indicating that an entity is no longer considered
current or valid.
from_schema: https:/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
- 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
- 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
- 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
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: label type
multivalued: true