Class: Abbreviation
Maps an abbreviation string to its decoded meaning. Optionally the abbreviation can be linked to one or more entities it denotes.
URI: [bican:Abbreviation](https://identifiers.org/brain-bican/vocab/Abbreviation)
[String](String.md) | Unique identifier for this abbreviation entry | direct | | [term](term.md) | 0..1
[String](String.md) | An abbreviation term as it appears in a cell type or cell set name | direct | | [meaning](meaning.md) | 0..1
[String](String.md) | The decoded meaning of the abbreviation term | direct | | [entity_type](entity_type.md) | 0..1
[AbbreviationEntityType](AbbreviationEntityType.md) | The entity type which the abbreviation term denotes | direct | | [was_derived_from](was_derived_from.md) | 0..1
[ProvEntity](ProvEntity.md) | A derivation is a transformation of an entity into another, an update of an e... | [ProvEntity](ProvEntity.md) | | [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) | | [mapping_relation](mapping_relation.md) | *
[OntologyClass](OntologyClass.md) | A mapping of unspecified kind | [OntologyMappable](OntologyMappable.md) | | [exact_match](exact_match.md) | *
[OntologyClass](OntologyClass.md) | The external concept is interchangeable with this entity | [OntologyMappable](OntologyMappable.md) | | [close_match](close_match.md) | *
[OntologyClass](OntologyClass.md) | Close enough to be used interchangeably in some applications | [OntologyMappable](OntologyMappable.md) | | [broad_match](broad_match.md) | *
[OntologyClass](OntologyClass.md) | The external concept is broader than this entity | [OntologyMappable](OntologyMappable.md) | | [narrow_match](narrow_match.md) | *
[OntologyClass](OntologyClass.md) | The external concept is narrower than this entity | [OntologyMappable](OntologyMappable.md) | | [related_match](related_match.md) | *
[OntologyClass](OntologyClass.md) | Associatively related | [OntologyMappable](OntologyMappable.md) | | [iri](iri.md) | 0..1
[IriType](IriType.md) | An IRI for an entity | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [type](type.md) | *
[String](String.md) | | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [name](name.md) | 0..1
[LabelType](LabelType.md) | A human-readable name for an attribute or entity | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [description](description.md) | 0..1
[NarrativeText](NarrativeText.md) | a human-readable description of an entity | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [has_attribute](has_attribute.md) | *
[Attribute](Attribute.md) | connects any entity to an attribute | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [deprecated](deprecated.md) | 0..1
[Boolean](Boolean.md) | A boolean flag indicating that an entity is no longer considered current or v... | [Entity](Entity.md), [NamedThing](NamedThing.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) | [has_abbreviation](has_abbreviation.md) | range | [Abbreviation](Abbreviation.md) | | [CellTypeTaxon](CellTypeTaxon.md) | [has_abbreviation](has_abbreviation.md) | range | [Abbreviation](Abbreviation.md) | ## Identifier and Mapping Information ### Schema Source * from schema: https://w3id.org/brain-bican/cell-taxonomy ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | bican:Abbreviation | | native | bican:Abbreviation | ## LinkML Source ### Direct
### Induced
classDiagram
class Abbreviation
click Abbreviation href "../Abbreviation/"
ProvEntity <|-- Abbreviation
click ProvEntity href "../ProvEntity/"
OntologyMappable <|-- Abbreviation
click OntologyMappable href "../OntologyMappable/"
NamedThing <|-- Abbreviation
click NamedThing href "../NamedThing/"
Abbreviation : broad_match
Abbreviation --> "*" OntologyClass : broad_match
click OntologyClass href "../OntologyClass/"
Abbreviation : category
Abbreviation : close_match
Abbreviation --> "*" OntologyClass : close_match
click OntologyClass href "../OntologyClass/"
Abbreviation : deprecated
Abbreviation : description
Abbreviation : entity_type
Abbreviation --> "0..1" AbbreviationEntityType : entity_type
click AbbreviationEntityType href "../AbbreviationEntityType/"
Abbreviation : equivalent_identifiers
Abbreviation : exact_match
Abbreviation --> "*" OntologyClass : exact_match
click OntologyClass href "../OntologyClass/"
Abbreviation : full_name
Abbreviation : has_attribute
Abbreviation --> "*" Attribute : has_attribute
click Attribute href "../Attribute/"
Abbreviation : id
Abbreviation : information_content
Abbreviation : iri
Abbreviation : mapping_relation
Abbreviation --> "*" OntologyClass : mapping_relation
click OntologyClass href "../OntologyClass/"
Abbreviation : meaning
Abbreviation : name
Abbreviation : named_thing_category
Abbreviation : narrow_match
Abbreviation --> "*" OntologyClass : narrow_match
click OntologyClass href "../OntologyClass/"
Abbreviation : provided_by
Abbreviation : related_match
Abbreviation --> "*" OntologyClass : related_match
click OntologyClass href "../OntologyClass/"
Abbreviation : synonym
Abbreviation : term
Abbreviation : type
Abbreviation : was_derived_from
Abbreviation --> "0..1" ProvEntity : was_derived_from
click ProvEntity href "../ProvEntity/"
Abbreviation : was_generated_by
Abbreviation --> "0..1" ProvActivity : was_generated_by
click ProvActivity href "../ProvActivity/"
Abbreviation : xref
## Inheritance
* [Entity](Entity.md)
* [NamedThing](NamedThing.md)
* **Abbreviation** [ [ProvEntity](ProvEntity.md) [OntologyMappable](OntologyMappable.md)]
## Slots
| Name | Cardinality and Range | Description | Inheritance |
| --- | --- | --- | --- |
| [id](id.md) | 1 [String](String.md) | Unique identifier for this abbreviation entry | direct | | [term](term.md) | 0..1
[String](String.md) | An abbreviation term as it appears in a cell type or cell set name | direct | | [meaning](meaning.md) | 0..1
[String](String.md) | The decoded meaning of the abbreviation term | direct | | [entity_type](entity_type.md) | 0..1
[AbbreviationEntityType](AbbreviationEntityType.md) | The entity type which the abbreviation term denotes | direct | | [was_derived_from](was_derived_from.md) | 0..1
[ProvEntity](ProvEntity.md) | A derivation is a transformation of an entity into another, an update of an e... | [ProvEntity](ProvEntity.md) | | [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) | | [mapping_relation](mapping_relation.md) | *
[OntologyClass](OntologyClass.md) | A mapping of unspecified kind | [OntologyMappable](OntologyMappable.md) | | [exact_match](exact_match.md) | *
[OntologyClass](OntologyClass.md) | The external concept is interchangeable with this entity | [OntologyMappable](OntologyMappable.md) | | [close_match](close_match.md) | *
[OntologyClass](OntologyClass.md) | Close enough to be used interchangeably in some applications | [OntologyMappable](OntologyMappable.md) | | [broad_match](broad_match.md) | *
[OntologyClass](OntologyClass.md) | The external concept is broader than this entity | [OntologyMappable](OntologyMappable.md) | | [narrow_match](narrow_match.md) | *
[OntologyClass](OntologyClass.md) | The external concept is narrower than this entity | [OntologyMappable](OntologyMappable.md) | | [related_match](related_match.md) | *
[OntologyClass](OntologyClass.md) | Associatively related | [OntologyMappable](OntologyMappable.md) | | [iri](iri.md) | 0..1
[IriType](IriType.md) | An IRI for an entity | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [type](type.md) | *
[String](String.md) | | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [name](name.md) | 0..1
[LabelType](LabelType.md) | A human-readable name for an attribute or entity | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [description](description.md) | 0..1
[NarrativeText](NarrativeText.md) | a human-readable description of an entity | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [has_attribute](has_attribute.md) | *
[Attribute](Attribute.md) | connects any entity to an attribute | [Entity](Entity.md), [NamedThing](NamedThing.md) | | [deprecated](deprecated.md) | 0..1
[Boolean](Boolean.md) | A boolean flag indicating that an entity is no longer considered current or v... | [Entity](Entity.md), [NamedThing](NamedThing.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) | [has_abbreviation](has_abbreviation.md) | range | [Abbreviation](Abbreviation.md) | | [CellTypeTaxon](CellTypeTaxon.md) | [has_abbreviation](has_abbreviation.md) | range | [Abbreviation](Abbreviation.md) | ## Identifier and Mapping Information ### Schema Source * from schema: https://w3id.org/brain-bican/cell-taxonomy ## Mappings | Mapping Type | Mapped Value | | --- | --- | | self | bican:Abbreviation | | native | bican:Abbreviation | ## LinkML Source ### Direct
name: Abbreviation
description: Maps an abbreviation string to its decoded meaning. Optionally the abbreviation
can be linked to one or more entities it denotes.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
is_a: named thing
mixins:
- ProvEntity
- OntologyMappable
slots:
- id
slot_usage:
id:
name: id
annotations:
ait_location:
tag: ait_location
value: (synthesized)
description: Unique identifier for this abbreviation entry.
in_subset:
- uns
- annotations
range: string
attributes:
term:
name: term
annotations:
ait_location:
tag: ait_location
value: uns.cluster_info.tokens_<level> (data only)
ait_separator:
tag: ait_separator
value: '|'
description: An abbreviation term as it appears in a cell type or cell set name.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
domain_of:
- Abbreviation
range: string
meaning:
name: meaning
description: The decoded meaning of the abbreviation term.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
domain_of:
- Abbreviation
range: string
entity_type:
name: entity_type
description: The entity type which the abbreviation term denotes.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
domain_of:
- Abbreviation
range: AbbreviationEntityType
name: Abbreviation
description: Maps an abbreviation string to its decoded meaning. Optionally the abbreviation
can be linked to one or more entities it denotes.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
is_a: named thing
mixins:
- ProvEntity
- OntologyMappable
slot_usage:
id:
name: id
annotations:
ait_location:
tag: ait_location
value: (synthesized)
description: Unique identifier for this abbreviation entry.
in_subset:
- uns
- annotations
range: string
attributes:
term:
name: term
annotations:
ait_location:
tag: ait_location
value: uns.cluster_info.tokens_<level> (data only)
ait_separator:
tag: ait_separator
value: '|'
description: An abbreviation term as it appears in a cell type or cell set name.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
owner: Abbreviation
domain_of:
- Abbreviation
range: string
meaning:
name: meaning
description: The decoded meaning of the abbreviation term.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
owner: Abbreviation
domain_of:
- Abbreviation
range: string
entity_type:
name: entity_type
description: The entity type which the abbreviation term denotes.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
owner: Abbreviation
domain_of:
- Abbreviation
range: AbbreviationEntityType
id:
name: id
definition_uri: https://w3id.org/biolink/vocab/id
annotations:
ait_location:
tag: ait_location
value: (synthesized)
description: Unique identifier for this abbreviation entry.
in_subset:
- uns
- annotations
from_schema: https://w3id.org/brain-bican/cell-taxonomy
exact_mappings:
- AGRKB:primaryId
- gff3:ID
- gpi:DB_Object_ID
rank: 1000
domain: entity
slot_uri: biolink:id
identifier: true
owner: Abbreviation
domain_of:
- ontology class
- entity
- Cell
- CellTypeSet
- CellTypeTaxon
- CellTypeTaxonomy
- ClusterSet
- Cluster
- ExpressionMatrix
- Embedding
- Abbreviation
- ColorPalette
- DisplayColor
- attribute
- named thing
- taxonomic rank
- organism taxon
- study result
- relative frequency analysis result
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: string
required: true
was_derived_from:
name: was_derived_from
description: A derivation is a transformation of an entity into another, an update
of an entity resulting in a new one, or the construction of a new entity based
on a pre-existing entity.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: prov:wasDerivedFrom
owner: Abbreviation
domain_of:
- CellTypeTaxonomy
- ClusterSet
- ProvEntity
range: ProvEntity
was_generated_by:
name: was_generated_by
description: Generation is the completion of production of a new entity by an
activity. This entity did not exist before generation and becomes available
for usage after this generation.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: prov:wasGeneratedBy
owner: Abbreviation
domain_of:
- ProvEntity
range: ProvActivity
mapping_relation:
name: mapping_relation
description: 'A mapping of unspecified kind. The honest choice when the relationship
is not established: it entails nothing, being neither symmetric nor transitive
and carrying no direction.'
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: skos:mappingRelation
owner: Abbreviation
domain_of:
- OntologyMappable
range: ontology class
multivalued: true
exact_match:
name: exact_match
description: 'The external concept is interchangeable with this entity. Symmetric
AND transitive, so it chains through third-party mappings. Do not use where
several of our entities map to one external concept: the entailment would then
assert that those entities are equivalent to each other.'
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: skos:exactMatch
owner: Abbreviation
domain_of:
- OntologyMappable
range: ontology class
multivalued: true
close_match:
name: close_match
description: Close enough to be used interchangeably in some applications. Symmetric
but not transitive. Asserts similarity at the same level, so it is not a substitute
for broad_match where a hierarchy exists.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: skos:closeMatch
owner: Abbreviation
domain_of:
- OntologyMappable
range: ontology class
multivalued: true
broad_match:
name: broad_match
description: The external concept is broader than this entity. Use where several
of our entities map to a single external concept.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: skos:broadMatch
owner: Abbreviation
domain_of:
- OntologyMappable
range: ontology class
multivalued: true
narrow_match:
name: narrow_match
description: The external concept is narrower than this entity.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: skos:narrowMatch
owner: Abbreviation
domain_of:
- OntologyMappable
range: ontology class
multivalued: true
related_match:
name: related_match
description: Associatively related. Note that this positively asserts that the
concepts are NOT equivalent and NOT hierarchically related, so it is a claim
in its own right rather than a neutral fallback.
from_schema: https://w3id.org/brain-bican/cell-taxonomy
rank: 1000
slot_uri: skos:relatedMatch
owner: Abbreviation
domain_of:
- OntologyMappable
range: ontology class
multivalued: true
iri:
name: iri
definition_uri: https://w3id.org/biolink/vocab/iri
description: An IRI for an entity. This is determined by the id using expansion
rules.
in_subset:
- translator_minimal
- samples
from_schema: https://w3id.org/brain-bican/cell-taxonomy
exact_mappings:
- WIKIDATA_PROPERTY:P854
rank: 1000
slot_uri: biolink:iri
owner: Abbreviation
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: Abbreviation
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: Abbreviation
domain_of:
- attribute
- entity
- macromolecular machine mixin
- CellTypeSet
- CellTypeTaxon
- ClusterSet
- Cluster
- ColorPalette
- named thing
- organism taxon
- study result
- relative frequency analysis result
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: 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: Abbreviation
domain_of:
- entity
- ColorPalette
- attribute
- named thing
- organism taxon
- study result
- relative frequency analysis result
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: narrative text
has attribute:
name: has attribute
definition_uri: https://w3id.org/biolink/vocab/has_attribute
description: connects any entity to an attribute
in_subset:
- samples
from_schema: https://w3id.org/brain-bican/cell-taxonomy
exact_mappings:
- SIO:000008
close_mappings:
- OBI:0001927
narrow_mappings:
- OBAN:association_has_subject_property
- OBAN:association_has_object_property
- CPT:has_possibly_included_panel_element
- DRUGBANK:category
- EFO:is_executed_in
- HANCESTRO:0301
- LOINC:has_action_guidance
- LOINC:has_adjustment
- LOINC:has_aggregation_view
- LOINC:has_approach_guidance
- LOINC:has_divisor
- LOINC:has_exam
- LOINC:has_method
- LOINC:has_modality_subtype
- LOINC:has_object_guidance
- LOINC:has_scale
- LOINC:has_suffix
- LOINC:has_time_aspect
- LOINC:has_time_modifier
- LOINC:has_timing_of
- NCIT:R88
- NCIT:eo_disease_has_property_or_attribute
- NCIT:has_data_element
- NCIT:has_pharmaceutical_administration_method
- NCIT:has_pharmaceutical_basic_dose_form
- NCIT:has_pharmaceutical_intended_site
- NCIT:has_pharmaceutical_release_characteristics
- NCIT:has_pharmaceutical_state_of_matter
- NCIT:has_pharmaceutical_transformation
- NCIT:is_qualified_by
- NCIT:qualifier_applies_to
- NCIT:role_has_domain
- NCIT:role_has_range
- INO:0000154
- HANCESTRO:0308
- orphanet:C016
- orphanet:C017
- RO:0000053
- RO:0000086
- RO:0000087
- SNOMED:has_access
- SNOMED:has_clinical_course
- SNOMED:has_count_of_base_of_active_ingredient
- SNOMED:has_dose_form_administration_method
- SNOMED:has_dose_form_release_characteristic
- SNOMED:has_dose_form_transformation
- SNOMED:has_finding_context
- SNOMED:has_finding_informer
- SNOMED:has_inherent_attribute
- SNOMED:has_intent
- SNOMED:has_interpretation
- SNOMED:has_laterality
- SNOMED:has_measurement_method
- SNOMED:has_method
- SNOMED:has_priority
- SNOMED:has_procedure_context
- SNOMED:has_process_duration
- SNOMED:has_property
- SNOMED:has_revision_status
- SNOMED:has_scale_type
- SNOMED:has_severity
- SNOMED:has_specimen
- SNOMED:has_state_of_matter
- SNOMED:has_subject_relationship_context
- SNOMED:has_surgical_approach
- SNOMED:has_technique
- SNOMED:has_temporal_context
- SNOMED:has_time_aspect
- SNOMED:has_units
- UMLS:has_structural_class
- UMLS:has_supported_concept_property
- UMLS:has_supported_concept_relationship
- UMLS:may_be_qualified_by
rank: 1000
domain: entity
slot_uri: biolink:has_attribute
alias: has_attribute
owner: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
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: Abbreviation
domain_of:
- entity
is_class_field: true
range: uriorcurie
required: true
multivalued: true