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Class: BiologicalEntity

  • NOTE: this is an abstract class and should not be instantiated directly

URI: biolink:BiologicalEntity

classDiagram class BiologicalEntity click BiologicalEntity href "../BiologicalEntity" ThingWithTaxon <|-- BiologicalEntity click ThingWithTaxon href "../ThingWithTaxon" NamedThing <|-- BiologicalEntity click NamedThing href "../NamedThing" BiologicalEntity <|-- Gene click Gene href "../Gene" BiologicalEntity <|-- Genome click Genome href "../Genome" BiologicalEntity : category BiologicalEntity : deprecated BiologicalEntity : description BiologicalEntity : full_name BiologicalEntity : has_attribute BiologicalEntity --> "*" Attribute : has_attribute click Attribute href "../Attribute" BiologicalEntity : id BiologicalEntity : in_taxon BiologicalEntity --> "*" OrganismTaxon : in_taxon click OrganismTaxon href "../OrganismTaxon" BiologicalEntity : in_taxon_label BiologicalEntity : iri BiologicalEntity : name BiologicalEntity : provided_by BiologicalEntity : synonym BiologicalEntity : type BiologicalEntity : xref

Inheritance

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
provided_by *
String		 The value in this node property represents the knowledge provider that create... direct
xref *
Uriorcurie		 A database cross reference or alternative identifier for a NamedThing or edge... direct
full_name 0..1
LabelType		 a long-form human readable name for a thing direct
synonym *
LabelType		 Alternate human-readable names for a thing direct
in_taxon *
OrganismTaxon		 connects an entity to its taxonomic classification direct
in_taxon_label 0..1
LabelType		 The human readable scientific name for the taxon of the entity direct

Aliases

  • bioentity

Identifier and Mapping Information

Schema Source

  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema

Mappings

Mapping Type Mapped Value
self biolink:BiologicalEntity
native bican:BiologicalEntity
narrow WIKIDATA:Q28845870, STY:T050, SIO:010046, STY:T129

LinkML Source

Direct

name: biological entity
definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
aliases:
- bioentity
narrow_mappings:
- WIKIDATA:Q28845870
- STY:T050
- SIO:010046
- STY:T129
is_a: named thing
abstract: true
mixins:
- thing with taxon
slots:
- id
- iri
- category
- type
- name
- description
- has attribute
- deprecated
- provided by
- xref
- full name
- synonym
- in taxon
- in taxon label
class_uri: biolink:BiologicalEntity

Induced

name: biological entity
definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
aliases:
- bioentity
narrow_mappings:
- WIKIDATA:Q28845870
- STY:T050
- SIO:010046
- STY:T129
is_a: named thing
abstract: true
mixins:
- thing with taxon
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: biological 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: biological 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: biological 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: biological 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: biological 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: biological 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: biological 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: biological 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
  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://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:provided_by
    alias: provided_by
    owner: biological entity
    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
  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://identifiers.org/brain-bican/genome-annotation-schema
    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: biological entity
    domain_of:
    - named thing
    - gene
    - attribute
    - organism taxon
    - 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://identifiers.org/brain-bican/genome-annotation-schema
    rank: 1000
    is_a: node property
    domain: named thing
    slot_uri: biolink:full_name
    alias: full_name
    owner: biological entity
    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://identifiers.org/brain-bican/genome-annotation-schema
    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: biological entity
    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
  in taxon:
    name: in taxon
    definition_uri: https://w3id.org/biolink/vocab/in_taxon
    annotations:
      canonical_predicate:
        tag: canonical_predicate
        value: true
    description: connects an entity to its taxonomic classification. Only certain
      kinds of entities can be taxonomically classified; see 'thing with taxon'
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    aliases:
    - instance of
    - is organism source of gene product
    - organism has gene
    - gene found in organism
    - gene product has organism source
    exact_mappings:
    - RO:0002162
    - WIKIDATA_PROPERTY:P703
    narrow_mappings:
    - RO:0002160
    rank: 1000
    is_a: related to at instance level
    domain: thing with taxon
    slot_uri: biolink:in_taxon
    inherited: true
    alias: in_taxon
    owner: biological entity
    domain_of:
    - thing with taxon
    - biological entity
    - gene
    - genome
    range: organism taxon
    multivalued: true
  in taxon label:
    name: in taxon label
    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
    annotations:
      denormalized:
        tag: denormalized
        value: true
    description: The human readable scientific name for the taxon of the entity.
    in_subset:
    - translator_minimal
    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
    exact_mappings:
    - WIKIDATA_PROPERTY:P225
    rank: 1000
    is_a: node property
    domain: thing with taxon
    slot_uri: biolink:in_taxon_label
    alias: in_taxon_label
    owner: biological entity
    domain_of:
    - thing with taxon
    - biological entity
    - gene
    - genome
    range: label type
class_uri: biolink:BiologicalEntity