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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 : adjusted_p_value 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 : has_supporting_studies GeneAffectsChemicalAssociation --|> Study : has_supporting_studies 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 : p_value 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

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 mutation, late stage, severe, transplant, chemical analog
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 stability, abundance, expression, exposure
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 mutation, late stage, severe, transplant, chemical analog
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 stability, abundance, expression, exposure
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 metabolite
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 blood, cerebral cortext
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 zebrafish, human
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
GeneOrGeneProduct		 Association
predicate:
A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes. 		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
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 		*
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

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
    range: gene or gene product
  subject form or variant qualifier:
    name: subject form or variant qualifier
    range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  subject part qualifier:
    name: subject part qualifier
    range: GeneOrGeneProductOrChemicalPartQualifierEnum
  subject aspect qualifier:
    name: subject aspect qualifier
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  subject context qualifier:
    name: subject context qualifier
    range: anatomical entity
  subject direction qualifier:
    name: subject direction qualifier
    range: DirectionQualifierEnum
  predicate:
    name: predicate
    subproperty_of: affects
  qualified predicate:
    name: qualified predicate
    subproperty_of: causes
  object:
    name: object
    range: chemical entity
  object form or variant qualifier:
    name: object form or variant qualifier
    range: ChemicalOrGeneOrGeneProductFormOrVariantEnum
  object part qualifier:
    name: object part qualifier
    range: GeneOrGeneProductOrChemicalPartQualifierEnum
  object derivative qualifier:
    name: object derivative qualifier
    range: ChemicalEntityDerivativeEnum
  object aspect qualifier:
    name: object aspect qualifier
    range: GeneOrGeneProductOrChemicalEntityAspectEnum
  object context qualifier:
    name: object context qualifier
    range: anatomical entity
  object direction qualifier:
    name: object direction qualifier
    range: DirectionQualifierEnum
  causal mechanism qualifier:
    name: causal mechanism qualifier
    range: CausalMechanismQualifierEnum
  anatomical context qualifier:
    name: anatomical context qualifier
    range: anatomical entity
  species context qualifier:
    name: species context qualifier
    range: organism taxon