Class: GeneToGeneAssociation
Description: parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction.
Aliases: molecular or genetic interaction
classDiagram
class GeneToGeneAssociation
Association <|-- GeneToGeneAssociation
GeneToGeneAssociation <|-- GeneToGeneHomologyAssociation
GeneToGeneAssociation <|-- GeneToGeneCoexpressionAssociation
GeneToGeneAssociation <|-- PairwiseGeneToGeneInteraction
GeneToGeneAssociation : adjusted_p_value
GeneToGeneAssociation : agent_type
GeneToGeneAssociation --|> AgentTypeEnum : agent_type
GeneToGeneAssociation : aggregator_knowledge_source
GeneToGeneAssociation : category
GeneToGeneAssociation : causal_mechanism_qualifier
GeneToGeneAssociation --|> CausalMechanismQualifierEnum : causal_mechanism_qualifier
GeneToGeneAssociation : deprecated
GeneToGeneAssociation : description
GeneToGeneAssociation : elevate_to_prediction
GeneToGeneAssociation : evidence_count
GeneToGeneAssociation : has_attribute
GeneToGeneAssociation --|> Attribute : has_attribute
GeneToGeneAssociation : has_confidence_score
GeneToGeneAssociation : has_evidence
GeneToGeneAssociation --|> InformationContentEntity : has_evidence
GeneToGeneAssociation : has_evidence_of_type
GeneToGeneAssociation --|> EvidenceType : has_evidence_of_type
GeneToGeneAssociation : has_supporting_studies
GeneToGeneAssociation --|> Study : has_supporting_studies
GeneToGeneAssociation : id
GeneToGeneAssociation : iri
GeneToGeneAssociation : knowledge_level
GeneToGeneAssociation --|> KnowledgeLevelEnum : knowledge_level
GeneToGeneAssociation : knowledge_source
GeneToGeneAssociation : name
GeneToGeneAssociation : negated
GeneToGeneAssociation : object
GeneToGeneAssociation --|> GeneOrGeneProduct : object
GeneToGeneAssociation : object_activity_qualifier
GeneToGeneAssociation --|> MolecularActivity : object_activity_qualifier
GeneToGeneAssociation : object_aspect_qualifier
GeneToGeneAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : object_aspect_qualifier
GeneToGeneAssociation : object_category
GeneToGeneAssociation --|> OntologyClass : object_category
GeneToGeneAssociation : object_category_closure
GeneToGeneAssociation --|> OntologyClass : object_category_closure
GeneToGeneAssociation : object_closure
GeneToGeneAssociation : object_context_qualifier
GeneToGeneAssociation --|> AnatomicalEntity : object_context_qualifier
GeneToGeneAssociation : object_direction_qualifier
GeneToGeneAssociation --|> DirectionQualifierEnum : object_direction_qualifier
GeneToGeneAssociation : object_feature_name
GeneToGeneAssociation : object_label_closure
GeneToGeneAssociation : object_namespace
GeneToGeneAssociation : object_process_qualifier
GeneToGeneAssociation --|> BiologicalProcess : object_process_qualifier
GeneToGeneAssociation : original_object
GeneToGeneAssociation : original_predicate
GeneToGeneAssociation : original_subject
GeneToGeneAssociation : p_value
GeneToGeneAssociation : predicate
GeneToGeneAssociation : primary_knowledge_source
GeneToGeneAssociation : publications
GeneToGeneAssociation --|> Publication : publications
GeneToGeneAssociation : qualified_predicate
GeneToGeneAssociation : qualifier
GeneToGeneAssociation : qualifiers
GeneToGeneAssociation --|> OntologyClass : qualifiers
GeneToGeneAssociation : retrieval_source_ids
GeneToGeneAssociation --|> RetrievalSource : retrieval_source_ids
GeneToGeneAssociation : semmed_agreement_count
GeneToGeneAssociation : sources
GeneToGeneAssociation --|> RetrievalSource : sources
GeneToGeneAssociation : species_context_qualifier
GeneToGeneAssociation --|> OrganismTaxon : species_context_qualifier
GeneToGeneAssociation : subject
GeneToGeneAssociation --|> GeneOrGeneProduct : subject
GeneToGeneAssociation : subject_activity_qualifier
GeneToGeneAssociation --|> MolecularActivity : subject_activity_qualifier
GeneToGeneAssociation : subject_aspect_qualifier
GeneToGeneAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier
GeneToGeneAssociation : subject_category
GeneToGeneAssociation --|> OntologyClass : subject_category
GeneToGeneAssociation : subject_category_closure
GeneToGeneAssociation --|> OntologyClass : subject_category_closure
GeneToGeneAssociation : subject_closure
GeneToGeneAssociation : subject_context_qualifier
GeneToGeneAssociation --|> AnatomicalEntity : subject_context_qualifier
GeneToGeneAssociation : subject_direction_qualifier
GeneToGeneAssociation --|> DirectionQualifierEnum : subject_direction_qualifier
GeneToGeneAssociation : subject_feature_name
GeneToGeneAssociation : subject_label_closure
GeneToGeneAssociation : subject_namespace
GeneToGeneAssociation : subject_process_qualifier
GeneToGeneAssociation --|> BiologicalProcess : subject_process_qualifier
GeneToGeneAssociation : supporting_text
GeneToGeneAssociation : timepoint
GeneToGeneAssociation : type
GeneToGeneAssociation : update_date
Inheritance
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| subject_aspect_qualifier: Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement). |
0..1 GeneOrGeneProductOrChemicalEntityAspectEnum |
direct | stability, abundance, expression, exposure |
| subject_direction_qualifier: Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement). |
0..1 DirectionQualifierEnum |
direct | increased, downregulated |
| object_aspect_qualifier: Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement). |
0..1 GeneOrGeneProductOrChemicalEntityAspectEnum |
direct | stability, abundance, expression, exposure |
| object_direction_qualifier: Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement). |
0..1 DirectionQualifierEnum |
direct | increased, downregulated |
| causal_mechanism_qualifier: A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated |
0..1 CausalMechanismQualifierEnum |
direct | agonism, inhibition |
| qualified_predicate: Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. |
0..1 Uriorcurie |
direct | biolink:causes |
| species_context_qualifier: A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place. |
0..1 OrganismTaxon |
direct | NCBITaxon:7955, NCBITaxon:9606 |
| subject: the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa. |
1 GeneOrGeneProduct |
direct | |
| subject_activity_qualifier: None |
0..1 MolecularActivity |
direct | |
| subject_process_qualifier: None |
0..1 BiologicalProcess |
direct | |
| subject_context_qualifier: A qualifier describing the context in which the subject of an association holds. |
0..1 AnatomicalEntity |
direct | |
| predicate: Has a value from the Biolink 'related_to' hierarchy. In RDF, this corresponds to rdf:predicate and in Neo4j this corresponds to the relationship type. The convention is for an edge label in snake_case form. For example, biolink:related_to, biolink:causes, biolink:treats |
1 Uriorcurie |
direct | |
| qualified_predicate: Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. Has a value from the Biolink 'related_to' hierarchy, for example, biolink:related_to, biolink:causes, biolink:treats This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading. |
0..1 Uriorcurie |
direct | biolink:causes |
| object: the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa. |
1 GeneOrGeneProduct |
direct | |
| object_activity_qualifier: None |
0..1 MolecularActivity |
direct | |
| object_process_qualifier: None |
0..1 BiologicalProcess |
direct | |
| object_context_qualifier: A qualifier describing the context in which the object of an association holds. |
0..1 AnatomicalEntity |
direct | |
| 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 | |
| sources: A set of RetrievalSources, which traces where the statement expressed in an Association came from. For example, the provenance of a Gene-Chemical Edge might be traced through the Translator Resource that provided it (e.g. MolePro) to one or more intermediate aggregator resources (e.g. ChEMBL), and finally to the resource that originally created/curated it (e.g. ClinicalTrials.org). |
* RetrievalSource |
Association | |
| has_evidence_of_type: Connects an association to an evidence type ontology term. Generally represents terms from the ECO ontology. |
* EvidenceType |
Association | |
| has_evidence: Connects an association to detailed information providing supporting evidence. |
* InformationContentEntity |
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_feature_name: Used to describe a subordinate feature of the associated subject for example, a particular sequence variant of a gene |
0..1 String |
Association | |
| object_feature_name: Used to describe a subordinate feature of the associated object for example, a symptom diagnosis of a disease |
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 | ['BRCA1'] |
| 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 | |
| supporting_text: The segment of text from a document that supports the mined assertion. |
* String |
Association | Here, we report two new cases of rivaroxaban-induced hepatitis. |
| has_supporting_studies: Studies that produced information used as evidence to generate the knowledge expressed in an Association. |
* Study |
Association | |
| update_date: date on which an entity was updated. This can be applied to nodes or edges |
0..1 Date |
Association | |
| has_confidence_score: connects an association to a quantitative (numeric) value that can be interpreted as an indicator of the degree of confidence that a piece of information is true, and accurately reflects the aspect of reality it is about. |
0..1 Float |
Association | |
| elevate_to_prediction: A boolean flag indicating whether a clinical trial finding should be elevated to a prediction. |
0..1 Boolean |
Association | |
| evidence_count: The number of evidence instances that are connected to an association. |
0..1 Integer |
Association | |
| semmed_agreement_count: The number of times this concept has been asserted in the SemMedDB literature database. |
0..1 Integer |
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 gene association
description: parent class for different kinds of gene-gene or gene product to gene
product relationships. Includes homology and interaction.
from_schema: https://w3id.org/biolink/vocab/
aliases:
- molecular or genetic interaction
is_a: association
slots:
- subject aspect qualifier
- subject direction qualifier
- object aspect qualifier
- object direction qualifier
- causal mechanism qualifier
- qualified predicate
- species context qualifier
- subject
- subject activity qualifier
- subject process qualifier
- subject context qualifier
- predicate
- qualified predicate
- object
- object activity qualifier
- object process qualifier
- object context qualifier
slot_usage:
subject:
name: subject
description: the subject gene in the association. If the relation is symmetric,
subject vs object is arbitrary. We allow a gene product to stand as a proxy
for the gene or vice versa.
range: gene or gene product
subject activity qualifier:
name: subject activity qualifier
range: molecular activity
subject process qualifier:
name: subject process qualifier
range: biological process
subject context qualifier:
name: subject context qualifier
range: anatomical entity
object:
name: object
description: the object gene in the association. If the relation is symmetric,
subject vs object is arbitrary. We allow a gene product to stand as a proxy
for the gene or vice versa.
range: gene or gene product
object activity qualifier:
name: object activity qualifier
range: molecular activity
object process qualifier:
name: object process qualifier
range: biological process
object context qualifier:
name: object context qualifier
range: anatomical entity
defining_slots:
- subject
- object