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Class: Association

An association between an object--typically an entity such as a protein or a feature--and a classification system or ontology, such as the Gene Ontology, the Enzyme Classification, or TIGRFAMS domains.

URI: kb_cdm:Association

classDiagram class Association click Association href "../Association" Table <|-- Association click Table href "../Table" Association : aggregator_knowledge_source Association : annotation_date Association : association_id Association : comments Association : evidence_type Association : negated Association : object Association : predicate Association : primary_knowledge_source Association : subject Association --> "1" Any : subject click Any href "../Any"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
association_id 1
UUID		 Internal (CDM) unique identifier for an association direct
subject 1
Any or 
Feature or 
Protein or 
ContigCollection		 The subject of an association direct
object 1
LocalCurie		 The object of an association direct
predicate 0..1
LocalCurie		 The relationship between subject and object in an association direct
negated 0..1
Boolean		 If true, the relationship between the subject and object is negated direct
evidence_type 0..1
LocalCurie		 The type of evidence supporting the association direct
primary_knowledge_source 0..1
Uriorcurie		 The knowledge source that created the association direct
aggregator_knowledge_source 0..1
Uriorcurie		 The knowledge source that aggregated the association direct
annotation_date 0..1
Iso8601		 The date when the annotation was made direct
comments 0..1
String		 Any comments about the association direct

Aliases

  • annotation
  • functional annotation
  • gene annotation
  • structural annotation
  • protein annotation

Identifier and Mapping Information

Schema Source

  • from schema: http://kbase.github.io/cdm-schema/cdm_schema

Mappings

Mapping Type Mapped Value
self kb_cdm:Association
native kb_cdm:Association

LinkML Source

Direct

name: Association
description: An association between an object--typically an entity such as a protein
  or a feature--and a classification system or ontology, such as the Gene Ontology,
  the Enzyme Classification, or TIGRFAMS domains.
from_schema: http://kbase.github.io/cdm-schema/cdm_schema
aliases:
- annotation
- functional annotation
- gene annotation
- structural annotation
- protein annotation
is_a: Table
slots:
- association_id
- subject
- object
- predicate
slot_usage:
  association_id:
    name: association_id
    identifier: true
  subject:
    name: subject
    description: The subject of an association.
    range: Any
    required: true
    any_of:
    - range: Feature
    - range: Protein
    - range: ContigCollection
  predicate:
    name: predicate
    description: The relationship between subject and object in an association. Should
      be a term from the Relation Ontology.
    range: local_curie
  object:
    name: object
    description: The object of an association. Should be an ontology term or database
      cross-reference.
    range: local_curie
    required: true
attributes:
  negated:
    name: negated
    description: If true, the relationship between the subject and object is negated.
      For example, consider an association where the subject is a protein ID, the
      object is the GO term for "glucose biosynthesis", and the predicate is "involved
      in". With the "negated" field set to false, the association is interpreted as
      "<protein ID> is involved in glucose biosynthesis". With the "negated" field
      set to true, the association is interpreted as "<protein ID> is not involved
      in glucose biosynthesis".
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Association
    range: boolean
  evidence_type:
    name: evidence_type
    description: The type of evidence supporting the association. Should be a term
      from the Evidence and Conclusion Ontology (ECO).
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Association
    range: local_curie
    pattern: ^ECO:\d+$
  primary_knowledge_source:
    name: primary_knowledge_source
    description: The knowledge source that created the association. Should be a UUID
      from the DataSource table.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Association
    range: uriorcurie
  aggregator_knowledge_source:
    name: aggregator_knowledge_source
    description: The knowledge source that aggregated the association. Should be a
      UUID from the DataSource table.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Association
    range: uriorcurie
  annotation_date:
    name: annotation_date
    description: The date when the annotation was made.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Association
    range: iso8601
  comments:
    name: comments
    description: Any comments about the association.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    domain_of:
    - Association
    - DataSource

Induced

name: Association
description: An association between an object--typically an entity such as a protein
  or a feature--and a classification system or ontology, such as the Gene Ontology,
  the Enzyme Classification, or TIGRFAMS domains.
from_schema: http://kbase.github.io/cdm-schema/cdm_schema
aliases:
- annotation
- functional annotation
- gene annotation
- structural annotation
- protein annotation
is_a: Table
slot_usage:
  association_id:
    name: association_id
    identifier: true
  subject:
    name: subject
    description: The subject of an association.
    range: Any
    required: true
    any_of:
    - range: Feature
    - range: Protein
    - range: ContigCollection
  predicate:
    name: predicate
    description: The relationship between subject and object in an association. Should
      be a term from the Relation Ontology.
    range: local_curie
  object:
    name: object
    description: The object of an association. Should be an ontology term or database
      cross-reference.
    range: local_curie
    required: true
attributes:
  negated:
    name: negated
    description: If true, the relationship between the subject and object is negated.
      For example, consider an association where the subject is a protein ID, the
      object is the GO term for "glucose biosynthesis", and the predicate is "involved
      in". With the "negated" field set to false, the association is interpreted as
      "<protein ID> is involved in glucose biosynthesis". With the "negated" field
      set to true, the association is interpreted as "<protein ID> is not involved
      in glucose biosynthesis".
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: negated
    owner: Association
    domain_of:
    - Association
    range: boolean
  evidence_type:
    name: evidence_type
    description: The type of evidence supporting the association. Should be a term
      from the Evidence and Conclusion Ontology (ECO).
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: evidence_type
    owner: Association
    domain_of:
    - Association
    range: local_curie
    pattern: ^ECO:\d+$
  primary_knowledge_source:
    name: primary_knowledge_source
    description: The knowledge source that created the association. Should be a UUID
      from the DataSource table.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: primary_knowledge_source
    owner: Association
    domain_of:
    - Association
    range: uriorcurie
  aggregator_knowledge_source:
    name: aggregator_knowledge_source
    description: The knowledge source that aggregated the association. Should be a
      UUID from the DataSource table.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: aggregator_knowledge_source
    owner: Association
    domain_of:
    - Association
    range: uriorcurie
  annotation_date:
    name: annotation_date
    description: The date when the annotation was made.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: annotation_date
    owner: Association
    domain_of:
    - Association
    range: iso8601
  comments:
    name: comments
    description: Any comments about the association.
    from_schema: http://kbase.github.io/cdm-schema/cdm_components
    rank: 1000
    alias: comments
    owner: Association
    domain_of:
    - Association
    - DataSource
    range: string
  association_id:
    name: association_id
    description: Internal (CDM) unique identifier for an association.
    from_schema: http://kbase.github.io/cdm-schema/cdm_schema
    rank: 1000
    identifier: true
    alias: association_id
    owner: Association
    domain_of:
    - Association_X_Publication
    - Association_X_SupportingObject
    - Association
    range: UUID
    required: true
  subject:
    name: subject
    description: The subject of an association.
    todos:
    - set range appropriately for ontology and association use
    from_schema: http://kbase.github.io/cdm-schema/cdm_schema
    aliases:
    - about
    - source
    - head
    - subject_id
    rank: 1000
    slot_uri: rdf:subject
    alias: subject
    owner: Association
    domain_of:
    - Association
    - Statements
    - EntailedEdge
    range: Any
    required: true
    any_of:
    - range: Feature
    - range: Protein
    - range: ContigCollection
  object:
    name: object
    description: The object of an association. Should be an ontology term or database
      cross-reference.
    todos:
    - set range appropriately for ontology and association use
    from_schema: http://kbase.github.io/cdm-schema/cdm_schema
    aliases:
    - target
    - sink
    - tail
    - object_id
    rank: 1000
    slot_uri: rdf:object
    alias: object
    owner: Association
    domain_of:
    - Association
    - Statements
    - EntailedEdge
    range: local_curie
    required: true
  predicate:
    name: predicate
    description: The relationship between subject and object in an association. Should
      be a term from the Relation Ontology.
    todos:
    - set range appropriately for ontology and association use
    from_schema: http://kbase.github.io/cdm-schema/cdm_schema
    aliases:
    - relationship
    - relationship type
    - property
    - predicate_id
    rank: 1000
    slot_uri: rdf:predicate
    alias: predicate
    owner: Association
    domain_of:
    - Association
    - Statements
    - EntailedEdge
    range: local_curie