NCBITaxonTerm

None

classDiagram OntologyTerm <|-- NCBITaxonTerm NCBITaxonTerm : ancestors NCBITaxonTerm : child_count NCBITaxonTerm : created_by NCBITaxonTerm : cross_references NCBITaxonTerm : curie NCBITaxonTerm : date_created NCBITaxonTerm : date_updated NCBITaxonTerm : db_date_created NCBITaxonTerm : db_date_updated NCBITaxonTerm : dbkey NCBITaxonTerm : definition NCBITaxonTerm : definition_urls NCBITaxonTerm : descendant_count NCBITaxonTerm : descendants NCBITaxonTerm : internal NCBITaxonTerm : name NCBITaxonTerm : namespace NCBITaxonTerm : obsolete NCBITaxonTerm : secondary_identifiers NCBITaxonTerm : subsets NCBITaxonTerm : synonyms NCBITaxonTerm : type NCBITaxonTerm : updated_by

URI: alliance:NCBITaxonTerm

Parent Classes

AuditedObject
- CurieObject
  - OntologyTerm
    - NCBITaxonTerm

Slots

Name	Description
ancestors	The ancestors of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like "develops_from", ancestors are the terms from which this term develops (not a true parent/child or ancestor/descendant relationship).
child_count	None
created_by	The individual that created the entity.
cross_references	Holds between an object and its CrossReferences.
curie	A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
date_created	The date on which an entity was created. This can be applied to nodes or edges.
date_updated	Date on which an entity was last modified.
db_date_created	The date on which an entity was created in the Alliance database. This is distinct from date_created, which represents the date when the entity was originally created (i.e. at the MOD for imported data).
db_date_updated	Date on which an entity was last modified in the Alliance database. This is distinct from date_updated, which represents the date when the entity was last modified and may predate import into the Alliance database.
dbkey	Typically the primary key on the table. Should be a global sequence in the database to insure uniqueness over the entire suite of tables. Alternatively, could be a serial8 identifier. Tables with a dbkey should have an alternate key to establish uniqueness based on the data in the table.
definition	The definition of the ontology term. This is a reference to an object that holds the text description of the term and a collection of URLs that further define the term.
definition_urls	None
descendant_count	None
descendants	The descendants of this term in the ontology, including the term itself. This language works well for the majority of use cases, however for a relationship like "develops_from", ancestors are the terms to which this term develops into (not a true parent/child or ancestor/descendant relationship).
internal	Classifies the entity as private (for internal use) or not (for public use).
name	a human-readable name for an entity
namespace	the namespace of the ontology.
obsolete	Entity is no longer current.
secondary_identifiers	None
subsets	None
synonyms	A generic free-text field for objects that only have string representation of one or more synonyms and do not require meta data or attribution; if meta data or attribution are required to be captured for individual synonyms, consider the NameSlotAnnotation class
type	None
updated_by	The individual that last modified the entity.

Mappings

Mapping Type	Mapped Value
self	['alliance:NCBITaxonTerm']
native	['alliance:NCBITaxonTerm']

LinkML Specification

Direct

name: NCBITaxonTerm
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: OntologyTerm

Induced

name: NCBITaxonTerm
from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
is_a: OntologyTerm
attributes:
  curie:
    name: curie
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://github.com/alliance-genome/agr_curation_schema/core.yaml
    multivalued: false
    identifier: true
    alias: curie
    owner: NCBITaxonTerm
    domain_of:
    - CurieObject
    - Identifier
    - OntologyTerm
    - Laboratory
    - Annotation
    - ExternalDataBaseEntityDTO
    - GeneNomenclatureSet
    range: uriorcurie
    required: true
  dbkey:
    name: dbkey
    description: Typically the primary key on the table.  Should be a global sequence
      in the database to insure uniqueness over the entire suite of tables.  Alternatively,
      could be a serial8 identifier. Tables with a dbkey should have an alternate
      key to establish uniqueness based on the data in the table.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: dbkey
    owner: NCBITaxonTerm
    domain_of:
    - ExternalDatabaseLink
    - OntologyTerm
    range: string
  name:
    name: name
    description: a human-readable name for an entity
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: false
    alias: name
    owner: NCBITaxonTerm
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Antibody
    - AntibodyDTO
    - Transcript
    - TranscriptDTO
    - Exon
    - ExonDTO
    - CodingSequence
    - CodingSequenceDTO
    - Chromosome
    - ChromosomeDTO
    - AssemblyComponent
    - AssemblyComponentDTO
    - Protein
    - ProteinDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - ResourceDescriptorPage
    - VocabularyTerm
    - Vocabulary
    - VocabularyTermSet
    - OntologyTerm
    - HTPExpressionDatasetAnnotation
    - HTPExpressionDatasetAnnotationDTO
    - CurationReportGroup
    - CurationReport
    - BulkLoadGroup
    - BulkLoad
    range: string
  definition:
    name: definition
    description: The definition of the ontology term. This is a reference to an object
      that holds the text description of the term and a collection of URLs that further
      define the term.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: definition
    owner: NCBITaxonTerm
    domain_of:
    - VocabularyTerm
    - OntologyTerm
    range: string
  definition_urls:
    name: definition_urls
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: definition_urls
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: string
  type:
    name: type
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: type
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: uriorcurie
  cross_references:
    name: cross_references
    description: Holds between an object and its CrossReferences.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - xrefs
    singular_name: cross_reference
    multivalued: true
    alias: cross_references
    owner: NCBITaxonTerm
    domain_of:
    - Antibody
    - AuthorReference
    - GenomicEntity
    - GenomeAssembly
    - OntologyTerm
    - ExternalDataBaseEntity
    - GeneInteraction
    range: CrossReference
  synonyms:
    name: synonyms
    description: A generic free-text field for objects that only have string representation
      of one or more synonyms and do not require meta data or attribution; if meta
      data or attribution are required to be captured for individual synonyms, consider
      the NameSlotAnnotation class
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: synonyms
    owner: NCBITaxonTerm
    domain_of:
    - VariantDTO
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - AffectedGenomicModel
    - AffectedGenomicModelDTO
    - ResourceDescriptor
    - VocabularyTerm
    - OntologyTerm
    - Resource
    - Variant
    - GeneNomenclatureSet
    range: string
    required: false
  namespace:
    name: namespace
    description: the namespace of the ontology.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: namespace
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: string
  subsets:
    name: subsets
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: subsets
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: string
  secondary_identifiers:
    name: secondary_identifiers
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - secondary_ids
    multivalued: true
    alias: secondary_identifiers
    owner: NCBITaxonTerm
    domain_of:
    - SequenceTargetingReagent
    - SequenceTargetingReagentDTO
    - Reagent
    - ReagentDTO
    - OntologyTerm
    - Figure
    - Image
    - ExternalDataBaseEntity
    - ExternalDataBaseEntityDTO
    range: uriorcurie
  ancestors:
    name: ancestors
    description: The ancestors of this term in the ontology, including the term itself.
      This language works well for the majority of use cases, however for a relationship
      like "develops_from", ancestors are the terms from which this term develops
      (not a true parent/child or ancestor/descendant relationship).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: ancestors
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: OntologyTermClosure
  descendants:
    name: descendants
    description: The descendants of this term in the ontology, including the term
      itself. This language works well for the majority of use cases, however for
      a relationship like "develops_from", ancestors are the terms to which this term
      develops into (not a true parent/child or ancestor/descendant relationship).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    multivalued: true
    alias: descendants
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: OntologyTermClosure
  child_count:
    name: child_count
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: child_count
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: integer
  descendant_count:
    name: descendant_count
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: descendant_count
    owner: NCBITaxonTerm
    domain_of:
    - OntologyTerm
    range: integer
  created_by:
    name: created_by
    description: The individual that created the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: created_by
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    range: Person
  date_created:
    name: date_created
    description: The date on which an entity was created. This can be applied to nodes
      or edges.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - creation_date
    exact_mappings:
    - dct:createdOn
    - WIKIDATA_PROPERTY:P577
    alias: date_created
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  updated_by:
    name: updated_by
    description: The individual that last modified the entity.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    domain: AuditedObject
    multivalued: false
    alias: updated_by
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    range: Person
  date_updated:
    name: date_updated
    description: Date on which an entity was last modified.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    aliases:
    - date_last_modified
    alias: date_updated
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_created:
    name: db_date_created
    description: The date on which an entity was created in the Alliance database.  This
      is distinct from date_created, which represents the date when the entity was
      originally created (i.e. at the MOD for imported data).
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_created
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  db_date_updated:
    name: db_date_updated
    description: Date on which an entity was last modified in the Alliance database.  This
      is distinct from date_updated, which represents the date when the entity was
      last modified and may predate import into the Alliance database.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: db_date_updated
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: datetime
  internal:
    name: internal
    description: Classifies the entity as private (for internal use) or not (for public
      use).
    notes:
    - Default value is true.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: internal
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean
    required: true
  obsolete:
    name: obsolete
    description: Entity is no longer current.
    notes:
    - Obsolete entities are preserved in the database for posterity but should not
      be publicly displayed.
    from_schema: https://github.com/alliance-genome/agr_curation_schema/alliance_schema
    alias: obsolete
    owner: NCBITaxonTerm
    domain_of:
    - AuditedObject
    - AuditedObjectDTO
    range: boolean