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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. Should be an ontology term or database cross-reference. direct
predicate 0..1
LocalCurie		 The relationship between subject and object in an association. Should be a term from the Relation Ontology. direct
negated 0..1
Boolean		 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 " is involved in glucose biosynthesis". With the "negated" field set to true, the association is interpreted as " is not involved in glucose biosynthesis". direct
evidence_type 0..1
LocalCurie		 The type of evidence supporting the association. Should be a term from the Evidence and Conclusion Ontology (ECO). direct
primary_knowledge_source 0..1
Uriorcurie		 The knowledge source that created the association. Should be a UUID from the DataSource table. direct
aggregator_knowledge_source 0..1
Uriorcurie		 The knowledge source that aggregated the association. Should be a UUID from the DataSource table. 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