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Class: GeneToExpressionSiteAssociation

An association between a gene and a gene expression site, possibly qualified by stage/timing info.

URI: biolink:GeneToExpressionSiteAssociation

classDiagram class GeneToExpressionSiteAssociation Association <|-- GeneToExpressionSiteAssociation GeneToExpressionSiteAssociation : aggregator_knowledge_source GeneToExpressionSiteAssociation : category GeneToExpressionSiteAssociation : description GeneToExpressionSiteAssociation : has_attribute GeneToExpressionSiteAssociation --|> attribute : has_attribute GeneToExpressionSiteAssociation : has_evidence GeneToExpressionSiteAssociation --|> evidence type : has_evidence GeneToExpressionSiteAssociation : id GeneToExpressionSiteAssociation : iri GeneToExpressionSiteAssociation : knowledge_source GeneToExpressionSiteAssociation : name GeneToExpressionSiteAssociation : negated GeneToExpressionSiteAssociation : object GeneToExpressionSiteAssociation --|> anatomical entity : object GeneToExpressionSiteAssociation : object_category GeneToExpressionSiteAssociation --|> ontology class : object_category GeneToExpressionSiteAssociation : object_category_closure GeneToExpressionSiteAssociation --|> ontology class : object_category_closure GeneToExpressionSiteAssociation : object_closure GeneToExpressionSiteAssociation : object_label_closure GeneToExpressionSiteAssociation : object_namespace GeneToExpressionSiteAssociation : original_object GeneToExpressionSiteAssociation : original_predicate GeneToExpressionSiteAssociation : original_subject GeneToExpressionSiteAssociation : predicate GeneToExpressionSiteAssociation : primary_knowledge_source GeneToExpressionSiteAssociation : publications GeneToExpressionSiteAssociation --|> publication : publications GeneToExpressionSiteAssociation : qualifiers GeneToExpressionSiteAssociation --|> ontology class : qualifiers GeneToExpressionSiteAssociation : quantifier_qualifier GeneToExpressionSiteAssociation --|> ontology class : quantifier_qualifier GeneToExpressionSiteAssociation : retrieval_source_ids GeneToExpressionSiteAssociation --|> retrieval source : retrieval_source_ids GeneToExpressionSiteAssociation : stage_qualifier GeneToExpressionSiteAssociation --|> life stage : stage_qualifier GeneToExpressionSiteAssociation : subject GeneToExpressionSiteAssociation --|> gene or gene product : subject GeneToExpressionSiteAssociation : subject_category GeneToExpressionSiteAssociation --|> ontology class : subject_category GeneToExpressionSiteAssociation : subject_category_closure GeneToExpressionSiteAssociation --|> ontology class : subject_category_closure GeneToExpressionSiteAssociation : subject_closure GeneToExpressionSiteAssociation : subject_label_closure GeneToExpressionSiteAssociation : subject_namespace GeneToExpressionSiteAssociation : timepoint GeneToExpressionSiteAssociation : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
stage_qualifier 0..1
LifeStage		 stage at which the gene is expressed in the site direct
quantifier_qualifier 0..1
OntologyClass		 can be used to indicate magnitude, or also ranking direct
subject 1..1
GeneOrGeneProduct		 Gene or gene product positively within the specified anatomical entity (or su... Association
predicate 1..1
PredicateType		 expression relationship Association
object 1..1
AnatomicalEntity		 location in which the gene is expressed Association
negated 0..1
Boolean		 if set to true, then the association is negated i Association
qualifiers 0..*
OntologyClass		 connects an association to qualifiers that modify or qualify the meaning of t... Association
publications 0..*
Publication		 One or more publications that report the statement expressed in an Associati... Association
has_evidence 0..*
EvidenceType		 connects an association to an instance of supporting evidence Association
knowledge_source 0..1
String		 An Information Resource from which the knowledge expressed in an Association ... Association
primary_knowledge_source 0..1
String		 The most upstream source of the knowledge expressed in an Association that an... Association
aggregator_knowledge_source 0..*
String		 An intermediate aggregator resource from which knowledge expressed in an Asso... Association
timepoint 0..1
TimeType		 a point in time Association
original_subject 0..1
String		 used to hold the original subject of a relation (or predicate) that an extern... Association
original_predicate 0..1
Uriorcurie		 used to hold the original relation/predicate that an external knowledge sourc... Association
original_object 0..1
String		 used to hold the original object of a relation (or predicate) that an externa... Association
subject_category 0..1
OntologyClass		 Used to hold the biolink class/category of an association Association
object_category 0..1
OntologyClass		 Used to hold the biolink class/category of an association Association
subject_closure 0..*
String		 Used to hold the subject closure of an association Association
object_closure 0..*
String		 Used to hold the object closure of an association Association
subject_category_closure 0..*
OntologyClass		 Used to hold the subject category closure of an association Association
object_category_closure 0..*
OntologyClass		 Used to hold the object category closure of an association Association
subject_namespace 0..1
String		 Used to hold the subject namespace of an association Association
object_namespace 0..1
String		 Used to hold the object namespace of an association Association
subject_label_closure 0..*
String		 Used to hold the subject label closure of an association Association
object_label_closure 0..*
String		 Used to hold the object label closure of an association Association
retrieval_source_ids 0..*
RetrievalSource		 A list of retrieval sources that served as a source of knowledge expressed in... Association
id 1..1
String		 A unique identifier for an entity Entity
iri 0..1
IriType		 An IRI for an entity Entity
category 0..*
CategoryType		 Name of the high level ontology class in which this entity is categorized Entity
type 0..*
String		 rdf:type of biolink:Association should be fixed at rdf:Statement Entity
name 0..1
LabelType		 A human-readable name for an attribute or entity Entity
description 0..1
NarrativeText		 a human-readable description of an entity Entity
has_attribute 0..*
Attribute		 connects any entity to an attribute Entity

See Also

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/biolink/biolink-model

Mappings

Mapping Type Mapped Value
self biolink:GeneToExpressionSiteAssociation
native biolink:GeneToExpressionSiteAssociation

LinkML Source

Direct

name: gene to expression site association
description: An association between a gene and a gene expression site, possibly qualified
  by stage/timing info.
notes:
- 'TBD: introduce subclasses for distinction between wild-type and experimental conditions?'
from_schema: https://w3id.org/biolink/biolink-model
see_also:
- https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee
is_a: association
slots:
- stage qualifier
- quantifier qualifier
slot_usage:
  subject:
    name: subject
    description: Gene or gene product positively within the specified anatomical entity
      (or subclass, i.e. cellular component) location.
    domain_of:
    - association
    range: gene or gene product
  object:
    name: object
    description: location in which the gene is expressed
    examples:
    - value: UBERON:0002037
      description: cerebellum
    domain_of:
    - association
    range: anatomical entity
  predicate:
    name: predicate
    description: expression relationship
    domain_of:
    - predicate mapping
    - association
    subproperty_of: expressed in
  stage qualifier:
    name: stage qualifier
    description: stage at which the gene is expressed in the site
    examples:
    - value: UBERON:0000069
      description: larval stage
    domain_of:
    - gene expression mixin
    - gene to expression site association
    range: life stage
  quantifier qualifier:
    name: quantifier qualifier
    description: can be used to indicate magnitude, or also ranking
    domain_of:
    - gene expression mixin
    - gene to expression site association
defining_slots:
- subject
- predicate
- object