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response to predicate additions #1525

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104 changes: 100 additions & 4 deletions biolink-model.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -263,7 +263,7 @@
- qud:Unit

time type:
uri: xsd:time
uri: xsd:string
typeof: time

biological sequence:
Expand Down Expand Up @@ -1168,12 +1168,26 @@
- SNOMED:has_route_of_administration


response context qualifier:
description: >-
a biological response (general, study, cohort, etc.) with a specific set of characteristics to constrain
an association.
is_a: context qualifier
range: ResponseEnum

response target context qualifier:
description: >-
a biological response target (a patient, a cohort, a model system, a cell line, a sample of biological material,
etc.)
is_a: context qualifier
range: ResponseTargetEnum

population context qualifier:
description: >-
a biological population (general, study, cohort, etc.) with a specific
set of characteristics to constrain an association.
is_a: qualifier
range: population of individual organisms
range: population of individual organisms # TODO: harmonize with 'response target context qualifier'

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temporal context qualifier:
description: >-
Expand Down Expand Up @@ -2584,8 +2598,38 @@
another existing entity.
inverse: affects

associated with sensitivity to:
associated with response to:
is_a: associated with
description: >-
A statistical association used to indicate that the object of a statement using this predicate
induces a response of some kind in the subject entity. Intentionally broad in definition, this predicate
should be used with qualifiers to narrow the type of response (E.g. whether the response is therapeutic,
phenotypic, detrimental, resistant, etc. is captured in context, direction, and
aspect qualifiers).
annotations:
canonical_predicate: true
comments: >-
subject: NCBIGene:2064 # HER2
subject_aspect: Amplification
predicate: associated with response to
object: CHEBI:10035 # Trastuzumab
response_type_qualifier: therapeutic_sensitivity
response_direction_qualifer: increased
response_target_qualifier: human patient
disease_context_qualifier: MONDO:0007254 # breast cancer

subject: MONDO:0007254
predicate: associated with response to
qualified_predicate: associated with
object: CHEBI:10035 # Trastuzumab
response_context_qualifier: therapeutic_sensitivity

response associated with:
is_a: associated with
inverse: associated with response to

associated with sensitivity to:
is_a: associated with response to
description: >-
A relation that holds between a named thing and a chemical
that specifies that the change in the named
Expand All @@ -2606,7 +2650,7 @@
domain: chemical entity

associated with resistance to:
is_a: associated with
is_a: associated with response to
description: >-
A relation that holds between a named thing and a chemical
that specifies that the change in the named
Expand Down Expand Up @@ -9389,6 +9433,30 @@
- owl:Axiom


disease associated with response to chemical entity association:
description: >-
A statistical association between a disease and a chemical entity where the
chemical entity has a therapeutic or adverse effect on the disease progression, symptoms or outcomes
in a patient, cell line, or any model system.
is_a: association
slots:
- response context qualifier
- response target context qualifier
defining_slots:
- subject
- predicate
- object
- response context qualifier
- response target context qualifier
slot_usage:
subject:
range: disease
object:
range: chemical entity
predicate:
subproperty_of: associated with response to


chemical entity assesses named thing association:
is_a: association
slot_usage:
Expand Down Expand Up @@ -11566,6 +11634,34 @@

enums:

ResponseEnum:
description: >-
A response to a treatment or intervention
permissible_values:
therapeutic_response:
description: >-
A positive response to a treatment or intervention
negative:
description: >-
A negative response to a treatment or intervention

ResponseTargetEnum:
description: >-
The target of a treatment or intervention
permissible_values:
cohort:
description: >-
A group of individuals that are the target of a treatment or intervention
cell line:
description: >-
A cell line that is the target of a treatment or intervention
individual:
description: >-
An individual that is the target of a treatment or intervention
sample:
description: >-
A biological materialsample that is the target of a treatment or intervention

ApprovalStatusEnum:
description: >-
permissible_values:
Expand Down
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