Class: GeneAffectsChemicalAssociation
Description: Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)
classDiagram
class GeneAffectsChemicalAssociation
Association <|-- GeneAffectsChemicalAssociation
GeneAffectsChemicalAssociation : agent_type
GeneAffectsChemicalAssociation --|> AgentTypeEnum : agent_type
GeneAffectsChemicalAssociation : aggregator_knowledge_source
GeneAffectsChemicalAssociation : anatomical_context_qualifier
GeneAffectsChemicalAssociation --|> AnatomicalEntity : anatomical_context_qualifier
GeneAffectsChemicalAssociation : category
GeneAffectsChemicalAssociation : causal_mechanism_qualifier
GeneAffectsChemicalAssociation --|> CausalMechanismQualifierEnum : causal_mechanism_qualifier
GeneAffectsChemicalAssociation : deprecated
GeneAffectsChemicalAssociation : description
GeneAffectsChemicalAssociation : has_attribute
GeneAffectsChemicalAssociation --|> Attribute : has_attribute
GeneAffectsChemicalAssociation : has_evidence
GeneAffectsChemicalAssociation --|> EvidenceType : has_evidence
GeneAffectsChemicalAssociation : id
GeneAffectsChemicalAssociation : iri
GeneAffectsChemicalAssociation : knowledge_level
GeneAffectsChemicalAssociation --|> KnowledgeLevelEnum : knowledge_level
GeneAffectsChemicalAssociation : knowledge_source
GeneAffectsChemicalAssociation : name
GeneAffectsChemicalAssociation : negated
GeneAffectsChemicalAssociation : object
GeneAffectsChemicalAssociation --|> ChemicalEntity : object
GeneAffectsChemicalAssociation : object_aspect_qualifier
GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : object_aspect_qualifier
GeneAffectsChemicalAssociation : object_category
GeneAffectsChemicalAssociation --|> OntologyClass : object_category
GeneAffectsChemicalAssociation : object_category_closure
GeneAffectsChemicalAssociation --|> OntologyClass : object_category_closure
GeneAffectsChemicalAssociation : object_closure
GeneAffectsChemicalAssociation : object_context_qualifier
GeneAffectsChemicalAssociation --|> AnatomicalEntity : object_context_qualifier
GeneAffectsChemicalAssociation : object_derivative_qualifier
GeneAffectsChemicalAssociation --|> ChemicalEntityDerivativeEnum : object_derivative_qualifier
GeneAffectsChemicalAssociation : object_direction_qualifier
GeneAffectsChemicalAssociation --|> DirectionQualifierEnum : object_direction_qualifier
GeneAffectsChemicalAssociation : object_form_or_variant_qualifier
GeneAffectsChemicalAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : object_form_or_variant_qualifier
GeneAffectsChemicalAssociation : object_label_closure
GeneAffectsChemicalAssociation : object_namespace
GeneAffectsChemicalAssociation : object_part_qualifier
GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalPartQualifierEnum : object_part_qualifier
GeneAffectsChemicalAssociation : original_object
GeneAffectsChemicalAssociation : original_predicate
GeneAffectsChemicalAssociation : original_subject
GeneAffectsChemicalAssociation : predicate
GeneAffectsChemicalAssociation : primary_knowledge_source
GeneAffectsChemicalAssociation : publications
GeneAffectsChemicalAssociation --|> Publication : publications
GeneAffectsChemicalAssociation : qualified_predicate
GeneAffectsChemicalAssociation : qualifier
GeneAffectsChemicalAssociation : qualifiers
GeneAffectsChemicalAssociation --|> OntologyClass : qualifiers
GeneAffectsChemicalAssociation : retrieval_source_ids
GeneAffectsChemicalAssociation --|> RetrievalSource : retrieval_source_ids
GeneAffectsChemicalAssociation : species_context_qualifier
GeneAffectsChemicalAssociation --|> OrganismTaxon : species_context_qualifier
GeneAffectsChemicalAssociation : subject
GeneAffectsChemicalAssociation --|> GeneOrGeneProduct : subject
GeneAffectsChemicalAssociation : subject_aspect_qualifier
GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalEntityAspectEnum : subject_aspect_qualifier
GeneAffectsChemicalAssociation : subject_category
GeneAffectsChemicalAssociation --|> OntologyClass : subject_category
GeneAffectsChemicalAssociation : subject_category_closure
GeneAffectsChemicalAssociation --|> OntologyClass : subject_category_closure
GeneAffectsChemicalAssociation : subject_closure
GeneAffectsChemicalAssociation : subject_context_qualifier
GeneAffectsChemicalAssociation --|> AnatomicalEntity : subject_context_qualifier
GeneAffectsChemicalAssociation : subject_derivative_qualifier
GeneAffectsChemicalAssociation : subject_direction_qualifier
GeneAffectsChemicalAssociation --|> DirectionQualifierEnum : subject_direction_qualifier
GeneAffectsChemicalAssociation : subject_form_or_variant_qualifier
GeneAffectsChemicalAssociation --|> ChemicalOrGeneOrGeneProductFormOrVariantEnum : subject_form_or_variant_qualifier
GeneAffectsChemicalAssociation : subject_label_closure
GeneAffectsChemicalAssociation : subject_namespace
GeneAffectsChemicalAssociation : subject_part_qualifier
GeneAffectsChemicalAssociation --|> GeneOrGeneProductOrChemicalPartQualifierEnum : subject_part_qualifier
GeneAffectsChemicalAssociation : timepoint
GeneAffectsChemicalAssociation : type
Inheritance
- Entity
- Association
- GeneAffectsChemicalAssociation
- Association
Slots
Name | Cardinality and Range | Inheritance | Examples |
---|---|---|---|
subject_form_or_variant_qualifier: A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement). |
0..1 ChemicalOrGeneOrGeneProductFormOrVariantEnum |
direct | |
subject_part_qualifier: defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement). |
0..1 GeneOrGeneProductOrChemicalPartQualifierEnum |
direct | |
subject_derivative_qualifier: A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement). |
0..1 String |
direct | metabolite |
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 | |
subject_context_qualifier: None |
0..1 AnatomicalEntity |
direct | |
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 | |
object_form_or_variant_qualifier: A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement). |
0..1 ChemicalOrGeneOrGeneProductFormOrVariantEnum |
direct | |
object_part_qualifier: defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement). |
0..1 GeneOrGeneProductOrChemicalPartQualifierEnum |
direct | |
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 | |
object_context_qualifier: None |
0..1 AnatomicalEntity |
direct | |
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 | |
object_derivative_qualifier: A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement). |
0..1 ChemicalEntityDerivativeEnum |
direct | |
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 (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker') |
0..1 CausalMechanismQualifierEnum |
direct | |
anatomical_context_qualifier: A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location). |
0..1 AnatomicalEntity |
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. 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 String |
direct | |
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 | |
subject: connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. |
1..1 GeneOrGeneProduct |
Association | |
predicate: A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. |
1..1 PredicateType |
Association | |
object: connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object. |
1..1 ChemicalEntity |
Association | |
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 |
0..* OntologyClass |
Association | |
publications: One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement. |
0..* Publication |
Association | |
has_evidence: connects an association to an instance of supporting evidence |
0..* 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. |
0..* 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..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..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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* 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. |
0..* RetrievalSource |
Association | |
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI |
1..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} |
0..* Uriorcurie |
Entity | |
type: rdf:type of biolink:Association should be fixed at rdf:Statement |
0..* 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 |
0..* Attribute |
Entity | |
deprecated: A boolean flag indicating that an entity is no longer considered current or valid. |
0..1 Boolean |
Entity |
Example values
Slot Name | Value |
---|---|
GeneAffectsChemicalAssociation | JsonObj(subject='TRPC4', predicate='affects', qualified_predicte='causes', object='Barium', object_aspect_qualifier='transport', object_direction_qualifier='increased') |
LinkML Source
name: gene affects chemical association
description: Describes an effect that a gene or gene product has on a chemical entity
(e.g. an impact of on its abundance, activity, localization, processing, transport,
etc.)
examples:
- value: JsonObj(subject='TRPC4', predicate='affects', qualified_predicte='causes',
object='Barium', object_aspect_qualifier='transport', object_direction_qualifier='increased')
from_schema: https://w3id.org/biolink/biolink-model
is_a: association
slots:
- subject form or variant qualifier
- subject part qualifier
- subject derivative qualifier
- subject aspect qualifier
- subject context qualifier
- subject direction qualifier
- object form or variant qualifier
- object part qualifier
- object aspect qualifier
- object context qualifier
- object direction qualifier
- object derivative qualifier
- causal mechanism qualifier
- anatomical context qualifier
- qualified predicate
- species context qualifier
slot_usage:
subject:
name: subject
domain_of:
- association
- cell line to entity association mixin
- chemical entity to entity association mixin
- drug to entity association mixin
- chemical to entity association mixin
- case to entity association mixin
- chemical to chemical association
- named thing associated with likelihood of named thing association
- material sample to entity association mixin
- material sample derivation association
- disease to entity association mixin
- entity to exposure event association mixin
- entity to outcome association mixin
- frequency qualifier mixin
- entity to phenotypic feature association mixin
- disease or phenotypic feature to entity association mixin
- entity to disease or phenotypic feature association mixin
- genotype to entity association mixin
- gene to entity association mixin
- variant to entity association mixin
- model to disease association mixin
- macromolecular machine to entity association mixin
- organism taxon to entity association
range: gene or gene product
subject form or variant qualifier:
name: subject form or variant qualifier
domain_of:
- predicate mapping
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
- gene has variant that contributes to disease association
range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
subject part qualifier:
name: subject part qualifier
domain_of:
- predicate mapping
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
range: GeneOrGeneProductOrChemicalPartQualifierEnum
subject aspect qualifier:
name: subject aspect qualifier
domain_of:
- predicate mapping
- named thing associated with likelihood of named thing association
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
- gene to disease or phenotypic feature association
range: GeneOrGeneProductOrChemicalEntityAspectEnum
subject context qualifier:
name: subject context qualifier
domain_of:
- predicate mapping
- named thing associated with likelihood of named thing association
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
range: anatomical entity
subject direction qualifier:
name: subject direction qualifier
domain_of:
- predicate mapping
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
range: DirectionQualifierEnum
predicate:
name: predicate
domain_of:
- predicate mapping
- association
- cell line to entity association mixin
- chemical entity to entity association mixin
- drug to entity association mixin
- chemical to entity association mixin
- case to entity association mixin
- chemical to chemical association
- named thing associated with likelihood of named thing association
- material sample to entity association mixin
- material sample derivation association
- disease to entity association mixin
- entity to exposure event association mixin
- entity to outcome association mixin
- frequency qualifier mixin
- entity to phenotypic feature association mixin
- disease or phenotypic feature to entity association mixin
- entity to disease or phenotypic feature association mixin
- genotype to entity association mixin
- gene to entity association mixin
- variant to entity association mixin
- model to disease association mixin
- macromolecular machine to entity association mixin
- organism taxon to entity association
subproperty_of: affects
qualified predicate:
name: qualified predicate
domain_of:
- predicate mapping
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
subproperty_of: causes
object:
name: object
domain_of:
- association
- cell line to entity association mixin
- chemical entity to entity association mixin
- drug to entity association mixin
- chemical to entity association mixin
- case to entity association mixin
- chemical to chemical association
- named thing associated with likelihood of named thing association
- material sample to entity association mixin
- material sample derivation association
- disease to entity association mixin
- entity to exposure event association mixin
- entity to outcome association mixin
- frequency qualifier mixin
- entity to phenotypic feature association mixin
- disease or phenotypic feature to entity association mixin
- entity to disease or phenotypic feature association mixin
- genotype to entity association mixin
- gene to entity association mixin
- variant to entity association mixin
- model to disease association mixin
- macromolecular machine to entity association mixin
- organism taxon to entity association
range: chemical entity
object form or variant qualifier:
name: object form or variant qualifier
domain_of:
- predicate mapping
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
object part qualifier:
name: object part qualifier
domain_of:
- predicate mapping
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
range: GeneOrGeneProductOrChemicalPartQualifierEnum
object derivative qualifier:
name: object derivative qualifier
domain_of:
- predicate mapping
- gene affects chemical association
range: ChemicalEntityDerivativeEnum
object aspect qualifier:
name: object aspect qualifier
domain_of:
- predicate mapping
- named thing associated with likelihood of named thing association
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
range: GeneOrGeneProductOrChemicalEntityAspectEnum
object context qualifier:
name: object context qualifier
domain_of:
- predicate mapping
- named thing associated with likelihood of named thing association
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
range: anatomical entity
object direction qualifier:
name: object direction qualifier
domain_of:
- predicate mapping
- chemical affects gene association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- feature or disease qualifiers to entity mixin
- gene to disease or phenotypic feature association
- chemical entity or gene or gene product regulates gene association
range: DirectionQualifierEnum
causal mechanism qualifier:
name: causal mechanism qualifier
domain_of:
- predicate mapping
- chemical affects gene association
- gene affects chemical association
range: CausalMechanismQualifierEnum
anatomical context qualifier:
name: anatomical context qualifier
domain_of:
- predicate mapping
- chemical gene interaction association
- chemical affects gene association
- gene affects chemical association
range: anatomical entity
species context qualifier:
name: species context qualifier
domain_of:
- predicate mapping
- chemical affects gene association
- gene affects chemical association
range: organism taxon