Slot: subject_form_or_variant_qualifier

Description: 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).

Domain: Association
Range: String

Inheritance

• association_slot
  • qualifier
    • form_or_variant_qualifier
      • subject_form_or_variant_qualifier

Applicable Classes

Name	Description	Modifies Slot
GeneAffectsChemicalAssociation	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.)	yes
CausalGeneToDiseaseAssociation	An association between a gene and a disease where variation in the gene has been shown to have a causal role in the disease.	no
GeneToDiseaseAssociation	An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease.	yes
ChemicalGeneSensitivityAssociation	Describes a relationship in which a chemical entity affects the sensitivity or susceptibility of a biological system to a gene or gene product (e.g. a chemical that increases or decreases the response to a gene or gene product). This covers 'response to substance' style interactions from sources such as CTD that map to the 'affects sensitivity to' predicate hierarchy, as opposed to the abundance/activity/processing effects covered by ChemicalAffectsGeneAssociation.	yes
ChemicalGeneInteractionAssociation	describes an interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)	yes
PredicateMapping	A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place.	no
ChemicalAffectsBiologicalEntityAssociation	Describes an effect that a chemical has on a biological entity (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)	yes
GeneHasVariantThatContributesToDiseaseAssociation	A gene-to-disease association that is asserted on the grounds that the gene harbours a sequence variant that contributes to the disease. Qualifies the gene with the form or variant that underlies the contribution.	no
MacromolecularMachineHasSubstrateAssociation	Describes the relationship between an enzyme (usually a macromolecular complex or gene product) and the molecules it acts on (substrate). The substrate can be a chemical, a polypeptide, or a protein.	no
GeneToPhenotypicFeatureAssociation	An association between a gene or gene product and a phenotypic feature, where variation in the gene is correlated with the phenotypic feature.	yes
CorrelatedGeneToDiseaseAssociation	An association between a gene (or gene product) and a disease for which the gene is statistically correlated with the disease rather than asserted as causal. Such associations typically derive from GWAS, co-occurrence analyses, or other statistical methods, and are annotated with scores such as a z-score or a diseases confidence score.	no

Example values

Slot Name	Value
subject_form_or_variant_qualifier	mutation
subject_form_or_variant_qualifier	late stage
subject_form_or_variant_qualifier	severe
subject_form_or_variant_qualifier	transplant
subject_form_or_variant_qualifier	chemical analog

LinkML Source

name: subject form or variant qualifier
description: '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).'
examples:
- value: mutation
- value: late stage
- value: severe
- value: transplant
- value: chemical analog
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/vocab/
is_a: form or variant qualifier
domain: association
alias: subject_form_or_variant_qualifier
domain_of:
- predicate mapping
- chemical gene interaction association
- macromolecular machine has substrate association
- chemical affects biological entity association
- chemical gene sensitivity association
- gene affects chemical association
- gene to phenotypic feature association
- gene to disease association
- causal gene to disease association
- correlated gene to disease association
- gene has variant that contributes to disease association
range: string