Class: Entity
Root Biolink Model class for all things and informational relationships, real or imagined.
- NOTE: this is an abstract class and should not be instantiated directly
URI: biolink:Entity
classDiagram
class Entity
click Entity href "../Entity"
Entity <|-- NamedThing
click NamedThing href "../NamedThing"
Entity <|-- Checksum
click Checksum href "../Checksum"
Entity : category
Entity : deprecated
Entity : description
Entity : has_attribute
Entity --> "*" Attribute : has_attribute
click Attribute href "../Attribute"
Entity : id
Entity : iri
Entity : name
Entity : type
Inheritance
- Entity
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| id | 1 String |
A unique identifier for an entity | direct |
| iri | 0..1 IriType |
An IRI for an entity | direct |
| category | * Curie |
Name of the high level ontology class in which this entity is categorized | direct |
| type | * String |
direct | |
| name | 0..1 LabelType |
A human-readable name for an attribute or entity | direct |
| description | 0..1 NarrativeText |
a human-readable description of an entity | direct |
| has_attribute | * Attribute |
connects any entity to an attribute | direct |
| deprecated | 0..1 Boolean |
A boolean flag indicating that an entity is no longer considered current or v... | direct |
Usages
Identifier and Mapping Information
Schema Source
- from schema: https://identifiers.org/brain-bican/genome-annotation-schema
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | biolink:Entity |
| native | bican:Entity |
LinkML Source
Direct
name: entity
definition_uri: https://w3id.org/biolink/vocab/Entity
description: Root Biolink Model class for all things and informational relationships,
real or imagined.
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
abstract: true
slots:
- id
- iri
- category
- type
- name
- description
- has attribute
- deprecated
class_uri: biolink:Entity
Induced
name: entity
definition_uri: https://w3id.org/biolink/vocab/Entity
description: Root Biolink Model class for all things and informational relationships,
real or imagined.
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
abstract: true
attributes:
id:
name: id
definition_uri: https://w3id.org/biolink/vocab/id
description: A unique identifier for an entity. Must be either a CURIE shorthand
for a URI or a complete URI
in_subset:
- translator_minimal
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
exact_mappings:
- AGRKB:primaryId
- gff3:ID
- gpi:DB_Object_ID
rank: 1000
domain: entity
slot_uri: biolink:id
identifier: true
alias: id
owner: entity
domain_of:
- ontology class
- entity
- 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
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://identifiers.org/brain-bican/genome-annotation-schema
exact_mappings:
- WIKIDATA_PROPERTY:P854
rank: 1000
slot_uri: biolink:iri
alias: iri
owner: entity
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://identifiers.org/brain-bican/genome-annotation-schema
rank: 1000
is_a: type
domain: entity
slot_uri: biolink:category
designates_type: true
alias: category
owner: entity
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://identifiers.org/brain-bican/genome-annotation-schema
mappings:
- rdf:type
exact_mappings:
- gff3:type
- gpi:DB_Object_Type
rank: 1000
domain: entity
slot_uri: rdf:type
alias: type
owner: entity
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
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://identifiers.org/brain-bican/genome-annotation-schema
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: entity
domain_of:
- attribute
- entity
- macromolecular machine mixin
- named thing
- organism taxon
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene or gene product
- 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://identifiers.org/brain-bican/genome-annotation-schema
aliases:
- definition
mappings:
- dct:description
exact_mappings:
- IAO:0000115
- skos:definitions
narrow_mappings:
- gff3:Description
rank: 1000
slot_uri: dct:description
alias: description
owner: entity
domain_of:
- entity
- attribute
- named thing
- organism taxon
- 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://identifiers.org/brain-bican/genome-annotation-schema
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: entity
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://identifiers.org/brain-bican/genome-annotation-schema
exact_mappings:
- oboInOwl:ObsoleteClass
rank: 1000
slot_uri: biolink:deprecated
alias: deprecated
owner: entity
domain_of:
- entity
- attribute
- named thing
- organism taxon
- information content entity
- dataset
- physical entity
- activity
- procedure
- material sample
- biological entity
- gene
- genome
range: boolean
class_uri: biolink:Entity