Class: PredicateMapping

Description: 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.

classDiagram class PredicateMapping PredicateMapping : anatomical_context_qualifier PredicateMapping : broad_match PredicateMapping --|> NamedThing : broad_match PredicateMapping : causal_mechanism_qualifier PredicateMapping --|> CausalMechanismQualifierEnum : causal_mechanism_qualifier PredicateMapping : exact_match PredicateMapping --|> NamedThing : exact_match PredicateMapping : mapped_predicate PredicateMapping : narrow_match PredicateMapping --|> NamedThing : narrow_match PredicateMapping : object_aspect_qualifier PredicateMapping : object_context_qualifier PredicateMapping : object_derivative_qualifier PredicateMapping : object_direction_qualifier PredicateMapping --|> DirectionQualifierEnum : object_direction_qualifier PredicateMapping : object_form_or_variant_qualifier PredicateMapping : object_part_qualifier PredicateMapping : predicate PredicateMapping : qualified_predicate PredicateMapping : species_context_qualifier PredicateMapping --|> OrganismTaxon : species_context_qualifier PredicateMapping : subject_aspect_qualifier PredicateMapping : subject_context_qualifier PredicateMapping : subject_derivative_qualifier PredicateMapping : subject_direction_qualifier PredicateMapping --|> DirectionQualifierEnum : subject_direction_qualifier PredicateMapping : subject_form_or_variant_qualifier PredicateMapping : subject_part_qualifier

Slots

Name	Cardinality and Range	Inheritance	Examples
mapped_predicate: The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs.	0..1 String	direct
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 String	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
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 String	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 String	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_context_qualifier: None	0..1 String	direct
predicate: A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.	1..1 PredicateType	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
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 String	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
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 String	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 String	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 String	direct	metabolite
object_context_qualifier: None	0..1 String	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 String	direct	blood, cerebral cortext
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
exact_match: holds between two entities that have strictly equivalent meanings, with a high degree of confidence	0..* NamedThing	direct
narrow_match: a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree.	0..* NamedThing	direct
broad_match: a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree.	0..* NamedThing	direct

Usages

used by	used in	type	used
MappingCollection	predicate_mappings	range	PredicateMapping

LinkML Source

name: predicate mapping
description: 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.
from_schema: https://w3id.org/biolink/biolink-model
slots:
- mapped predicate
- subject aspect qualifier
- subject direction qualifier
- subject form or variant qualifier
- subject part qualifier
- subject derivative qualifier
- subject context qualifier
- predicate
- qualified predicate
- object aspect qualifier
- object direction qualifier
- object form or variant qualifier
- object part qualifier
- object derivative qualifier
- object context qualifier
- causal mechanism qualifier
- anatomical context qualifier
- species context qualifier
- exact match
- narrow match
- broad match