Class: ThingWithTaxon

A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes

URI: biolink:ThingWithTaxon

classDiagram class ThingWithTaxon click ThingWithTaxon href "../ThingWithTaxon" ThingWithTaxon <|-- GenomeAssembly click GenomeAssembly href "../GenomeAssembly" ThingWithTaxon <|-- BiologicalEntity click BiologicalEntity href "../BiologicalEntity" ThingWithTaxon : in_taxon ThingWithTaxon --> "*" OrganismTaxon : in_taxon click OrganismTaxon href "../OrganismTaxon" ThingWithTaxon : in_taxon_label

Slots

Name	Cardinality and Range	Description	Inheritance
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

Mixin Usage

mixed into	description
GenomeAssembly	Genome assembly to contain version and label information
BiologicalEntity

Usages

used by	used in	type	used
GeneAnnotation	in_taxon	domain	ThingWithTaxon
GeneAnnotation	in_taxon_label	domain	ThingWithTaxon
GenomeAnnotation	in_taxon	domain	ThingWithTaxon
GenomeAnnotation	in_taxon_label	domain	ThingWithTaxon
GenomeAssembly	in_taxon	domain	ThingWithTaxon
GenomeAssembly	in_taxon_label	domain	ThingWithTaxon
ThingWithTaxon	in_taxon	domain	ThingWithTaxon
ThingWithTaxon	in_taxon_label	domain	ThingWithTaxon
BiologicalEntity	in_taxon	domain	ThingWithTaxon
BiologicalEntity	in_taxon_label	domain	ThingWithTaxon
Gene	in_taxon	domain	ThingWithTaxon
Gene	in_taxon_label	domain	ThingWithTaxon
Genome	in_taxon	domain	ThingWithTaxon
Genome	in_taxon_label	domain	ThingWithTaxon

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	biolink:ThingWithTaxon
native	bican:ThingWithTaxon

LinkML Source

Direct

name: thing with taxon
definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon
description: A mixin that can be used on any entity that can be taxonomically classified.
  This includes individual organisms; genes, their products and other molecular entities;
  body parts; biological processes
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
mixin: true
slots:
- in taxon
- in taxon label
class_uri: biolink:ThingWithTaxon

Induced

name: thing with taxon
definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon
description: A mixin that can be used on any entity that can be taxonomically classified.
  This includes individual organisms; genes, their products and other molecular entities;
  body parts; biological processes
from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
mixin: true
attributes:
  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
    multivalued: true
    inherited: true
    alias: in_taxon
    owner: thing with taxon
    domain_of:
    - thing with taxon
    - biological entity
    - gene
    - genome
    range: organism taxon
  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: thing with taxon
    domain_of:
    - thing with taxon
    - biological entity
    - gene
    - genome
    range: label type
class_uri: biolink:ThingWithTaxon