Class: TaxonTerm

A taxon used to state the organisms to which a biological observation, method, or claim applies: a species by its scientific or common name, or a broader grouping such as a genus, family, order, or class, identified by its NCBI Taxonomy ID where one exists. In EMOD a taxon term can be attached to a line of evidence, an assay, or an applicability statement on an AOP, Key Event, or Key Event Relationship. An applicability statement may be asserted during AOP development, or derived from the taxa recorded on cited evidence; where evidence is cited, the taxon claimed can be traced to an Observation.

URI: http://example.org/aopwiki-emod/TaxonTerm

classDiagram class TaxonTerm click TaxonTerm href "../TaxonTerm/" TaxonTerm : created_at TaxonTerm : id TaxonTerm : ncbi_id TaxonTerm : scientific_term TaxonTerm : source TaxonTerm : source_id TaxonTerm : term TaxonTerm : term_class TaxonTerm --> "0..1" TaxonTermClassEnum : term_class click TaxonTermClassEnum href "../TaxonTermClassEnum/" TaxonTerm : updated_at

Slots

Name	Cardinality and Range	Description	Inheritance
created_at	0..1 Datetime	Timestamp of when the record was created	direct
updated_at	0..1 Datetime	Timestamp of when the record was last updated	direct
id	0..1 Integer		direct
term_class	0..1 TaxonTermClassEnum		direct
term	0..1 String		direct
source	0..1 String		direct
ncbi_id	0..1 String		direct
scientific_term	0..1 String		direct
source_id	0..1 String		direct

Usages

used by	used in	type	used
Assay	taxon_terms	range	TaxonTerm
Evidence	taxon_term_id	range	TaxonTerm
AopToTaxon	taxon_term_id	range	TaxonTerm
EventToTaxon	taxon_term_id	range	TaxonTerm
KeRelationshipToTaxon	taxon_term_id	range	TaxonTerm

Identifier and Mapping Information

Schema Source

from schema: http://example.org/aopwiki-emod

Mappings

Mapping Type	Mapped Value
self	http://example.org/aopwiki-emod/TaxonTerm
native	http://example.org/aopwiki-emod/TaxonTerm

LinkML Source

Direct

name: TaxonTerm
description: 'A taxon used to state the organisms to which a biological observation,
  method, or claim applies: a species by its scientific or common name, or a broader
  grouping such as a genus, family, order, or class, identified by its NCBI Taxonomy
  ID where one exists. In EMOD a taxon term can be attached to a line of evidence,
  an assay, or an applicability statement on an AOP, Key Event, or Key Event Relationship.
  An applicability statement may be asserted during AOP development, or derived from
  the taxa recorded on cited evidence; where evidence is cited, the taxon claimed
  can be traced to an Observation.'
from_schema: http://example.org/aopwiki-emod
slots:
- created_at
- updated_at
attributes:
  id:
    name: id
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    - User
    range: integer
  term_class:
    name: term_class
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - TaxonTerm
    range: TaxonTermClassEnum
  term:
    name: term
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - CellTerm
    - ConfidenceLevel
    - Directness
    - LifeStageTerm
    - OrganTerm
    - SexTerm
    - TaxonTerm
  source:
    name: source
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - CellTerm
    - OrganTerm
    - TaxonTerm
  ncbi_id:
    name: ncbi_id
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - TaxonTerm
  scientific_term:
    name: scientific_term
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    domain_of:
    - TaxonTerm
  source_id:
    name: source_id
    from_schema: http://example.org/aopwiki-emod
    domain_of:
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - CellTerm
    - OrganTerm
    - TaxonTerm

Induced

name: TaxonTerm
description: 'A taxon used to state the organisms to which a biological observation,
  method, or claim applies: a species by its scientific or common name, or a broader
  grouping such as a genus, family, order, or class, identified by its NCBI Taxonomy
  ID where one exists. In EMOD a taxon term can be attached to a line of evidence,
  an assay, or an applicability statement on an AOP, Key Event, or Key Event Relationship.
  An applicability statement may be asserted during AOP development, or derived from
  the taxa recorded on cited evidence; where evidence is cited, the taxon claimed
  can be traced to an Observation.'
from_schema: http://example.org/aopwiki-emod
attributes:
  id:
    name: id
    from_schema: http://example.org/aopwiki-emod
    alias: id
    owner: TaxonTerm
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    - User
    range: integer
  term_class:
    name: term_class
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: term_class
    owner: TaxonTerm
    domain_of:
    - TaxonTerm
    range: TaxonTermClassEnum
  term:
    name: term
    from_schema: http://example.org/aopwiki-emod
    alias: term
    owner: TaxonTerm
    domain_of:
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - CellTerm
    - ConfidenceLevel
    - Directness
    - LifeStageTerm
    - OrganTerm
    - SexTerm
    - TaxonTerm
    range: string
  source:
    name: source
    from_schema: http://example.org/aopwiki-emod
    alias: source
    owner: TaxonTerm
    domain_of:
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - CellTerm
    - OrganTerm
    - TaxonTerm
    range: string
  ncbi_id:
    name: ncbi_id
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: ncbi_id
    owner: TaxonTerm
    domain_of:
    - TaxonTerm
    range: string
  scientific_term:
    name: scientific_term
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: scientific_term
    owner: TaxonTerm
    domain_of:
    - TaxonTerm
    range: string
  source_id:
    name: source_id
    from_schema: http://example.org/aopwiki-emod
    alias: source_id
    owner: TaxonTerm
    domain_of:
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - CellTerm
    - OrganTerm
    - TaxonTerm
    range: string
  created_at:
    name: created_at
    description: Timestamp of when the record was created
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: created_at
    owner: TaxonTerm
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    range: datetime
  updated_at:
    name: updated_at
    description: Timestamp of when the record was last updated
    from_schema: http://example.org/aopwiki-emod
    rank: 1000
    alias: updated_at
    owner: TaxonTerm
    domain_of:
    - Aop
    - Event
    - KeRelationship
    - Assay
    - Observation
    - Evidence
    - Stressor
    - Citation
    - BiologicalAction
    - BiologicalObject
    - BiologicalProcess
    - LevelOfBiologicalOrganization
    - AopToEvent
    - AopToLifeStage
    - AopToKeRelationship
    - AopToSex
    - AopToPrototypicalStressor
    - AopToTaxon
    - AssignedLicense
    - BioTargetFamily
    - CellTerm
    - ConfidenceLevel
    - Directness
    - EventToLifeStage
    - EventToSex
    - EventToTaxon
    - ExperimentSetup
    - ExperimentType
    - Handbook
    - HarmonizedAop
    - HarmonizedEvent
    - License
    - LifeStageTerm
    - OecdStatus
    - OrganTerm
    - KeRelationshipToLifeStage
    - KeRelationshipToSex
    - KeRelationshipToTaxon
    - SexTerm
    - EventComponent
    - TaxonTerm
    - TestGuideline
    range: datetime