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Class: GeneToExpressionSiteAssociation

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?

classDiagram class GeneToExpressionSiteAssociation Association <|-- GeneToExpressionSiteAssociation GeneToExpressionSiteAssociation : adjusted_p_value GeneToExpressionSiteAssociation : agent_type GeneToExpressionSiteAssociation --|> AgentTypeEnum : agent_type GeneToExpressionSiteAssociation : aggregator_knowledge_source GeneToExpressionSiteAssociation : category GeneToExpressionSiteAssociation : deprecated GeneToExpressionSiteAssociation : description GeneToExpressionSiteAssociation : has_attribute GeneToExpressionSiteAssociation --|> Attribute : has_attribute GeneToExpressionSiteAssociation : has_evidence GeneToExpressionSiteAssociation --|> EvidenceType : has_evidence GeneToExpressionSiteAssociation : has_supporting_studies GeneToExpressionSiteAssociation --|> Study : has_supporting_studies GeneToExpressionSiteAssociation : id GeneToExpressionSiteAssociation : iri GeneToExpressionSiteAssociation : knowledge_level GeneToExpressionSiteAssociation --|> KnowledgeLevelEnum : knowledge_level GeneToExpressionSiteAssociation : knowledge_source GeneToExpressionSiteAssociation : name GeneToExpressionSiteAssociation : negated GeneToExpressionSiteAssociation : object GeneToExpressionSiteAssociation --|> AnatomicalEntity : object GeneToExpressionSiteAssociation : object_category GeneToExpressionSiteAssociation --|> OntologyClass : object_category GeneToExpressionSiteAssociation : object_category_closure GeneToExpressionSiteAssociation --|> OntologyClass : object_category_closure GeneToExpressionSiteAssociation : object_closure GeneToExpressionSiteAssociation : object_label_closure GeneToExpressionSiteAssociation : object_namespace GeneToExpressionSiteAssociation : original_object GeneToExpressionSiteAssociation : original_predicate GeneToExpressionSiteAssociation : original_subject GeneToExpressionSiteAssociation : p_value GeneToExpressionSiteAssociation : predicate GeneToExpressionSiteAssociation : primary_knowledge_source GeneToExpressionSiteAssociation : publications GeneToExpressionSiteAssociation --|> Publication : publications GeneToExpressionSiteAssociation : qualifier GeneToExpressionSiteAssociation : qualifiers GeneToExpressionSiteAssociation --|> OntologyClass : qualifiers GeneToExpressionSiteAssociation : quantifier_qualifier GeneToExpressionSiteAssociation --|> OntologyClass : quantifier_qualifier GeneToExpressionSiteAssociation : retrieval_source_ids GeneToExpressionSiteAssociation --|> RetrievalSource : retrieval_source_ids GeneToExpressionSiteAssociation : stage_qualifier GeneToExpressionSiteAssociation --|> LifeStage : stage_qualifier GeneToExpressionSiteAssociation : subject GeneToExpressionSiteAssociation --|> GeneOrGeneProduct : subject GeneToExpressionSiteAssociation : subject_category GeneToExpressionSiteAssociation --|> OntologyClass : subject_category GeneToExpressionSiteAssociation : subject_category_closure GeneToExpressionSiteAssociation --|> OntologyClass : subject_category_closure GeneToExpressionSiteAssociation : subject_closure GeneToExpressionSiteAssociation : subject_label_closure GeneToExpressionSiteAssociation : subject_namespace GeneToExpressionSiteAssociation : timepoint GeneToExpressionSiteAssociation : type

Inheritance

Slots

Name Cardinality and Range Inheritance Examples
stage_qualifier:
stage at which the gene is expressed in the site
0..1
LifeStage		 direct UBERON:0000069
quantifier_qualifier:
can be used to indicate magnitude, or also ranking 		0..1
OntologyClass		 direct
subject:
Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location. 		1
GeneOrGeneProduct		 Association
predicate:
expression relationship 		1
PredicateType		 Association
object:
location in which the gene is expressed 		1
AnatomicalEntity		 Association UBERON:0002037
negated:
if set to true, then the association is negated i.e. is not true 		0..1
Boolean		 Association
qualifier:
grouping slot for all qualifiers on an edge. useful for testing compliance with association classes 		0..1
String		 Association
qualifiers:
connects an association to qualifiers that modify or qualify the meaning of that association 		*
OntologyClass		 Association
publications:
One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. 		*
Publication		 Association
has_evidence:
connects an association to an instance of supporting evidence 		*
EvidenceType		 Association
knowledge_source:
An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property. 		0..1
String		 Association
primary_knowledge_source:
The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. "aggregator knowledge source" can be used to capture non-primary sources. 		0..1
String		 Association
aggregator_knowledge_source:
An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form. 		*
String		 Association
knowledge_level:
Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true. 		1
KnowledgeLevelEnum		 Association knowledge_assertion, prediction, statistical_association
agent_type:
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information. 		1
AgentTypeEnum		 Association manual_agent, automated_agent, computational_model, text_mining_agent
timepoint:
a point in time 		0..1
TimeType		 Association
original_subject:
used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
String		 Association
original_predicate:
used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
Uriorcurie		 Association
original_object:
used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification. 		0..1
String		 Association
subject_category:
Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
OntologyClass		 Association biolink:Gene
object_category:
Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
OntologyClass		 Association biolink:Disease
subject_closure:
Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association
object_closure:
Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association ['MONDO:0000167', 'MONDO:0005395']
subject_category_closure:
Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
OntologyClass		 Association ['biolink:Gene", "biolink:NamedThing']
object_category_closure:
Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
OntologyClass		 Association ['biolink:Disease", "biolink:NamedThing']
subject_namespace:
Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
String		 Association NCBIGene
object_namespace:
Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		0..1
String		 Association MONDO
subject_label_closure:
Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association ['BRACA1']
object_label_closure:
Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX. 		*
String		 Association breast cancer, cancer
retrieval_source_ids:
A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge. 		*
RetrievalSource		 Association
p_value:
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone. 		0..1
Float		 Association
adjusted_p_value:
The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<. 		0..1
Float		 Association
has_supporting_studies:
A study that produced information used as evidence to generate the knowledge expressed in an Association. 		*
Study		 Association
id:
A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI 		1
String		 Entity
iri:
An IRI for an entity. This is determined by the id using expansion rules. 		0..1
IriType		 Entity
category:
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values biolink:Protein, biolink:GeneProduct, biolink:MolecularEntity. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing} 		*
Uriorcurie		 Entity
type:
rdf:type of biolink:Association should be fixed at rdf:Statement 		*
String		 Entity
name:
A human-readable name for an attribute or entity. 		0..1
LabelType		 Entity
description:
a human-readable description of an entity 		0..1
NarrativeText		 Entity
has_attribute:
connects any entity to an attribute 		*
Attribute		 Entity
deprecated:
A boolean flag indicating that an entity is no longer considered current or valid. 		0..1
Boolean		 Entity

LinkML Source

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.
    range: gene or gene product
  object:
    name: object
    description: location in which the gene is expressed
    examples:
    - value: UBERON:0002037
      description: cerebellum
    range: anatomical entity
  predicate:
    name: predicate
    description: expression relationship
    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
    range: life stage
  quantifier qualifier:
    name: quantifier qualifier
    description: can be used to indicate magnitude, or also ranking
defining_slots:
- subject
- predicate
- object