Slot: qualified_predicate

Description: 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.

Notes: to express the statement that “Chemical X causes increased expression of Gene Y”, the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes, object:GeneY, object_aspect: expression, object_direction:increased. The predicate ‘affects’ is needed for the core triple reading, but does not make sense in the full statement reading (because “Chemical X affects increased expression of Gene Y'' is not what we mean to say here: it causes increased expression of Gene Y)

Domain: Association
Range: Uriorcurie

Inheritance

• association_slot
  • qualifier
    • qualified_predicate

Applicable Classes

Name	Description	Modifies Slot
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
ChemicalEntityToBiologicalProcessAssociation	An association between a chemical entity and a biological process, where the chemical entity has some effect on the biological process.	no
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)	no
GeneRegulatesGeneAssociation	Describes a regulatory relationship between two genes or gene products.	yes
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
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
FeatureOrDiseaseQualifiersToEntityMixin	Qualifiers for disease or phenotype to entity associations.	no
EntityToFeatureOrGeneQualifiersMixin	Qualifiers for entity to gene associations.	no
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
EntityToFeatureOrVariantQualifiersMixin	Qualifiers for entity to variant associations.	no
GeneToDiseaseAssociation	An association between a gene or gene product and a disease, where variation in the gene is correlated with the disease.	no
EntityToFeatureOrDiseaseQualifiersMixin	Qualifiers for entity to disease or phenotype associations.	no
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
qualified_predicate	biolink:causes

LinkML Source

name: qualified predicate
description: 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.
notes:
- 'to express the statement that “Chemical X causes increased expression of Gene Y”,
  the core triple is read using the fields subject:ChemX, predicate:affects, object:GeneY
  . . . and the full statement is read using the fields subject:ChemX, qualified_predicate:causes,
  object:GeneY, object_aspect: expression, object_direction:increased. The predicate
  ‘affects’ is needed for the core triple reading, but does not make sense in the
  full statement reading  (because “Chemical X affects increased expression of Gene
  Y'''' is not what we mean to say here: it causes increased expression of Gene Y)'
examples:
- value: biolink:causes
  description: used with `affects` predicate to express causal statements
from_schema: https://w3id.org/biolink/vocab/
is_a: qualifier
domain: association
alias: qualified_predicate
domain_of:
- predicate mapping
- chemical entity to biological process association
- chemical gene interaction association
- gene regulates gene association
- chemical affects biological entity association
- gene affects chemical association
- entity to feature or disease qualifiers mixin
- entity to feature or variant qualifiers mixin
- entity to feature or gene qualifiers mixin
- feature or disease qualifiers to entity mixin
- gene to disease association
- causal gene to disease association
- correlated gene to disease association
range: uriorcurie