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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: cdm:Association

classDiagram class Association click Association href "../Association" 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 : publications Association --> "*" Publication : publications click Publication href "../Publication" Association : subject Association --> "1" Any : subject click Any href "../Any" Association : supporting_objects Association --> "*" Any : supporting_objects click Any href "../Any"

Slots

Name Cardinality and Range Description Inheritance
subject 1
Any or 
Feature or 
Protein		 The subject of an association direct
object 1
Curie		 The object of an association direct
predicate 0..1
Curie		 The relationship between subject and object in an association direct
association_id 1
UUID		 Unique ID for the association direct
negated 0..1
Boolean		 If true, the relationship between the subject and object is negated direct
evidence_type 0..1
Curie		 The type of evidence supporting the association direct
publications *
Publication		 Publications that support the association direct
supporting_objects *
Any or 
Feature or 
Protein		 Objects that support 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
Date		 The date when the annotation was made direct
comments *
String		 Any comments about the association direct

Usages

used by used in type used
AssociationXPublication association_id range Association
AssociationXEntity association_id range Association

Aliases

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

Identifier and Mapping Information

Schema Source

  • from schema: https://github.com/kbase/cdm-schema

Mappings

Mapping Type Mapped Value
self cdm:Association
native 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: https://github.com/kbase/cdm-schema
aliases:
- annotation
- functional annotation
- gene annotation
- structural annotation
- protein annotation
slots:
- subject
- object
- predicate
slot_usage:
  subject:
    name: subject
    description: The subject of an association.
    alias: subject_id
    range: Any
    required: true
    any_of:
    - range: Feature
    - range: Protein
  predicate:
    name: predicate
    description: The relationship between subject and object in an association. Should
      be a term from the OBO relations ontology.
    alias: relationship
    range: curie
  object:
    name: object
    description: The object of an association. Should be an ontology term or database
      cross-reference.
    alias: object_id
    range: curie
    required: true
attributes:
  association_id:
    name: association_id
    description: Unique ID for the association.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    domain_of:
    - Association_x_Publication
    - Association_X_Entity
    - Association
    range: UUID
    required: true
  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: https://github.com/kbase/cdm-schema
    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: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    range: curie
    pattern: ^ECO:\d+$
  publications:
    name: publications
    description: Publications that support the association.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    range: Publication
    multivalued: true
  supporting_objects:
    name: supporting_objects
    description: Objects that support the association. Should be URLs or CURIEs. Where
      possible, CDM identifiers should be used.
    todos:
    - work out range of supporting objects
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    range: Any
    multivalued: true
    any_of:
    - range: Feature
    - range: Protein
  primary_knowledge_source:
    name: primary_knowledge_source
    description: The knowledge source that created the association.
    todos:
    - generate a controlled vocab for this field.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    range: uriorcurie
  aggregator_knowledge_source:
    name: aggregator_knowledge_source
    description: The knowledge source that aggregated the association.
    todos:
    - generate a controlled vocab for this field.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    range: uriorcurie
  annotation_date:
    name: annotation_date
    description: The date when the annotation was made.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    range: date
  comments:
    name: comments
    description: Any comments about the association.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    domain_of:
    - Association
    - DataSource
    multivalued: true

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: https://github.com/kbase/cdm-schema
aliases:
- annotation
- functional annotation
- gene annotation
- structural annotation
- protein annotation
slot_usage:
  subject:
    name: subject
    description: The subject of an association.
    alias: subject_id
    range: Any
    required: true
    any_of:
    - range: Feature
    - range: Protein
  predicate:
    name: predicate
    description: The relationship between subject and object in an association. Should
      be a term from the OBO relations ontology.
    alias: relationship
    range: curie
  object:
    name: object
    description: The object of an association. Should be an ontology term or database
      cross-reference.
    alias: object_id
    range: curie
    required: true
attributes:
  association_id:
    name: association_id
    description: Unique ID for the association.
    from_schema: https://github.com/kbase/cdm-schema
    identifier: true
    alias: association_id
    owner: Association
    domain_of:
    - Association_x_Publication
    - Association_X_Entity
    - Association
    range: UUID
    required: true
  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: https://github.com/kbase/cdm-schema
    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: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: evidence_type
    owner: Association
    domain_of:
    - Association
    range: curie
    pattern: ^ECO:\d+$
  publications:
    name: publications
    description: Publications that support the association.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: publications
    owner: Association
    domain_of:
    - Association
    range: Publication
    multivalued: true
  supporting_objects:
    name: supporting_objects
    description: Objects that support the association. Should be URLs or CURIEs. Where
      possible, CDM identifiers should be used.
    todos:
    - work out range of supporting objects
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: supporting_objects
    owner: Association
    domain_of:
    - Association
    range: Any
    multivalued: true
    any_of:
    - range: Feature
    - range: Protein
  primary_knowledge_source:
    name: primary_knowledge_source
    description: The knowledge source that created the association.
    todos:
    - generate a controlled vocab for this field.
    from_schema: https://github.com/kbase/cdm-schema
    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.
    todos:
    - generate a controlled vocab for this field.
    from_schema: https://github.com/kbase/cdm-schema
    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: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: annotation_date
    owner: Association
    domain_of:
    - Association
    range: date
  comments:
    name: comments
    description: Any comments about the association.
    from_schema: https://github.com/kbase/cdm-schema
    rank: 1000
    alias: comments
    owner: Association
    domain_of:
    - Association
    - DataSource
    range: string
    multivalued: true
  subject:
    name: subject
    description: The subject of an association.
    todos:
    - set range appropriately for ontology and association use
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - about
    - source
    - head
    rank: 1000
    slot_uri: rdf:subject
    alias: subject_id
    owner: Association
    domain_of:
    - Association
    - Statements
    - EntailedEdge
    range: Any
    required: true
    any_of:
    - range: Feature
    - range: Protein
  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: https://github.com/kbase/cdm-schema
    aliases:
    - target
    - sink
    - tail
    rank: 1000
    slot_uri: rdf:object
    alias: object_id
    owner: Association
    domain_of:
    - Association
    - Statements
    - EntailedEdge
    range: curie
    required: true
  predicate:
    name: predicate
    description: The relationship between subject and object in an association. Should
      be a term from the OBO relations ontology.
    todos:
    - set range appropriately for ontology and association use
    from_schema: https://github.com/kbase/cdm-schema
    aliases:
    - relationship type
    - property
    rank: 1000
    slot_uri: rdf:predicate
    alias: relationship
    owner: Association
    domain_of:
    - Association
    - Statements
    - EntailedEdge
    range: curie