Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments.
+
+
+
preclinical_research_phase
+
None
+
Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo.
+
+
+
fda_clinical_research_phase
+
None
+
Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer.
+
+
+
fda_review_phase_4
+
None
+
FDA Review
+
+
+
fda_post_market_safety_review
+
None
+
FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.
+
+
+
fda_clinical_research_phase_1
+
None
+
In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 – 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase.
+
+
+
fda_clinical_research_phase_2
+
None
+
In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur.
+
+
+
fda_clinical_research_phase_3
+
None
+
In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 – 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions.
+
+
+
fda_clinical_research_phase_4
+
None
+
In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review.
+
+
+
fda_fast_track
+
None
+
Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track
+
+
+
fda_breakthrough_therapy
+
None
+
Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy
+
+
+
fda_accelerated_approval
+
None
+
When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as “clinical benefit”. Mindful of the fact that it may take an extended period of time to measure a drug’s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval
+
+
+
fda_priority_review
+
None
+
Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times – Standard Review and Priority Review. A Priority Review designation means FDA’s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review
+
+
+
regular_fda_approval
+
None
+
Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations.
name: ApprovalStatusEnum
+description: ''
+from_schema: https://w3id.org/biolink/biolink-model
+permissible_values:
+ discovery_and_development_phase:
+ text: discovery_and_development_phase
+ description: Discovery & Development Phase. Discovery involves researchers finding
+ new possibilities for medication through testing molecular compounds, noting
+ unexpected effects from existing treatments, or the creation of new technology
+ that allows novel ways of targeting medical products to sites in the body. Drug
+ development occurs after researchers identify potential compounds for experiments.
+ preclinical_research_phase:
+ text: preclinical_research_phase
+ description: 'Preclinical Research Phase. Once researchers have examined the
+ possibilities a new drug may contain, they must do preliminary research to determine
+ its potential for harm (toxicity). This is categorized as preclinical research
+ and can be one of two types: in vitro or in vivo.'
+ fda_clinical_research_phase:
+ text: fda_clinical_research_phase
+ description: Clinical Research Phase. Clinical research involves trials of the
+ drug on people, and it is one of the most involved stages in the drug development
+ and approval process. Clinical trials must answer specific questions and follow
+ a protocol determined by the drug researcher or manufacturer.
+ fda_review_phase_4:
+ text: fda_review_phase_4
+ description: FDA Review
+ fda_post_market_safety_review:
+ text: fda_post_market_safety_review
+ description: FDA Post-Market Safety Monitoring. The last phase of drug approval
+ is an ongoing one while the drug is on the marketplace. If a developer wants
+ to change anything about the drug formulation or approve it for a new use, they
+ must apply with the FDA. The FDA also frequently reviews the drug’s advertising
+ and its manufacturing facility to make sure everything involved in its creation
+ and marketing is in compliance with regulations.
+ fda_clinical_research_phase_1:
+ text: fda_clinical_research_phase_1
+ description: In the FDA Clinical Research Phase, the Clinical Research Phase 1
+ involves 20 – 100 study participants and lasts several months. This phase is
+ used to determine the safety and dosage of the drug, and about 70% of these
+ drugs move on to the next clinical research phase.
+ fda_clinical_research_phase_2:
+ text: fda_clinical_research_phase_2
+ description: In the FDA Clinical Research Phase, the Clinical Research Phase 2
+ involves up to several hundred people, who must have the disease or condition
+ the drug supposes to treat. This phase can last from a few months to two years,
+ and its purpose is to monitor the efficacy of the drug, as well as note side
+ effects that may occur.
+ fda_clinical_research_phase_3:
+ text: fda_clinical_research_phase_3
+ description: In the FDA Clinical Research Phase, the Clinical Research Phase 3
+ involves 300 – 3000 volunteers and can last up to four years. It is used to
+ continue monitoring the efficacy of the drug, as well as exploring any longer-term
+ adverse reactions.
+ fda_clinical_research_phase_4:
+ text: fda_clinical_research_phase_4
+ description: In the FDA Clinical Research Phase, the Clinical Research Phase 4
+ involves several thousands of volunteers who have the disease or condition and
+ continues to monitor safety and efficacy. If a drug passes this phase, it goes
+ on to FDA review.
+ fda_fast_track:
+ text: fda_fast_track
+ description: Fast track is a process designed to facilitate the development, and
+ expedite the review of drugs to treat serious conditions and fill an unmet medical
+ need. The purpose is to get important new drugs to the patient earlier. Fast
+ Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track
+ fda_breakthrough_therapy:
+ text: fda_breakthrough_therapy
+ description: Breakthrough Therapy designation is a process designed to expedite
+ the development and review of drugs that are intended to treat a serious condition
+ and preliminary clinical evidence indicates that the drug may demonstrate substantial
+ improvement over available therapy on a clinically significant endpoint(s).
+ For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy
+ fda_accelerated_approval:
+ text: fda_accelerated_approval
+ description: When studying a new drug, it can sometimes take many years to learn
+ whether a drug actually provides a real effect on how a patient survives, feels,
+ or functions. A positive therapeutic effect that is clinically meaningful in
+ the context of a given disease is known as “clinical benefit”. Mindful of the
+ fact that it may take an extended period of time to measure a drug’s intended
+ clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations.
+ These regulations allowed drugs for serious conditions that filled an unmet
+ medical need to be approved based on a surrogate endpoint. Using a surrogate
+ endpoint enabled the FDA to approve these drugs faster. For more information
+ https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval
+ fda_priority_review:
+ text: fda_priority_review
+ description: Prior to approval, each drug marketed in the United States must go
+ through a detailed FDA review process. In 1992, under the Prescription Drug
+ User Act (PDUFA), FDA agreed to specific goals for improving the drug review
+ time and created a two-tiered system of review times – Standard Review and Priority
+ Review. A Priority Review designation means FDA’s goal is to take action on
+ an application within 6 months (compared to 10 months under standard review).
+ For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review
+ regular_fda_approval:
+ text: regular_fda_approval
+ description: Regular FDA Approval. The last phase of drug approval is an ongoing
+ one while the drug is on the marketplace. If a developer wants to change anything
+ about the drug formulation or approve it for a new use, they must apply with
+ the FDA. The FDA also frequently reviews the drug’s advertising and its manufacturing
+ facility to make sure everything involved in its creation and marketing is in
+ compliance with regulations.
+ post_approval_withdrawal:
+ text: post_approval_withdrawal
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/Association/index.html b/Association/index.html
index 6bbd766ccc..8144ca6c28 100644
--- a/Association/index.html
+++ b/Association/index.html
@@ -314,6 +314,7 @@
Class: Association
Association <|-- MaterialSampleToDiseaseOrPhenotypicFeatureAssociation
Association <|-- DiseaseToExposureEventAssociation
Association <|-- ExposureEventToOutcomeAssociation
+ Association <|-- PhenotypicFeatureToPhenotypicFeatureAssociation
Association <|-- InformationContentEntityToNamedThingAssociation
Association <|-- DiseaseOrPhenotypicFeatureToLocationAssociation
Association <|-- DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation
@@ -479,6 +480,7 @@
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.
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.
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.
ChemicalMixture : highest_FDA_approval_status
+ ChemicalMixture --|> ApprovalStatusEnum : highest_FDA_approval_status
+
ChemicalMixture : id
ChemicalMixture : iri
@@ -394,13 +398,13 @@
Slots
highest_FDA_approval_status: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
highest_FDA_approval_status: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
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.
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.
Drug : drug_regulatory_status_world_wide
+ Drug --|> ApprovalStatusEnum : drug_regulatory_status_world_wide
+
Drug : full_name
Drug : has_attribute
@@ -323,6 +325,8 @@
Class: Drug
Drug : highest_FDA_approval_status
+ Drug --|> ApprovalStatusEnum : highest_FDA_approval_status
+
Drug : id
Drug : iri
@@ -384,7 +388,7 @@
Slots
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
highest_FDA_approval_status: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
subject: gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state.
Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.
Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment
Food : highest_FDA_approval_status
+ Food --|> ApprovalStatusEnum : highest_FDA_approval_status
+
Food : id
Food : iri
@@ -377,13 +381,13 @@
Slots
highest_FDA_approval_status: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
subject: A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.
subject: A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease.
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.
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.
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.
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
MolecularMixture : highest_FDA_approval_status
+ MolecularMixture --|> ApprovalStatusEnum : highest_FDA_approval_status
+
MolecularMixture : id
MolecularMixture : iri
@@ -384,13 +388,13 @@
Slots
highest_FDA_approval_status: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
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.
Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.
+Description: Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.
+
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.
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.
publications: One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.
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.
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.
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.
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.
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.
original_predicate: used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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<.
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}
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).
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).
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).
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).
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.
name: phenotypic feature to phenotypic feature association
+description: Association between two concept nodes of phenotypic character, qualified
+ by the predicate used. This association may typically be used to specify 'similar_to'
+ or 'member_of' relationships.
+from_schema: https://w3id.org/biolink/biolink-model
+is_a: association
+mixins:
+- phenotypic feature to entity association mixin
+- entity to phenotypic feature association mixin
+defining_slots:
+- subject
+- predicate
+- object
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/PhenotypicQuality/index.html b/PhenotypicQuality/index.html
index 2501034c2c..4249ad9c7d 100644
--- a/PhenotypicQuality/index.html
+++ b/PhenotypicQuality/index.html
@@ -391,7 +391,7 @@
Slots
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
highest_FDA_approval_status: Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
xref: A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references.
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.
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.
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.
Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)
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.)
Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)
describes a physical 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
@@ -679,11 +684,6 @@
Applicable Classes
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.
describes a physical 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
-
Example values
diff --git a/aspects.json b/aspects.json
index df27232a54..0de5978872 100644
--- a/aspects.json
+++ b/aspects.json
@@ -3,6 +3,10 @@
"name": "[root]",
"parent": null,
"children": [
+ {
+ "name": "absorption",
+ "parent": "[root]"
+ },
{
"name": "activity_or_abundance",
"parent": "[root]",
@@ -27,6 +31,10 @@
}
]
},
+ {
+ "name": "aggregation",
+ "parent": "[root]"
+ },
{
"name": "degradation",
"parent": "[root]",
@@ -45,6 +53,10 @@
"name": "folding",
"parent": "[root]"
},
+ {
+ "name": "interaction",
+ "parent": "[root]"
+ },
{
"name": "localization",
"parent": "[root]"
@@ -191,6 +203,10 @@
"name": "mutation_rate",
"parent": "[root]"
},
+ {
+ "name": "release",
+ "parent": "[root]"
+ },
{
"name": "splicing",
"parent": "[root]"
diff --git a/associations.json b/associations.json
index 13163c63d5..a9f4eae106 100644
--- a/associations.json
+++ b/associations.json
@@ -307,6 +307,10 @@
"name": "phenotypic_feature_to_disease_association",
"parent": "Association"
},
+ {
+ "name": "phenotypic_feature_to_phenotypic_feature_association",
+ "parent": "Association"
+ },
{
"name": "population_to_population_association",
"parent": "Association"
diff --git a/biolink-model.context.jsonld b/biolink-model.context.jsonld
index ad45d7e021..cd36d475a4 100644
--- a/biolink-model.context.jsonld
+++ b/biolink-model.context.jsonld
@@ -1,7 +1,7 @@
{
"comments": {
"description": "Auto generated by LinkML jsonld context generator",
- "generation_date": "2024-05-10T23:03:10",
+ "generation_date": "2024-07-26T14:52:24",
"source": "biolink_model.yaml"
},
"@context": {
@@ -347,8 +347,8 @@
"@prefix": true
},
"PFAM": "http://identifiers.org/pfam/",
- "PHARMGKB.CHEMICAL": "https://www.pharmgkb.org/chemical/",
"PHARMGKB.DISEASE": "https://www.pharmgkb.org/disease/",
+ "PHARMGKB.DRUG": "https://www.pharmgkb.org/chemical/",
"PHARMGKB.GENE": "https://www.pharmgkb.org/gene/",
"PHARMGKB.PATHWAYS": "https://www.pharmgkb.org/pathway/",
"PHARMGKB.VARIANT": "https://www.pharmgkb.org/variant/",
@@ -1025,6 +1025,12 @@
"@id": "dcat:downloadURL"
},
"drug_regulatory_status_world_wide": {
+ "@context": {
+ "@vocab": "@null",
+ "text": "skos:notation",
+ "description": "skos:prefLabel",
+ "meaning": "@id"
+ },
"@id": "drug_regulatory_status_world_wide"
},
"editor": {
@@ -1459,6 +1465,12 @@
"@id": "has_zygosity"
},
"highest_FDA_approval_status": {
+ "@context": {
+ "@vocab": "@null",
+ "text": "skos:notation",
+ "description": "skos:prefLabel",
+ "meaning": "@id"
+ },
"@id": "highest_FDA_approval_status"
},
"homologous_to": {
@@ -3141,6 +3153,9 @@
"PhenotypicFeatureToEntityAssociationMixin": {
"@id": "PhenotypicFeatureToEntityAssociationMixin"
},
+ "PhenotypicFeatureToPhenotypicFeatureAssociation": {
+ "@id": "PhenotypicFeatureToPhenotypicFeatureAssociation"
+ },
"PhenotypicQuality": {
"@id": "PhenotypicQuality"
},
diff --git a/biolink-model.graphql b/biolink-model.graphql
index 2ef5cc68f9..995ecc035a 100644
--- a/biolink-model.graphql
+++ b/biolink-model.graphql
@@ -1166,8 +1166,8 @@ type ChemicalMixture
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isSupplement: String
- highestFDAApprovalStatus: String
- drugRegulatoryStatusWorldWide: String
+ highestFDAApprovalStatus: ApprovalStatusEnum
+ drugRegulatoryStatusWorldWide: ApprovalStatusEnum
routesOfDelivery: [DrugDeliveryEnum]
}
@@ -1714,8 +1714,8 @@ type ComplexMolecularMixture
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isSupplement: String
- highestFDAApprovalStatus: String
- drugRegulatoryStatusWorldWide: String
+ highestFDAApprovalStatus: ApprovalStatusEnum
+ drugRegulatoryStatusWorldWide: ApprovalStatusEnum
routesOfDelivery: [DrugDeliveryEnum]
}
@@ -2246,8 +2246,8 @@ type Drug implements ChemicalOrDrugOrTreatment, OntologyClass
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isSupplement: String
- highestFDAApprovalStatus: String
- drugRegulatoryStatusWorldWide: String
+ highestFDAApprovalStatus: ApprovalStatusEnum
+ drugRegulatoryStatusWorldWide: ApprovalStatusEnum
routesOfDelivery: [DrugDeliveryEnum]
}
@@ -2899,8 +2899,8 @@ type Food
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isSupplement: String
- highestFDAApprovalStatus: String
- drugRegulatoryStatusWorldWide: String
+ highestFDAApprovalStatus: ApprovalStatusEnum
+ drugRegulatoryStatusWorldWide: ApprovalStatusEnum
routesOfDelivery: [DrugDeliveryEnum]
}
@@ -4977,8 +4977,8 @@ type MolecularMixture
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isSupplement: String
- highestFDAApprovalStatus: String
- drugRegulatoryStatusWorldWide: String
+ highestFDAApprovalStatus: ApprovalStatusEnum
+ drugRegulatoryStatusWorldWide: ApprovalStatusEnum
routesOfDelivery: [DrugDeliveryEnum]
}
@@ -5833,6 +5833,59 @@ type PhenotypicFeatureToEntityAssociationMixin implements FrequencyQuantifier
hasPercentage: Double
}
+type PhenotypicFeatureToPhenotypicFeatureAssociation implements PhenotypicFeatureToEntityAssociationMixin, EntityToPhenotypicFeatureAssociationMixin
+ {
+ id: String!
+ iri: IriType
+ name: LabelType
+ description: NarrativeText
+ hasAttribute: [Attribute]
+ deprecated: Boolean
+ subject: NamedThing!
+ predicate: PredicateType!
+ object: NamedThing!
+ negated: Boolean
+ qualifier: String
+ qualifiers: [OntologyClass]
+ publications: [Publication]
+ hasEvidence: [EvidenceType]
+ knowledgeSource: String
+ primaryKnowledgeSource: String
+ aggregatorKnowledgeSource: [String]
+ knowledgeLevel: KnowledgeLevelEnum!
+ agentType: AgentTypeEnum!
+ timepoint: TimeType
+ originalSubject: String
+ originalPredicate: Uriorcurie
+ originalObject: String
+ subjectCategory: OntologyClass
+ objectCategory: OntologyClass
+ subjectClosure: [String]
+ objectClosure: [String]
+ subjectCategoryClosure: [OntologyClass]
+ objectCategoryClosure: [OntologyClass]
+ subjectNamespace: String
+ objectNamespace: String
+ subjectLabelClosure: [String]
+ objectLabelClosure: [String]
+ retrievalSourceIds: [RetrievalSource]
+ pValue: Float
+ adjustedPValue: Float
+ type: [String]
+ category: [Uriorcurie]
+ frequencyQualifier: FrequencyValue
+ subjectAspectQualifier: String
+ subjectDirectionQualifier: DirectionQualifierEnum
+ objectAspectQualifier: String
+ objectDirectionQualifier: DirectionQualifierEnum
+ qualifiedPredicate: String
+ sexQualifier: BiologicalSex
+ hasCount: Integer
+ hasTotal: Integer
+ hasQuotient: Double
+ hasPercentage: Double
+ }
+
type PhenotypicQuality
{
id: String!
@@ -6133,8 +6186,8 @@ type ProcessedMaterial
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isSupplement: String
- highestFDAApprovalStatus: String
- drugRegulatoryStatusWorldWide: String
+ highestFDAApprovalStatus: ApprovalStatusEnum
+ drugRegulatoryStatusWorldWide: ApprovalStatusEnum
routesOfDelivery: [DrugDeliveryEnum]
}
@@ -6678,6 +6731,7 @@ type SiRNA
type SmallMolecule
{
+ id: String!
iri: IriType
type: [String]
name: LabelType
@@ -6695,7 +6749,6 @@ type SmallMolecule
isToxic: Boolean
hasChemicalRole: [ChemicalRole]
isMetabolite: Boolean
- id: String!
}
type Snv
diff --git a/biolink-model.json b/biolink-model.json
index 3032275439..e6561a0348 100644
--- a/biolink-model.json
+++ b/biolink-model.json
@@ -800,6 +800,28 @@
"title": "AnatomicalEntityToAnatomicalEntityPartOfAssociation",
"type": "object"
},
+ "ApprovalStatusEnum": {
+ "description": "",
+ "enum": [
+ "discovery_and_development_phase",
+ "preclinical_research_phase",
+ "fda_clinical_research_phase",
+ "fda_review_phase_4",
+ "fda_post_market_safety_review",
+ "fda_clinical_research_phase_1",
+ "fda_clinical_research_phase_2",
+ "fda_clinical_research_phase_3",
+ "fda_clinical_research_phase_4",
+ "fda_fast_track",
+ "fda_breakthrough_therapy",
+ "fda_accelerated_approval",
+ "fda_priority_review",
+ "regular_fda_approval",
+ "post_approval_withdrawal"
+ ],
+ "title": "ApprovalStatusEnum",
+ "type": "string"
+ },
"Article": {
"additionalProperties": false,
"description": "a piece of writing on a particular topic presented as a stand-alone section of a larger publication",
@@ -5261,8 +5283,8 @@
"type": "string"
},
"drug_regulatory_status_world_wide": {
- "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA."
},
"full_name": {
"description": "a long-form human readable name for a thing",
@@ -5283,8 +5305,8 @@
"type": "array"
},
"highest_FDA_approval_status": {
- "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'"
},
"id": {
"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
@@ -7993,8 +8015,8 @@
"type": "string"
},
"drug_regulatory_status_world_wide": {
- "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA."
},
"full_name": {
"description": "a long-form human readable name for a thing",
@@ -8015,8 +8037,8 @@
"type": "array"
},
"highest_FDA_approval_status": {
- "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'"
},
"id": {
"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
@@ -10534,8 +10556,8 @@
"type": "string"
},
"drug_regulatory_status_world_wide": {
- "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA."
},
"full_name": {
"description": "a long-form human readable name for a thing",
@@ -10556,8 +10578,8 @@
"type": "array"
},
"highest_FDA_approval_status": {
- "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'"
},
"id": {
"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
@@ -13289,8 +13311,8 @@
"type": "string"
},
"drug_regulatory_status_world_wide": {
- "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA."
},
"full_name": {
"description": "a long-form human readable name for a thing",
@@ -13311,8 +13333,8 @@
"type": "array"
},
"highest_FDA_approval_status": {
- "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'"
},
"id": {
"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
@@ -14803,6 +14825,10 @@
"folding",
"localization",
"transport",
+ "absorption",
+ "aggregation",
+ "interaction",
+ "release",
"secretion",
"uptake",
"splicing",
@@ -22993,8 +23019,8 @@
"type": "string"
},
"drug_regulatory_status_world_wide": {
- "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA."
},
"full_name": {
"description": "a long-form human readable name for a thing",
@@ -23015,8 +23041,8 @@
"type": "array"
},
"highest_FDA_approval_status": {
- "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'"
},
"id": {
"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
@@ -26593,6 +26619,263 @@
"title": "PhenotypicFeatureToDiseaseAssociation",
"type": "object"
},
+ "PhenotypicFeatureToPhenotypicFeatureAssociation": {
+ "additionalProperties": false,
+ "description": "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.",
+ "properties": {
+ "adjusted_p_value": {
+ "description": "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<.",
+ "type": "number"
+ },
+ "agent_type": {
+ "$ref": "#/$defs/AgentTypeEnum",
+ "description": "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information."
+ },
+ "aggregator_knowledge_source": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "category": {
+ "description": "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}",
+ "enum": [
+ "biolink:PhenotypicFeatureToPhenotypicFeatureAssociation"
+ ],
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "deprecated": {
+ "description": "A boolean flag indicating that an entity is no longer considered current or valid.",
+ "type": "boolean"
+ },
+ "description": {
+ "description": "a human-readable description of an entity",
+ "type": "string"
+ },
+ "frequency_qualifier": {
+ "description": "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject",
+ "type": "string"
+ },
+ "has_attribute": {
+ "description": "connects any entity to an attribute",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "has_count": {
+ "description": "number of things with a particular property",
+ "type": "integer"
+ },
+ "has_evidence": {
+ "description": "connects an association to an instance of supporting evidence",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "has_percentage": {
+ "description": "equivalent to has quotient multiplied by 100",
+ "type": "number"
+ },
+ "has_quotient": {
+ "type": "number"
+ },
+ "has_total": {
+ "description": "total number of things in a particular reference set",
+ "type": "integer"
+ },
+ "id": {
+ "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
+ "type": "string"
+ },
+ "iri": {
+ "description": "An IRI for an entity. This is determined by the id using expansion rules.",
+ "type": "string"
+ },
+ "knowledge_level": {
+ "$ref": "#/$defs/KnowledgeLevelEnum",
+ "description": "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."
+ },
+ "knowledge_source": {
+ "description": "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.",
+ "type": "string"
+ },
+ "name": {
+ "description": "A human-readable name for an attribute or entity.",
+ "type": "string"
+ },
+ "negated": {
+ "description": "if set to true, then the association is negated i.e. is not true",
+ "type": "boolean"
+ },
+ "object": {
+ "description": "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.",
+ "type": "string"
+ },
+ "object_aspect_qualifier": {
+ "description": "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).",
+ "type": "string"
+ },
+ "object_category": {
+ "description": "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.",
+ "type": "string"
+ },
+ "object_category_closure": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "object_closure": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "object_direction_qualifier": {
+ "$ref": "#/$defs/DirectionQualifierEnum",
+ "description": "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)."
+ },
+ "object_label_closure": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "object_namespace": {
+ "description": "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.",
+ "type": "string"
+ },
+ "original_object": {
+ "description": "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.",
+ "type": "string"
+ },
+ "original_predicate": {
+ "description": "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification.",
+ "type": "string"
+ },
+ "original_subject": {
+ "description": "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.",
+ "type": "string"
+ },
+ "p_value": {
+ "description": "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.",
+ "type": "number"
+ },
+ "predicate": {
+ "description": "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes.",
+ "type": "string"
+ },
+ "primary_knowledge_source": {
+ "description": "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.",
+ "type": "string"
+ },
+ "publications": {
+ "description": "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "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. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a \u2018full statement\u2019 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.",
+ "type": "string"
+ },
+ "qualifier": {
+ "description": "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes",
+ "type": "string"
+ },
+ "qualifiers": {
+ "description": "connects an association to qualifiers that modify or qualify the meaning of that association",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "retrieval_source_ids": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "sex_qualifier": {
+ "description": "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex.",
+ "type": "string"
+ },
+ "subject": {
+ "description": "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.",
+ "type": "string"
+ },
+ "subject_aspect_qualifier": {
+ "description": "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).",
+ "type": "string"
+ },
+ "subject_category": {
+ "description": "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.",
+ "type": "string"
+ },
+ "subject_category_closure": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "subject_closure": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "subject_direction_qualifier": {
+ "$ref": "#/$defs/DirectionQualifierEnum",
+ "description": "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)."
+ },
+ "subject_label_closure": {
+ "description": "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.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "subject_namespace": {
+ "description": "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.",
+ "type": "string"
+ },
+ "timepoint": {
+ "description": "a point in time",
+ "format": "time",
+ "type": "string"
+ },
+ "type": {
+ "description": "rdf:type of biolink:Association should be fixed at rdf:Statement",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ }
+ },
+ "required": [
+ "subject",
+ "predicate",
+ "object",
+ "knowledge_level",
+ "agent_type",
+ "id"
+ ],
+ "title": "PhenotypicFeatureToPhenotypicFeatureAssociation",
+ "type": "object"
+ },
"PhenotypicQuality": {
"additionalProperties": false,
"description": "A property of a phenotype",
@@ -27981,8 +28264,8 @@
"type": "string"
},
"drug_regulatory_status_world_wide": {
- "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA.",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "An agglomeration of drug regulatory status worldwide. Not specific to FDA."
},
"full_name": {
"description": "a long-form human readable name for a thing",
@@ -28003,8 +28286,8 @@
"type": "array"
},
"highest_FDA_approval_status": {
- "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'",
- "type": "string"
+ "$ref": "#/$defs/ApprovalStatusEnum",
+ "description": "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'"
},
"id": {
"description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
@@ -33899,5 +34182,5 @@
"metamodel_version": "1.7.0",
"title": "Biolink-Model",
"type": "object",
- "version": "4.2.1"
+ "version": "4.2.2"
}
\ No newline at end of file
diff --git a/biolink-model.jsonld b/biolink-model.jsonld
index a1d0ac7765..34a3c27708 100644
--- a/biolink-model.jsonld
+++ b/biolink-model.jsonld
@@ -2,7 +2,7 @@
"name": "Biolink-Model",
"description": "Entity and association taxonomy and datamodel for life-sciences data",
"id": "https://w3id.org/biolink/biolink-model",
- "version": "4.2.1",
+ "version": "4.2.2",
"imports": [
"linkml:types"
],
@@ -365,7 +365,7 @@
"prefix_reference": "http://purl.org/pav/"
},
{
- "prefix_prefix": "PHARMGKB.CHEMICAL",
+ "prefix_prefix": "PHARMGKB.DRUG",
"prefix_reference": "https://www.pharmgkb.org/chemical/"
},
{
@@ -1010,6 +1010,73 @@
}
],
"enums": [
+ {
+ "name": "ApprovalStatusEnum",
+ "definition_uri": "https://w3id.org/biolink/vocab/ApprovalStatusEnum",
+ "description": "",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "permissible_values": [
+ {
+ "text": "discovery_and_development_phase",
+ "description": "Discovery & Development Phase. Discovery involves researchers finding new possibilities for medication through testing molecular compounds, noting unexpected effects from existing treatments, or the creation of new technology that allows novel ways of targeting medical products to sites in the body. Drug development occurs after researchers identify potential compounds for experiments."
+ },
+ {
+ "text": "preclinical_research_phase",
+ "description": "Preclinical Research Phase. Once researchers have examined the possibilities a new drug may contain, they must do preliminary research to determine its potential for harm (toxicity). This is categorized as preclinical research and can be one of two types: in vitro or in vivo."
+ },
+ {
+ "text": "fda_clinical_research_phase",
+ "description": "Clinical Research Phase. Clinical research involves trials of the drug on people, and it is one of the most involved stages in the drug development and approval process. Clinical trials must answer specific questions and follow a protocol determined by the drug researcher or manufacturer."
+ },
+ {
+ "text": "fda_review_phase_4",
+ "description": "FDA Review"
+ },
+ {
+ "text": "fda_post_market_safety_review",
+ "description": "FDA Post-Market Safety Monitoring. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug\u2019s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations."
+ },
+ {
+ "text": "fda_clinical_research_phase_1",
+ "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 1 involves 20 \u2013 100 study participants and lasts several months. This phase is used to determine the safety and dosage of the drug, and about 70% of these drugs move on to the next clinical research phase."
+ },
+ {
+ "text": "fda_clinical_research_phase_2",
+ "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 2 involves up to several hundred people, who must have the disease or condition the drug supposes to treat. This phase can last from a few months to two years, and its purpose is to monitor the efficacy of the drug, as well as note side effects that may occur."
+ },
+ {
+ "text": "fda_clinical_research_phase_3",
+ "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 3 involves 300 \u2013 3000 volunteers and can last up to four years. It is used to continue monitoring the efficacy of the drug, as well as exploring any longer-term adverse reactions."
+ },
+ {
+ "text": "fda_clinical_research_phase_4",
+ "description": "In the FDA Clinical Research Phase, the Clinical Research Phase 4 involves several thousands of volunteers who have the disease or condition and continues to monitor safety and efficacy. If a drug passes this phase, it goes on to FDA review."
+ },
+ {
+ "text": "fda_fast_track",
+ "description": "Fast track is a process designed to facilitate the development, and expedite the review of drugs to treat serious conditions and fill an unmet medical need. The purpose is to get important new drugs to the patient earlier. Fast Track addresses a broad range of serious conditions. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/fast-track"
+ },
+ {
+ "text": "fda_breakthrough_therapy",
+ "description": "Breakthrough Therapy designation is a process designed to expedite the development and review of drugs that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/breakthrough-therapy"
+ },
+ {
+ "text": "fda_accelerated_approval",
+ "description": "When studying a new drug, it can sometimes take many years to learn whether a drug actually provides a real effect on how a patient survives, feels, or functions. A positive therapeutic effect that is clinically meaningful in the context of a given disease is known as \u201cclinical benefit\u201d. Mindful of the fact that it may take an extended period of time to measure a drug\u2019s intended clinical benefit, in 1992 FDA instituted the Accelerated Approval regulations. These regulations allowed drugs for serious conditions that filled an unmet medical need to be approved based on a surrogate endpoint. Using a surrogate endpoint enabled the FDA to approve these drugs faster. For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/accelerated-approval"
+ },
+ {
+ "text": "fda_priority_review",
+ "description": "Prior to approval, each drug marketed in the United States must go through a detailed FDA review process. In 1992, under the Prescription Drug User Act (PDUFA), FDA agreed to specific goals for improving the drug review time and created a two-tiered system of review times \u2013 Standard Review and Priority Review. A Priority Review designation means FDA\u2019s goal is to take action on an application within 6 months (compared to 10 months under standard review). For more information https://www.fda.gov/patients/fast-track-breakthrough-therapy-accelerated-approval-priority-review/priority-review"
+ },
+ {
+ "text": "regular_fda_approval",
+ "description": "Regular FDA Approval. The last phase of drug approval is an ongoing one while the drug is on the marketplace. If a developer wants to change anything about the drug formulation or approve it for a new use, they must apply with the FDA. The FDA also frequently reviews the drug\u2019s advertising and its manufacturing facility to make sure everything involved in its creation and marketing is in compliance with regulations."
+ },
+ {
+ "text": "post_approval_withdrawal"
+ }
+ ]
+ },
{
"name": "ClinicalApprovalStatusEnum",
"definition_uri": "https://w3id.org/biolink/vocab/ClinicalApprovalStatusEnum",
@@ -1247,6 +1314,18 @@
{
"text": "transport"
},
+ {
+ "text": "absorption"
+ },
+ {
+ "text": "aggregation"
+ },
+ {
+ "text": "interaction"
+ },
+ {
+ "text": "release"
+ },
{
"text": "secretion",
"is_a": "transport"
@@ -3726,7 +3805,7 @@
"domain_of": [
"ChemicalMixture"
],
- "range": "string",
+ "range": "ApprovalStatusEnum",
"@type": "SlotDefinition"
},
{
@@ -3768,7 +3847,7 @@
"domain_of": [
"ChemicalMixture"
],
- "range": "string",
+ "range": "ApprovalStatusEnum",
"@type": "SlotDefinition"
},
{
@@ -8167,14 +8246,13 @@
],
"is_a": "related_to_at_instance_level",
"mixin": true,
- "domain": "DiseaseOrPhenotypicFeature",
+ "domain": "ChemicalOrDrugOrTreatment",
"slot_uri": "https://w3id.org/biolink/vocab/treats_or_applied_or_studied_to_treat",
"multivalued": true,
"inherited": true,
"owner": "treats_or_applied_or_studied_to_treat",
"inverse": "subject_of_treatment_application_or_study_for_treatment_by",
- "range": "ChemicalOrDrugOrTreatment",
- "inlined": true,
+ "range": "DiseaseOrPhenotypicFeature",
"@type": "SlotDefinition"
},
{
@@ -8183,13 +8261,14 @@
"from_schema": "https://w3id.org/biolink/biolink-model",
"is_a": "related_to_at_instance_level",
"mixin": true,
- "domain": "ChemicalOrDrugOrTreatment",
+ "domain": "DiseaseOrPhenotypicFeature",
"slot_uri": "https://w3id.org/biolink/vocab/subject_of_treatment_application_or_study_for_treatment_by",
"multivalued": true,
"inherited": true,
"owner": "subject_of_treatment_application_or_study_for_treatment_by",
"inverse": "treats_or_applied_or_studied_to_treat",
- "range": "DiseaseOrPhenotypicFeature",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
"@type": "SlotDefinition"
},
{
@@ -13402,41 +13481,6 @@
"range": "uriorcurie",
"@type": "SlotDefinition"
},
- {
- "name": "small_molecule_id",
- "definition_uri": "https://w3id.org/biolink/vocab/id",
- "description": "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI",
- "examples": [
- {
- "value": "CHEBI:29101",
- "description": "sodium ion",
- "@type": "Example"
- }
- ],
- "in_subset": [
- "translator_minimal"
- ],
- "from_schema": "https://w3id.org/biolink/biolink-model",
- "exact_mappings": [
- "https://www.alliancegenome.org/primaryId",
- "https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#ID",
- "https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#DB_Object_ID"
- ],
- "is_a": "id",
- "domain": "SmallMolecule",
- "slot_uri": "https://w3id.org/biolink/vocab/id",
- "identifier": true,
- "alias": "id",
- "owner": "SmallMolecule",
- "domain_of": [
- "SmallMolecule"
- ],
- "is_usage_slot": true,
- "usage_slot_name": "id",
- "range": "string",
- "required": true,
- "@type": "SlotDefinition"
- },
{
"name": "molecular_activity_has_input",
"definition_uri": "https://w3id.org/biolink/vocab/has_input",
@@ -24526,8 +24570,7 @@
"UMLSSG:DEVI",
"STY:T074",
"STY:T075",
- "STY:T203",
- "STY:T122"
+ "STY:T203"
],
"is_a": "NamedThing",
"slots": [
@@ -24881,10 +24924,10 @@
{
"name": "MolecularEntity",
"id_prefixes": [
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
"DRUGBANK",
"MESH",
"CAS",
@@ -24892,11 +24935,14 @@
"GTOPDB",
"HMDB",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
"SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
"KEGG.GLYCAN",
"KEGG.DRUG",
"KEGG.ENVIRON",
@@ -24943,23 +24989,25 @@
{
"name": "ChemicalEntity",
"id_prefixes": [
- "UNII",
"CHEBI",
- "MESH",
- "CAS",
- "ncats.drug",
- "PHARMGKB.CHEMICAL",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
+ "DRUGBANK",
+ "MESH",
+ "CAS",
"DrugCentral",
"GTOPDB",
"HMDB",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
"SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
"KEGG.GLYCAN",
"KEGG.DRUG",
"KEGG.ENVIRON",
@@ -25020,9 +25068,9 @@
"name": "SmallMolecule",
"id_prefixes": [
"CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
"DRUGBANK",
"MESH",
"CAS",
@@ -25030,13 +25078,13 @@
"GTOPDB",
"HMDB",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
"SIDER.DRUG",
"INCHI",
"INCHIKEY",
"BIGG.METABOLITE",
- "UMLS",
"foodb.compound",
"KEGG.GLYCAN",
"KEGG.DRUG",
@@ -25071,6 +25119,7 @@
],
"is_a": "MolecularEntity",
"slots": [
+ "id",
"iri",
"type",
"name",
@@ -25087,8 +25136,7 @@
"max_tolerated_dose",
"is_toxic",
"has_chemical_role",
- "is_metabolite",
- "small_molecule_id"
+ "is_metabolite"
],
"slot_usage": {},
"class_uri": "https://w3id.org/biolink/vocab/SmallMolecule",
@@ -25097,10 +25145,10 @@
{
"name": "ChemicalMixture",
"id_prefixes": [
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
"DRUGBANK",
"MESH",
"CAS",
@@ -25108,15 +25156,18 @@
"GTOPDB",
"HMDB",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
"SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
"KEGG.GLYCAN",
"KEGG.DRUG",
- "KEGG",
"KEGG.ENVIRON",
+ "KEGG",
"UMLS"
],
"definition_uri": "https://w3id.org/biolink/vocab/ChemicalMixture",
@@ -25361,10 +25412,10 @@
{
"name": "MolecularMixture",
"id_prefixes": [
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
"DRUGBANK",
"MESH",
"CAS",
@@ -25372,17 +25423,19 @@
"GTOPDB",
"HMDB",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
"SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
"KEGG.GLYCAN",
"KEGG.DRUG",
- "KEGG",
"KEGG.ENVIRON",
- "UMLS",
- "ncats.drug"
+ "KEGG",
+ "UMLS"
],
"definition_uri": "https://w3id.org/biolink/vocab/MolecularMixture",
"description": "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry.",
@@ -25766,29 +25819,31 @@
{
"name": "ProcessedMaterial",
"id_prefixes": [
- "UMLS",
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
+ "DRUGBANK",
"MESH",
"CAS",
+ "DrugCentral",
"GTOPDB",
"HMDB",
- "KEGG",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
+ "SIDER.DRUG",
"INCHI",
"INCHIKEY",
- "KEGG.GLYCAN",
- "KEGG.ENVIRON",
- "ChemBank",
- "SIDER.DRUG",
"BIGG.METABOLITE",
"foodb.compound",
- "UMLS",
- "foodb.food"
+ "foodb.food",
+ "KEGG.GLYCAN",
+ "KEGG.DRUG",
+ "KEGG.ENVIRON",
+ "KEGG",
+ "UMLS"
],
"definition_uri": "https://w3id.org/biolink/vocab/ProcessedMaterial",
"description": "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing.",
@@ -25831,26 +25886,29 @@
"RXCUI",
"NDC",
"UMLS",
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
+ "DRUGBANK",
"MESH",
"CAS",
+ "DrugCentral",
"GTOPDB",
"HMDB",
- "KEGG",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
+ "SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
"KEGG.GLYCAN",
"KEGG.ENVIRON",
- "ChemBank",
- "SIDER.DRUG",
- "BIGG.METABOLITE",
- "foodb.compound"
+ "KEGG.ENVIRON",
+ "KEGG"
],
"definition_uri": "https://w3id.org/biolink/vocab/Drug",
"description": "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease",
@@ -25905,30 +25963,31 @@
{
"name": "EnvironmentalFoodContaminant",
"id_prefixes": [
- "ncats.drug",
- "RXCUI",
- "NDC",
- "UMLS",
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
+ "DRUGBANK",
"MESH",
"CAS",
+ "DrugCentral",
"GTOPDB",
"HMDB",
- "KEGG",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
+ "SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
+ "foodb.food",
"KEGG.GLYCAN",
+ "KEGG.DRUG",
"KEGG.ENVIRON",
- "ChemBank",
- "SIDER.DRUG",
- "BIGG.METABOLITE",
- "foodb.compound"
+ "KEGG",
+ "UMLS"
],
"definition_uri": "https://w3id.org/biolink/vocab/EnvironmentalFoodContaminant",
"from_schema": "https://w3id.org/biolink/biolink-model",
@@ -25962,30 +26021,31 @@
{
"name": "FoodAdditive",
"id_prefixes": [
- "ncats.drug",
- "RXCUI",
- "NDC",
- "UMLS",
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
+ "DRUGBANK",
"MESH",
"CAS",
+ "DrugCentral",
"GTOPDB",
"HMDB",
- "KEGG",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
+ "SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
+ "foodb.compound",
+ "foodb.food",
"KEGG.GLYCAN",
+ "KEGG.DRUG",
"KEGG.ENVIRON",
- "ChemBank",
- "SIDER.DRUG",
- "BIGG.METABOLITE",
- "foodb.compound"
+ "KEGG",
+ "UMLS"
],
"definition_uri": "https://w3id.org/biolink/vocab/FoodAdditive",
"from_schema": "https://w3id.org/biolink/biolink-model",
@@ -26022,34 +26082,33 @@
"foodb.food",
"foodb.compound",
"FOODON",
- "UMLS",
- "NCIT",
+ "CHEBI",
+ "UNII",
"PUBCHEM.COMPOUND",
"CHEMBL.COMPOUND",
- "UNII",
- "CHEBI",
+ "DRUGBANK",
"MESH",
"CAS",
+ "DrugCentral",
"GTOPDB",
"HMDB",
- "KEGG",
"KEGG.COMPOUND",
+ "PHARMGKB.DRUG",
"ChemBank",
"PUBCHEM.SUBSTANCE",
+ "SIDER.DRUG",
"INCHI",
"INCHIKEY",
+ "BIGG.METABOLITE",
"KEGG.GLYCAN",
+ "KEGG.DRUG",
"KEGG.ENVIRON",
- "ChemBank",
- "SIDER.DRUG",
- "BIGG.METABOLITE"
+ "KEGG",
+ "UMLS"
],
"definition_uri": "https://w3id.org/biolink/vocab/Food",
"description": "A substance consumed by a living organism as a source of nutrition",
"from_schema": "https://w3id.org/biolink/biolink-model",
- "exact_mappings": [
- "STY:T168"
- ],
"is_a": "ChemicalMixture",
"slots": [
"id",
@@ -31567,6 +31626,76 @@
],
"@type": "ClassDefinition"
},
+ {
+ "name": "PhenotypicFeatureToPhenotypicFeatureAssociation",
+ "definition_uri": "https://w3id.org/biolink/vocab/PhenotypicFeatureToPhenotypicFeatureAssociation",
+ "description": "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships.",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "Association",
+ "mixins": [
+ "PhenotypicFeatureToEntityAssociationMixin",
+ "EntityToPhenotypicFeatureAssociationMixin"
+ ],
+ "slots": [
+ "id",
+ "iri",
+ "name",
+ "description",
+ "has_attribute",
+ "deprecated",
+ "subject",
+ "predicate",
+ "object",
+ "negated",
+ "qualifier",
+ "qualifiers",
+ "publications",
+ "has_evidence",
+ "knowledge_source",
+ "primary_knowledge_source",
+ "aggregator_knowledge_source",
+ "knowledge_level",
+ "agent_type",
+ "timepoint",
+ "original_subject",
+ "original_predicate",
+ "original_object",
+ "subject_category",
+ "object_category",
+ "subject_closure",
+ "object_closure",
+ "subject_category_closure",
+ "object_category_closure",
+ "subject_namespace",
+ "object_namespace",
+ "subject_label_closure",
+ "object_label_closure",
+ "retrieval_source_ids",
+ "p_value",
+ "adjusted_p_value",
+ "association_type",
+ "association_category",
+ "frequency_qualifier",
+ "subject_aspect_qualifier",
+ "subject_direction_qualifier",
+ "object_aspect_qualifier",
+ "object_direction_qualifier",
+ "qualified_predicate",
+ "sex_qualifier",
+ "has_count",
+ "has_total",
+ "has_quotient",
+ "has_percentage"
+ ],
+ "slot_usage": {},
+ "class_uri": "https://w3id.org/biolink/vocab/PhenotypicFeatureToPhenotypicFeatureAssociation",
+ "defining_slots": [
+ "subject",
+ "predicate",
+ "object"
+ ],
+ "@type": "ClassDefinition"
+ },
{
"name": "InformationContentEntityToNamedThingAssociation",
"definition_uri": "https://w3id.org/biolink/vocab/InformationContentEntityToNamedThingAssociation",
@@ -35037,9 +35166,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "biolink_model.yaml",
- "source_file_date": "2024-05-10T23:03:07",
- "source_file_size": 393015,
- "generation_date": "2024-05-10T23:03:12",
+ "source_file_date": "2024-07-26T14:52:20",
+ "source_file_size": 398264,
+ "generation_date": "2024-07-26T14:52:26",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/biolink_model.context.jsonld",
diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl
index ca2ea2f903..203f4c5e02 100644
--- a/biolink-model.owl.ttl
+++ b/biolink-model.owl.ttl
@@ -80,7 +80,7 @@
a owl:Ontology ;
rdfs:label "Biolink-Model" ;
dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
- pav:version "4.2.1" ;
+ pav:version "4.2.2" ;
skos:definition "Entity and association taxonomy and datamodel for life-sciences data" .
biolink:BehavioralOutcome a owl:Class ;
@@ -2498,8 +2498,8 @@ biolink:subclass_of a owl:ObjectProperty ;
biolink:subject_of_treatment_application_or_study_for_treatment_by a owl:ObjectProperty ;
rdfs:label "subject of treatment application or study for treatment by" ;
- rdfs:domain biolink:ChemicalOrDrugOrTreatment ;
- rdfs:range biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:treats_or_applied_or_studied_to_treat ;
skos:inScheme .
@@ -2601,16 +2601,16 @@ biolink:AccessibleDnaRegion a owl:Class ;
rdfs:label "accessible dna region" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:GenomicEntity ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenomicEntity ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
biolink:RegulatoryRegion ;
skos:altLabel "atac-seq accessible region",
"dnase-seq accessible region" ;
@@ -2657,13 +2657,7 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ;
rdfs:label "anatomical entity to anatomical entity ontogenic association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
owl:onProperty biolink:object ],
@@ -2676,12 +2670,18 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ;
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:AnatomicalEntityToAnatomicalEntityAssociation ;
skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ;
skos:inScheme .
@@ -2693,32 +2693,107 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:AnatomicalEntityToAnatomicalEntityAssociation ;
skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ;
skos:inScheme .
+ a owl:Class ;
+ rdfs:label "discovery_and_development_phase" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_accelerated_approval" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_breakthrough_therapy" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_clinical_research_phase" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_clinical_research_phase_1" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_clinical_research_phase_2" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_clinical_research_phase_3" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_clinical_research_phase_4" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_fast_track" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_post_market_safety_review" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_priority_review" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "fda_review_phase_4" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "post_approval_withdrawal" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "preclinical_research_phase" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
+ a owl:Class ;
+ rdfs:label "regular_fda_approval" ;
+ rdfs:subClassOf biolink:ApprovalStatusEnum,
+ linkml:PermissibleValue .
+
biolink:Bacterium a owl:Class ;
rdfs:label "bacterium" ;
rdfs:subClassOf biolink:OrganismalEntity ;
@@ -2730,26 +2805,26 @@ biolink:Bacterium a owl:Class ;
biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ;
rdfs:label "behavior to behavioral feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:BehavioralFeature ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Behavior ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:BehavioralFeature ;
- owl:onProperty biolink:object ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ;
skos:inScheme .
@@ -2778,18 +2853,18 @@ biolink:Book a owl:Class ;
rdfs:label "book" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:id ],
+ owl:onProperty biolink:type ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:type ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:type ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:id ],
biolink:Publication ;
skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ;
@@ -2816,29 +2891,29 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ;
biolink:CausalGeneToDiseaseAssociation a owl:Class ;
rdfs:label "causal gene to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Disease ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Disease ;
+ owl:onProperty biolink:object ],
biolink:GeneToDiseaseAssociation ;
skos:inScheme .
@@ -2931,17 +3006,17 @@ biolink:Cell a owl:Class ;
biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ;
rdfs:label "cell line as a model of disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:CellLine ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
+ owl:allValuesFrom biolink:CellLine ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
@@ -2957,167 +3032,167 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ;
biolink:ChemicalAffectsGeneAssociation a owl:Class ;
rdfs:label "chemical affects gene association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:object_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:onProperty biolink:subject_direction_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:allValuesFrom biolink:DirectionQualifierEnum ;
+ owl:onProperty biolink:subject_direction_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:object_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:OrganismTaxon ;
+ owl:onProperty biolink:species_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:CausalMechanismQualifierEnum ;
+ owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
- owl:onProperty biolink:subject_part_qualifier ],
+ owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:DirectionQualifierEnum ;
owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
+ owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_context_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_direction_qualifier ],
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DirectionQualifierEnum ;
- owl:onProperty biolink:subject_direction_qualifier ],
+ owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ;
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:causal_mechanism_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
- owl:onProperty biolink:subject_aspect_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntity ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
- owl:onProperty biolink:object_part_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:species_context_qualifier ],
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:CausalMechanismQualifierEnum ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:subject_derivative_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
+ owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_part_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_part_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_direction_qualifier ],
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:OrganismTaxon ;
- owl:onProperty biolink:species_context_qualifier ],
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
biolink:Association ;
skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ;
skos:inScheme .
@@ -3127,71 +3202,71 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:NamedThing ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ChemicalEntity ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
biolink:Association ;
skos:inScheme .
biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ;
rdfs:label "chemical entity or gene or gene product regulates gene association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:DirectionQualifierEnum ;
+ owl:onProperty biolink:object_direction_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:DirectionQualifierEnum ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:predicate ],
biolink:Association ;
skos:definition "A regulatory relationship between two genes" ;
skos:inScheme .
@@ -3199,107 +3274,107 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ;
biolink:ChemicalGeneInteractionAssociation a owl:Class ;
rdfs:label "chemical gene interaction association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
+ owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ;
owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
- owl:onProperty biolink:subject_part_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_part_qualifier ],
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
+ owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
owl:onProperty biolink:subject_form_or_variant_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntity ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_part_qualifier ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
biolink:Association ;
skos:definition "describes a physical 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)" ;
skos:exactMatch SIO:001257 ;
@@ -3308,19 +3383,19 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ;
biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ;
skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ;
@@ -3349,38 +3424,38 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation
biolink:ChemicalToChemicalDerivationAssociation a owl:Class ;
rdfs:label "chemical to chemical derivation association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:MacromolecularMachineMixin ;
- owl:onProperty biolink:catalyst_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:catalyst_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntity ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:catalyst_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:allValuesFrom biolink:MacromolecularMachineMixin ;
+ owl:onProperty biolink:catalyst_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
biolink:ChemicalToChemicalAssociation ;
skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ;
skos:inScheme .
@@ -3388,14 +3463,14 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ;
biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "chemical to disease or phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ;
- owl:onProperty biolink:object ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
+ owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
@@ -3412,24 +3487,24 @@ biolink:ChemicalToPathwayAssociation a owl:Class ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ChemicalEntity ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Pathway ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
biolink:Association ;
skos:definition "An interaction between a chemical entity and a biological process or pathway." ;
skos:exactMatch SIO:001250 ;
@@ -3479,10 +3554,10 @@ biolink:ClinicalMeasurement a owl:Class ;
owl:allValuesFrom owl:Thing ;
owl:onProperty biolink:has_attribute_type ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:has_attribute_type ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:has_attribute_type ],
biolink:ClinicalAttribute ;
skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ;
@@ -3545,28 +3620,28 @@ biolink:ContributorAssociation a owl:Class ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Agent ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:qualifiers ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom owl:Thing ;
owl:onProperty biolink:qualifiers ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:qualifiers ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:allValuesFrom biolink:InformationContentEntity ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:InformationContentEntity ;
+ owl:allValuesFrom biolink:Agent ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ;
@@ -3575,29 +3650,29 @@ biolink:ContributorAssociation a owl:Class ;
biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ;
rdfs:label "correlated gene to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Disease ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
+ owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Disease ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
biolink:GeneToDiseaseAssociation ;
skos:inScheme .
@@ -3626,26 +3701,26 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ;
biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ;
rdfs:label "disease or phenotypic feature to genetic inheritance association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:GeneticInheritance ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ;
skos:inScheme .
@@ -3659,10 +3734,10 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ;
owl:allValuesFrom biolink:AnatomicalEntity ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ;
@@ -3672,10 +3747,10 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ;
rdfs:label "disease to exposure event association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ],
+ owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin ],
+ owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ],
biolink:Association ;
skos:definition "An association between an exposure event and a disease." ;
skos:inScheme .
@@ -3683,41 +3758,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ;
biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "disease to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:Disease ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:onset_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Onset ;
owl:onProperty biolink:onset_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Disease ;
- owl:onProperty biolink:subject ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:onset_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:FrequencyQuantifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:onset_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:PhenotypicFeature ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:closeMatch dcid:DiseaseSymptomAssociation ;
skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ;
@@ -3769,16 +3844,16 @@ biolink:DrugToEntityAssociationMixin a owl:Class ;
biolink:DrugToGeneAssociation a owl:Class ;
rdfs:label "drug to gene association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:DrugToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An interaction between a drug and a gene or gene product." ;
@@ -3817,23 +3892,20 @@ biolink:DrugToGeneInteractionExposure a owl:Class ;
biolink:DruggableGeneToDiseaseAssociation a owl:Class ;
rdfs:label "druggable gene to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:has_evidence ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:DruggableGeneCategoryEnum ;
+ owl:onProperty biolink:has_evidence ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
@@ -3841,11 +3913,14 @@ biolink:DruggableGeneToDiseaseAssociation a owl:Class ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DruggableGeneCategoryEnum ;
- owl:onProperty biolink:has_evidence ],
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
biolink:GeneToDiseaseAssociation ;
skos:inScheme .
@@ -3855,8 +3930,11 @@ biolink:EntityToDiseaseAssociation a owl:Class ;
owl:minCardinality 0 ;
owl:onProperty biolink:max_research_phase ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ;
owl:onProperty biolink:clinical_approval_status ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:MaxResearchPhaseEnum ;
+ owl:onProperty biolink:max_research_phase ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:max_research_phase ],
@@ -3864,10 +3942,7 @@ biolink:EntityToDiseaseAssociation a owl:Class ;
owl:maxCardinality 1 ;
owl:onProperty biolink:clinical_approval_status ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:MaxResearchPhaseEnum ;
- owl:onProperty biolink:max_research_phase ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:clinical_approval_status ],
biolink:Association ;
skos:inScheme .
@@ -3887,23 +3962,23 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ;
biolink:EntityToPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "entity to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:clinical_approval_status ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:clinical_approval_status ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:max_research_phase ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:MaxResearchPhaseEnum ;
owl:onProperty biolink:max_research_phase ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ;
owl:onProperty biolink:clinical_approval_status ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:max_research_phase ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:max_research_phase ],
biolink:Association ;
skos:inScheme .
@@ -3944,23 +4019,23 @@ biolink:Event a owl:Class ;
biolink:ExonToTranscriptRelationship a owl:Class ;
rdfs:label "exon to transcript relationship" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Transcript ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Exon ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Transcript ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Exon ;
+ owl:onProperty biolink:subject ],
biolink:SequenceFeatureRelationship ;
skos:definition "A transcript is formed from multiple exons" ;
skos:inScheme .
@@ -3968,20 +4043,20 @@ biolink:ExonToTranscriptRelationship a owl:Class ;
biolink:ExposureEventToOutcomeAssociation a owl:Class ;
rdfs:label "exposure event to outcome association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
owl:onProperty biolink:population_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:time_type ;
- owl:onProperty biolink:temporal_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:population_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:temporal_context_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
- owl:onProperty biolink:population_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:temporal_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:time_type ;
+ owl:onProperty biolink:temporal_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:population_context_qualifier ],
@@ -3995,17 +4070,17 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ;
biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "exposure event to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:ExposureEvent ;
- owl:onProperty biolink:subject ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:ExposureEvent ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ;
skos:inScheme .
@@ -4040,7 +4115,6 @@ biolink:Food a owl:Class ;
rdfs:label "food" ;
rdfs:subClassOf biolink:ChemicalMixture ;
skos:definition "A substance consumed by a living organism as a source of nutrition" ;
- skos:exactMatch STY:T168 ;
skos:inScheme .
biolink:FoodAdditive a owl:Class ;
@@ -4063,176 +4137,176 @@ biolink:Fungus a owl:Class ;
biolink:GeneAffectsChemicalAssociation a owl:Class ;
rdfs:label "gene affects chemical association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_context_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_part_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_part_qualifier ],
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ;
- owl:onProperty biolink:object_derivative_qualifier ],
+ owl:allValuesFrom biolink:DirectionQualifierEnum ;
+ owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:DirectionQualifierEnum ;
owl:onProperty biolink:object_direction_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:qualified_predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:subject_derivative_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
+ owl:onProperty biolink:object_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:OrganismTaxon ;
+ owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:onProperty biolink:object_derivative_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_direction_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:ChemicalEntity ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_derivative_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:subject_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:species_context_qualifier ],
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
+ owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_derivative_qualifier ],
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:subject_part_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:CausalMechanismQualifierEnum ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_direction_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_aspect_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:DirectionQualifierEnum ;
- owl:onProperty biolink:subject_direction_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:species_context_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:OrganismTaxon ;
- owl:onProperty biolink:species_context_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:onProperty biolink:object_derivative_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ;
+ owl:onProperty biolink:object_derivative_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:CausalMechanismQualifierEnum ;
+ owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_derivative_qualifier ],
+ owl:onProperty biolink:species_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "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.)" ;
skos:inScheme .
@@ -4241,51 +4315,51 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ;
rdfs:label "gene as a model of disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
+ owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
biolink:GeneToDiseaseAssociation ;
skos:inScheme .
biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ;
rdfs:label "gene has variant that contributes to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:Disease ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Disease ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
@@ -4294,7 +4368,7 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:onProperty biolink:subject ],
biolink:GeneToDiseaseAssociation ;
skos:inScheme .
@@ -4303,6 +4377,11 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
.
+ a owl:Class ;
+ rdfs:label "absorption" ;
+ rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
+ linkml:PermissibleValue .
+
a owl:Class ;
rdfs:label "acetylation" ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
@@ -4318,6 +4397,11 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
.
+ a owl:Class ;
+ rdfs:label "aggregation" ;
+ rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
+ linkml:PermissibleValue .
+
a owl:Class ;
rdfs:label "alkylation" ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
@@ -4398,6 +4482,11 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
.
+ a owl:Class ;
+ rdfs:label "interaction" ;
+ rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
+ linkml:PermissibleValue .
+
a owl:Class ;
rdfs:label "lipidation" ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
@@ -4478,6 +4567,11 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
.
+ a owl:Class ;
+ rdfs:label "release" ;
+ rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
+ linkml:PermissibleValue .
+
a owl:Class ;
rdfs:label "ribosylation" ;
rdfs:subClassOf biolink:GeneOrGeneProductOrChemicalEntityAspectEnum,
@@ -4566,46 +4660,46 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ;
owl:onProperty biolink:quantifier_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:quantifier_qualifier ],
+ owl:onProperty biolink:stage_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:quantifier_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:LifeStage ;
owl:onProperty biolink:stage_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:stage_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:OntologyClass ;
- owl:onProperty biolink:quantifier_qualifier ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:OntologyClass ;
+ owl:onProperty biolink:quantifier_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:LifeStage ;
- owl:onProperty biolink:stage_qualifier ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ;
skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ;
@@ -4614,14 +4708,14 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ;
biolink:GeneToGeneCoexpressionAssociation a owl:Class ;
rdfs:label "gene to gene coexpression association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneExpressionMixin ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GeneExpressionMixin ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
@@ -4632,8 +4726,14 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ;
biolink:GeneToGeneFamilyAssociation a owl:Class ;
rdfs:label "gene to gene family association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:Gene ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
@@ -4643,21 +4743,15 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ;
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Gene ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneFamily ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:GeneFamily ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ;
skos:inScheme .
@@ -4667,18 +4761,15 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
@@ -4687,10 +4778,13 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
biolink:GeneToGeneAssociation ;
skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ;
skos:inScheme .
@@ -4698,22 +4792,16 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ;
biolink:GeneToGeneProductRelationship a owl:Class ;
rdfs:label "gene to gene product relationship" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneProductMixin ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Gene ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
@@ -4721,8 +4809,14 @@ biolink:GeneToGeneProductRelationship a owl:Class ;
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneProductMixin ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Gene ;
owl:onProperty biolink:subject ],
biolink:SequenceFeatureRelationship ;
skos:definition "A gene is transcribed and potentially translated to a gene product" ;
@@ -4731,22 +4825,22 @@ biolink:GeneToGeneProductRelationship a owl:Class ;
biolink:GeneToGoTermAssociation a owl:Class ;
rdfs:label "gene to go term association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
owl:allValuesFrom biolink:OntologyClass ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Gene ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
biolink:FunctionalAssociation ;
skos:altLabel "functional association" ;
@@ -4756,26 +4850,26 @@ biolink:GeneToGoTermAssociation a owl:Class ;
biolink:GeneToPathwayAssociation a owl:Class ;
rdfs:label "gene to pathway association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Pathway ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "An interaction between a gene or gene product and a biological process or pathway." ;
skos:inScheme .
@@ -4783,29 +4877,29 @@ biolink:GeneToPathwayAssociation a owl:Class ;
biolink:GeneToPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "gene to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
- [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:PhenotypicFeature ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ;
skos:exactMatch WBVocab:Gene-Phenotype-Association ;
skos:inScheme .
@@ -4817,10 +4911,10 @@ biolink:Genome a owl:Class ;
owl:someValuesFrom biolink:GenomicEntity ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
biolink:BiologicalEntity ;
skos:closeMatch dcid:GenomeAssemblyUnit ;
skos:definition "A genome is the sum of genetic material within a cell or virion." ;
@@ -4833,22 +4927,22 @@ biolink:GenomicBackgroundExposure a owl:Class ;
rdfs:label "genomic background exposure" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenomicEntity ],
+ owl:someValuesFrom biolink:ThingWithTaxon ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:ExposureEvent ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:GenomicEntity ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneGroupingMixin ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ExposureEvent ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ThingWithTaxon ],
+ owl:someValuesFrom biolink:GeneGroupingMixin ],
biolink:Attribute ;
skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ;
skos:inScheme .
@@ -4859,16 +4953,16 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Genotype ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Genotype ;
owl:onProperty biolink:subject ],
biolink:GenotypeToDiseaseAssociation ;
skos:inScheme .
@@ -4876,32 +4970,32 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ;
biolink:GenotypeToGeneAssociation a owl:Class ;
rdfs:label "genotype to gene association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Gene ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Genotype ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:Gene ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
biolink:Association ;
skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ;
skos:inScheme .
@@ -4909,32 +5003,32 @@ biolink:GenotypeToGeneAssociation a owl:Class ;
biolink:GenotypeToGenotypePartAssociation a owl:Class ;
rdfs:label "genotype to genotype part association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Genotype ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:Genotype ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Genotype ;
- owl:onProperty biolink:object ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:predicate ],
biolink:Association ;
skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ;
skos:inScheme .
@@ -4942,29 +5036,29 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ;
biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "genotype to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Genotype ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Genotype ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ;
skos:inScheme .
@@ -4973,13 +5067,13 @@ biolink:GenotypeToVariantAssociation a owl:Class ;
rdfs:label "genotype to variant association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Genotype ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:SequenceVariant ;
owl:onProperty biolink:object ],
@@ -4987,17 +5081,17 @@ biolink:GenotypeToVariantAssociation a owl:Class ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Genotype ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "Any association between a genotype and a sequence variant." ;
skos:inScheme .
@@ -5036,10 +5130,10 @@ biolink:GeographicExposure a owl:Class ;
biolink:GeographicLocationAtTime a owl:Class ;
rdfs:label "geographic location at time" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:time_type ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:timepoint ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:time_type ;
owl:onProperty biolink:timepoint ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
@@ -5063,14 +5157,14 @@ biolink:GrossAnatomicalStructure a owl:Class ;
biolink:Haplotype a owl:Class ;
rdfs:label "haplotype" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GenomicEntity ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:OntologyClass ],
biolink:BiologicalEntity ;
skos:definition "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ;
skos:exactMatch ,
@@ -5101,28 +5195,28 @@ biolink:Human a owl:Class ;
biolink:InformationContentEntityToNamedThingAssociation a owl:Class ;
rdfs:label "information content entity to named thing association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:NamedThing ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:allValuesFrom owl:Thing ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom owl:Thing ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:NamedThing ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
@@ -5205,16 +5299,16 @@ biolink:MacromolecularComplex a owl:Class ;
biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ;
rdfs:label "macromolecular machine to biological process association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:BiologicalProcess ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
biolink:FunctionalAssociation ;
skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ;
@@ -5223,11 +5317,11 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ;
biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ;
rdfs:label "macromolecular machine to cellular component association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:CellularComponent ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:CellularComponent ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
@@ -5241,16 +5335,16 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ;
biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ;
rdfs:label "macromolecular machine to molecular activity association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:MolecularActivity ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:MolecularActivity ;
owl:onProperty biolink:object ],
biolink:FunctionalAssociation ;
skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ;
@@ -5260,31 +5354,31 @@ biolink:MaterialSampleDerivationAssociation a owl:Class ;
rdfs:label "material sample derivation association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:predicate_type ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:NamedThing ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:MaterialSample ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "An association between a material sample and the material entity from which it is derived." ;
skos:inScheme .
@@ -5293,10 +5387,10 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "material sample to disease or phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ],
+ owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
+ owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ],
biolink:Association ;
skos:definition "An association between a material sample and a disease or phenotype." ;
skos:inScheme .
@@ -5351,11 +5445,8 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:MolecularActivity ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalEntity ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
@@ -5363,8 +5454,11 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:MolecularActivity ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:ChemicalEntity ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ;
skos:inScheme .
@@ -5373,22 +5467,22 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ;
rdfs:label "molecular activity to molecular activity association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:allValuesFrom biolink:MolecularActivity ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:MolecularActivity ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:MolecularActivity ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ;
skos:inScheme .
@@ -5396,32 +5490,32 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ;
biolink:MolecularActivityToPathwayAssociation a owl:Class ;
rdfs:label "molecular activity to pathway association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Pathway ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:MolecularActivity ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ;
skos:inScheme .
@@ -5429,76 +5523,76 @@ biolink:MolecularActivityToPathwayAssociation a owl:Class ;
biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ;
rdfs:label "named thing associated with likelihood of named thing association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:object_aspect_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
+ [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:population_context_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:predicate_type ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:predicate_type ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:OntologyClass ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
owl:onProperty biolink:population_context_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject_aspect_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OntologyClass ;
owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:population_context_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:NamedThing ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:NamedThing ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:NamedThing ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:OntologyClass ;
owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object_aspect_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:onProperty biolink:population_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:NamedThing ;
owl:onProperty biolink:object ],
biolink:Association ;
skos:inScheme .
@@ -5514,13 +5608,13 @@ biolink:NucleosomeModification a owl:Class ;
rdfs:label "nucleosome modification" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EpigenomicEntity ],
+ owl:someValuesFrom biolink:GenomicEntity ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneProductIsoformMixin ],
+ owl:someValuesFrom biolink:EpigenomicEntity ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenomicEntity ],
+ owl:someValuesFrom biolink:GeneProductIsoformMixin ],
biolink:BiologicalEntity ;
skos:definition "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ;
skos:inScheme .
@@ -5534,75 +5628,75 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ;
biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ;
rdfs:label "organism taxon to environment association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom owl:Thing ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom owl:Thing ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
biolink:Association ;
skos:inScheme .
biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ;
rdfs:label "organism taxon to organism taxon interaction" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:associated_environmental_context ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:associated_environmental_context ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:associated_environmental_context ],
+ owl:allValuesFrom biolink:OrganismTaxon ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:OrganismTaxon ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:associated_environmental_context ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:associated_environmental_context ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:associated_environmental_context ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
biolink:OrganismTaxonToOrganismTaxonAssociation ;
skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ;
@@ -5611,32 +5705,32 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ;
biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ;
rdfs:label "organism taxon to organism taxon specialization" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
biolink:OrganismTaxonToOrganismTaxonAssociation ;
skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ;
skos:inScheme .
@@ -5644,23 +5738,23 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ;
biolink:OrganismToOrganismAssociation a owl:Class ;
rdfs:label "organism to organism association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:IndividualOrganism ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:allValuesFrom biolink:IndividualOrganism ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:IndividualOrganism ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:inScheme .
@@ -5668,69 +5762,69 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ;
rdfs:label "organismal entity as a model of disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
+ owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismalEntity ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
+ owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
biolink:Association ;
skos:inScheme .
biolink:PairwiseMolecularInteraction a owl:Class ;
rdfs:label "pairwise molecular interaction" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:MolecularEntity ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:interacting_molecules_category ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:interacting_molecules_category ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:interacting_molecules_category ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OntologyClass ;
owl:onProperty biolink:interacting_molecules_category ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:MolecularEntity ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:MolecularEntity ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
biolink:PairwiseGeneToGeneInteraction ;
skos:definition "An interaction at the molecular level between two physical entities" ;
skos:inScheme .
@@ -5822,29 +5916,33 @@ biolink:Phenomenon a owl:Class ;
biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ;
rdfs:label "phenotypic feature to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ],
biolink:Association ;
skos:inScheme .
-biolink:PhenotypicFeatureToEntityAssociationMixin a owl:Class ;
- rdfs:label "phenotypic feature to entity association mixin" ;
+biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a owl:Class ;
+ rdfs:label "phenotypic feature to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:FrequencyQuantifier ],
- biolink:FeatureOrDiseaseQualifiersToEntityMixin ;
+ owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ],
+ biolink:Association ;
+ skos:definition "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ;
skos:inScheme .
biolink:PhenotypicQuality a owl:Class ;
@@ -5889,32 +5987,32 @@ biolink:Plant a owl:Class ;
biolink:PopulationToPopulationAssociation a owl:Class ;
rdfs:label "population to population association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between a two populations" ;
skos:inScheme .
@@ -5932,193 +6030,193 @@ biolink:PredicateMapping a owl:Class ;
rdfs:label "predicate mapping" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_context_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:narrow_match ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:object_derivative_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:OrganismTaxon ;
- owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:DirectionQualifierEnum ;
- owl:onProperty biolink:subject_direction_qualifier ],
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_derivative_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_part_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:mapped_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:broad_match ],
+ owl:onProperty biolink:subject_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:qualified_predicate ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_aspect_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:onProperty biolink:broad_match ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:narrow_match ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:mapped_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:exact_match ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:subject_part_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:predicate_type ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:broad_match ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object_part_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_aspect_qualifier ],
+ owl:onProperty biolink:narrow_match ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_part_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:narrow_match ],
+ owl:onProperty biolink:exact_match ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:onProperty biolink:exact_match ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:mapped_predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:object_derivative_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:exact_match ],
+ owl:allValuesFrom biolink:DirectionQualifierEnum ;
+ owl:onProperty biolink:subject_direction_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:allValuesFrom biolink:OrganismTaxon ;
+ owl:onProperty biolink:species_context_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:exact_match ],
+ owl:onProperty biolink:object_context_qualifier ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:narrow_match ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:species_context_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:qualified_predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:broad_match ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_form_or_variant_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject_direction_qualifier ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:CausalMechanismQualifierEnum ;
- owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_context_qualifier ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_derivative_qualifier ],
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_form_or_variant_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:subject_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:allValuesFrom biolink:CausalMechanismQualifierEnum ;
+ owl:onProperty biolink:causal_mechanism_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_derivative_qualifier ],
+ owl:onProperty biolink:object_derivative_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object_context_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DirectionQualifierEnum ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:broad_match ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:anatomical_context_qualifier ],
+ owl:onProperty biolink:subject_context_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:mapped_predicate ],
+ owl:onProperty biolink:subject_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object_context_qualifier ],
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:subject_part_qualifier ],
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject_direction_qualifier ],
+ owl:onProperty biolink:object_aspect_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:subject_derivative_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:narrow_match ],
+ owl:onProperty biolink:anatomical_context_qualifier ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:subject_context_qualifier ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:broad_match ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:subject_part_qualifier ],
+ owl:onProperty biolink:object_form_or_variant_qualifier ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:mapped_predicate ],
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:qualified_predicate ],
+ owl:onProperty biolink:object_part_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:object_aspect_qualifier ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:DirectionQualifierEnum ;
+ owl:onProperty biolink:object_direction_qualifier ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:causal_mechanism_qualifier ],
linkml:ClassDefinition ;
skos:definition "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." ;
skos:inScheme .
@@ -6142,10 +6240,10 @@ biolink:ProteinDomain a owl:Class ;
rdfs:label "protein domain" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneGroupingMixin ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
+ owl:someValuesFrom biolink:GeneGroupingMixin ],
biolink:BiologicalEntity ;
skos:definition "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ;
skos:exactMatch ,
@@ -6221,13 +6319,13 @@ biolink:RNAProductIsoform a owl:Class ;
biolink:ReactionToCatalystAssociation a owl:Class ;
rdfs:label "reaction to catalyst association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
biolink:ReactionToParticipantAssociation ;
skos:inScheme .
@@ -6236,10 +6334,10 @@ biolink:ReagentTargetedGene a owl:Class ;
rdfs:label "reagent targeted gene" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GenomicEntity ],
@@ -6289,22 +6387,22 @@ biolink:SequenceEnum a owl:Class ;
biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ;
rdfs:label "sequence variant modulates treatment association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:SequenceVariant ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:Treatment ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:SequenceVariant ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Treatment ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ;
@@ -6314,47 +6412,47 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ;
biolink:Serial a owl:Class ;
rdfs:label "serial" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:type ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:issue ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:type ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:issue ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:volume ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:iso_abbreviation ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:volume ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:volume ],
+ owl:onProperty biolink:issue ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:volume ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:type ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:issue ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:volume ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:iso_abbreviation ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
+ owl:onProperty biolink:issue ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:iso_abbreviation ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:issue ],
+ owl:onProperty biolink:volume ],
biolink:Publication ;
skos:altLabel "journal" ;
skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ;
@@ -6372,16 +6470,7 @@ biolink:SiRNA a owl:Class ;
biolink:SmallMolecule a owl:Class ;
rdfs:label "small molecule" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
- biolink:MolecularEntity ;
+ rdfs:subClassOf biolink:MolecularEntity ;
skos:altLabel "chemical substance" ;
skos:definition "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ;
skos:inScheme ;
@@ -6412,14 +6501,14 @@ biolink:Snv a owl:Class ;
biolink:SocioeconomicExposure a owl:Class ;
rdfs:label "socioeconomic exposure" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:has_attribute ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:ExposureEvent ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:SocioeconomicAttribute ;
owl:onProperty biolink:has_attribute ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:has_attribute ],
biolink:Attribute ;
skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ;
skos:inScheme .
@@ -6471,20 +6560,20 @@ biolink:StudyVariable a owl:Class ;
biolink:TaxonToTaxonAssociation a owl:Class ;
rdfs:label "taxon to taxon association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
@@ -6507,23 +6596,23 @@ biolink:TextMiningResult a owl:Class ;
biolink:TranscriptToGeneRelationship a owl:Class ;
rdfs:label "transcript to gene relationship" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom biolink:Gene ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Transcript ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Gene ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:Transcript ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
biolink:SequenceFeatureRelationship ;
skos:definition "A gene is a collection of transcripts" ;
skos:inScheme .
@@ -6532,16 +6621,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ;
rdfs:label "transcription factor binding site" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenomicEntity ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:GenomicEntity ],
biolink:RegulatoryRegion ;
skos:altLabel "binding site",
"tf binding site" ;
@@ -6552,20 +6641,20 @@ biolink:TranscriptionFactorBindingSite a owl:Class ;
biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ;
rdfs:label "variant as a model of disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
+ [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:SequenceVariant ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:SequenceVariant ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ],
biolink:VariantToDiseaseAssociation ;
skos:inScheme .
@@ -6575,13 +6664,13 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GeneExpressionMixin ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
biolink:VariantToGeneAssociation ;
skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ;
@@ -6590,14 +6679,14 @@ biolink:VariantToGeneExpressionAssociation a owl:Class ;
biolink:VariantToPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "variant to phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:SequenceVariant ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
@@ -6610,59 +6699,59 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ;
biolink:VariantToPopulationAssociation a owl:Class ;
rdfs:label "variant to population association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:FrequencyQualifierMixin ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:SequenceVariant ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_quotient ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:has_quotient ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:has_quotient ],
+ owl:onProperty biolink:has_total ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:FrequencyQuantifier ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:has_quotient ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:SequenceVariant ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:has_count ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
owl:onProperty biolink:has_total ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:has_count ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:has_total ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:has_count ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:has_count ],
+ owl:onProperty biolink:has_quotient ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:has_total ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:FrequencyQualifierMixin ],
biolink:Association ;
skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ;
skos:inScheme .
@@ -7236,41 +7325,41 @@ biolink:AdministrativeEntity a owl:Class ;
biolink:Article a owl:Class ;
rdfs:label "article" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:volume ],
- [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:iso_abbreviation ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:volume ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
owl:onProperty biolink:iso_abbreviation ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:published_in ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:issue ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:volume ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:anyURI ;
owl:onProperty biolink:published_in ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:issue ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:iso_abbreviation ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:volume ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:issue ],
+ owl:onProperty biolink:published_in ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:iso_abbreviation ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:published_in ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:volume ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:issue ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:published_in ],
biolink:Publication ;
skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ;
skos:exactMatch fabio:article,
@@ -7303,31 +7392,31 @@ biolink:BehavioralFeature a owl:Class ;
biolink:BookChapter a owl:Class ;
rdfs:label "book chapter" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:chapter ],
+ [ a owl:Restriction ;
owl:allValuesFrom xsd:anyURI ;
owl:onProperty biolink:published_in ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:volume ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:volume ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:chapter ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:published_in ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:chapter ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:volume ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:volume ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:chapter ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:published_in ],
biolink:Publication ;
skos:inScheme .
@@ -7346,19 +7435,19 @@ biolink:Case a owl:Class ;
biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "cell line to disease or phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ;
owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ;
@@ -7381,12 +7470,12 @@ biolink:ChemicalExposure a owl:Class ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:has_quantitative_value ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:QuantityValue ;
- owl:onProperty biolink:has_quantitative_value ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:ExposureEvent ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:QuantityValue ;
+ owl:onProperty biolink:has_quantitative_value ],
biolink:Attribute ;
skos:definition "A chemical exposure is an intake of a particular chemical entity." ;
skos:exactMatch ECTO:9000000,
@@ -7396,29 +7485,29 @@ biolink:ChemicalExposure a owl:Class ;
biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:FDA_adverse_event_level ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ;
owl:onProperty biolink:FDA_adverse_event_level ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ;
- owl:onProperty biolink:FDA_adverse_event_level ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:FDA_adverse_event_level ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
biolink:Association ;
skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary undesirable effect." ;
skos:inScheme .
@@ -7544,10 +7633,10 @@ biolink:GeneFamily a owl:Class ;
rdfs:label "gene family" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneGroupingMixin ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
+ owl:someValuesFrom biolink:GeneGroupingMixin ],
biolink:BiologicalEntity ;
skos:altLabel "orthogroup",
"protein family" ;
@@ -7563,76 +7652,76 @@ biolink:GenomicSequenceLocalization a owl:Class ;
rdfs:label "genomic sequence localization" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:genome_build ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:phase ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:StrandEnum ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:genome_build ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:strand ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:end_interbase_coordinate ],
+ owl:onProperty biolink:phase ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:StrandEnum ;
owl:onProperty biolink:genome_build ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:NucleicAcidEntity ;
- owl:onProperty biolink:subject ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:strand ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:start_interbase_coordinate ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:end_interbase_coordinate ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:start_interbase_coordinate ],
+ owl:onProperty biolink:end_interbase_coordinate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:StrandEnum ;
+ owl:onProperty biolink:strand ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:end_interbase_coordinate ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:phase ],
+ owl:onProperty biolink:genome_build ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:start_interbase_coordinate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:start_interbase_coordinate ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:PhaseEnum ;
owl:onProperty biolink:phase ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:phase ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:strand ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:NucleicAcidEntity ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:strand ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:StrandEnum ;
- owl:onProperty biolink:genome_build ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:end_interbase_coordinate ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:start_interbase_coordinate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:start_interbase_coordinate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:NucleicAcidEntity ;
+ owl:onProperty biolink:subject ],
biolink:SequenceAssociation ;
skos:broadMatch dcid:Chromosome ;
skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ;
@@ -7643,6 +7732,15 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ;
rdfs:label "genotype to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom owl:Thing ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
@@ -7650,30 +7748,21 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ;
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom owl:Thing ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom owl:Thing ;
- owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:inScheme ;
skos:note "TODO decide no how to model pathogenicity" .
@@ -7686,23 +7775,23 @@ biolink:GenotypeToEntityAssociationMixin a owl:Class ;
biolink:GeographicLocation a owl:Class ;
rdfs:label "geographic location" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:longitude ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:float ;
owl:onProperty biolink:latitude ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:float ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:latitude ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:float ;
owl:onProperty biolink:longitude ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:longitude ],
+ owl:onProperty biolink:latitude ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:latitude ],
+ owl:onProperty biolink:longitude ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:longitude ],
biolink:PlanetaryEntity ;
skos:definition "a location that can be described in lat/long coordinates" ;
skos:exactMatch STY:T083,
@@ -7744,19 +7833,27 @@ biolink:OrganismTaxonToEntityAssociation a owl:Class ;
biolink:PairwiseGeneToGeneInteraction a owl:Class ;
rdfs:label "pairwise gene to gene interaction" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
biolink:GeneToGeneAssociation ;
skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ;
skos:inScheme ;
skos:narrowMatch dcid:ProteinProteinInteraction .
+biolink:PhenotypicFeatureToEntityAssociationMixin a owl:Class ;
+ rdfs:label "phenotypic feature to entity association mixin" ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:FrequencyQuantifier ],
+ biolink:FeatureOrDiseaseQualifiersToEntityMixin ;
+ skos:inScheme .
+
biolink:Polypeptide a owl:Class ;
rdfs:label "polypeptide" ;
rdfs:subClassOf [ a owl:Restriction ;
@@ -7776,41 +7873,41 @@ biolink:Polypeptide a owl:Class ;
biolink:ReactionToParticipantAssociation a owl:Class ;
rdfs:label "reaction to participant association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:stoichiometry ],
+ owl:allValuesFrom biolink:MolecularEntity ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:reaction_direction ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:reaction_side ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:ReactionSideEnum ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:reaction_side ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:reaction_direction ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ReactionDirectionEnum ;
- owl:onProperty biolink:reaction_direction ],
+ owl:onProperty biolink:stoichiometry ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:integer ;
owl:onProperty biolink:stoichiometry ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:MolecularEntity ;
- owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:stoichiometry ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:reaction_side ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
+ owl:onProperty biolink:reaction_direction ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:reaction_direction ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:ReactionSideEnum ;
owl:onProperty biolink:reaction_side ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:ReactionDirectionEnum ;
+ owl:onProperty biolink:reaction_direction ],
biolink:ChemicalToChemicalAssociation ;
skos:inScheme .
@@ -7842,29 +7939,29 @@ biolink:StudyPopulation a owl:Class ;
biolink:Treatment a owl:Class ;
rdfs:label "treatment" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_device ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Procedure ;
- owl:onProperty biolink:has_procedure ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Device ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:has_device ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ],
+ owl:someValuesFrom biolink:ExposureEvent ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Drug ;
owl:onProperty biolink:has_drug ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ExposureEvent ],
+ owl:allValuesFrom biolink:Procedure ;
+ owl:onProperty biolink:has_procedure ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:has_drug ],
+ owl:onProperty biolink:has_procedure ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:has_procedure ],
+ owl:onProperty biolink:has_drug ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Device ;
+ owl:onProperty biolink:has_device ],
biolink:NamedThing ;
skos:altLabel "medical action",
"medical intervention" ;
@@ -7877,38 +7974,38 @@ biolink:Treatment a owl:Class ;
biolink:VariantToDiseaseAssociation a owl:Class ;
rdfs:label "variant to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:allValuesFrom owl:Thing ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom owl:Thing ;
- owl:onProperty biolink:subject ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom owl:Thing ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:allValuesFrom owl:Thing ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
biolink:Association ;
skos:inScheme ;
skos:note "TODO decide no how to model pathogenicity" .
@@ -7916,26 +8013,26 @@ biolink:VariantToDiseaseAssociation a owl:Class ;
biolink:VariantToGeneAssociation a owl:Class ;
rdfs:label "variant to gene association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Gene ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:VariantToEntityAssociationMixin ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:predicate ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Gene ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ;
skos:inScheme .
@@ -8031,8 +8128,9 @@ biolink:distribution_download_url a owl:DatatypeProperty ;
skos:exactMatch dcat:downloadURL ;
skos:inScheme .
-biolink:drug_regulatory_status_world_wide a owl:DatatypeProperty ;
+biolink:drug_regulatory_status_world_wide a owl:ObjectProperty ;
rdfs:label "drug regulatory status world wide" ;
+ rdfs:range biolink:ApprovalStatusEnum ;
skos:altLabel "max phase" ;
skos:definition "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ;
skos:exactMatch ;
@@ -8187,8 +8285,9 @@ biolink:has_zygosity a owl:ObjectProperty ;
rdfs:subPropertyOf biolink:node_property ;
skos:inScheme .
-biolink:highest_FDA_approval_status a owl:DatatypeProperty ;
+biolink:highest_FDA_approval_status a owl:ObjectProperty ;
rdfs:label "highest FDA approval status" ;
+ rdfs:range biolink:ApprovalStatusEnum ;
skos:definition "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ;
skos:inScheme .
@@ -8605,20 +8704,20 @@ biolink:ActivityAndBehavior a owl:Class ;
biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ;
rdfs:label "anatomical entity to anatomical entity association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:AnatomicalEntity ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:AnatomicalEntity ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:AnatomicalEntity ;
owl:onProperty biolink:object ],
@@ -8654,16 +8753,13 @@ biolink:ChemicalToChemicalAssociation a owl:Class ;
rdfs:label "chemical to chemical association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:NamedThing ;
owl:onProperty biolink:subject ],
@@ -8672,16 +8768,19 @@ biolink:ChemicalToChemicalAssociation a owl:Class ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ChemicalEntity ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ;
skos:inScheme .
@@ -8704,7 +8803,6 @@ biolink:Device a owl:Class ;
skos:inScheme ;
skos:narrowMatch STY:T074,
STY:T075,
- STY:T122,
STY:T203,
UMLSSG:DEVI .
@@ -8760,55 +8858,55 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ;
rdfs:label "gene to disease or phenotypic feature association" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:DirectionQualifierEnum ;
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:predicate ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:object_direction_qualifier ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:onProperty biolink:subject_aspect_qualifier ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DirectionQualifierEnum ;
- owl:onProperty biolink:object_direction_qualifier ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:predicate ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:subject_aspect_qualifier ],
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:predicate ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:subject_aspect_qualifier ],
biolink:Association ;
skos:inScheme ;
skos:narrowMatch WBVocab:Gene-Phenotype-Association,
@@ -8864,26 +8962,26 @@ biolink:Onset a owl:Class ;
biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ;
rdfs:label "organism taxon to organism taxon association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:minCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:OrganismTaxon ;
owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:OrganismTaxon ;
- owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "A relationship between two organism taxon nodes" ;
skos:inScheme .
@@ -8931,13 +9029,13 @@ biolink:RegulatoryRegion a owl:Class ;
rdfs:label "regulatory region" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GenomicEntity ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:PhysicalEssence ],
@@ -9273,13 +9371,13 @@ biolink:CellularComponent a owl:Class ;
biolink:DatasetDistribution a owl:Class ;
rdfs:label "dataset distribution" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:distribution_download_url ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:distribution_download_url ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:distribution_download_url ],
biolink:InformationContentEntity ;
skos:definition "an item that holds distribution level information about a dataset." ;
@@ -9289,23 +9387,23 @@ biolink:DatasetDistribution a owl:Class ;
biolink:DatasetSummary a owl:Class ;
rdfs:label "dataset summary" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:source_logo ],
+ [ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:source_web_page ],
+ owl:onProperty biolink:source_logo ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:source_web_page ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
owl:onProperty biolink:source_logo ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:source_web_page ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:source_logo ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:source_logo ],
+ owl:onProperty biolink:source_web_page ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:source_web_page ],
biolink:InformationContentEntity ;
skos:definition "an item that holds summary level information about a dataset." ;
skos:inScheme .
@@ -9332,23 +9430,23 @@ biolink:GeneProductIsoformMixin a owl:Class ;
biolink:GeneToGeneAssociation a owl:Class ;
rdfs:label "gene to gene association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:GeneOrGeneProduct ;
+ owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
biolink:Association ;
skos:altLabel "molecular or genetic interaction" ;
skos:definition "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ;
@@ -9430,23 +9528,23 @@ biolink:Protein a owl:Class ;
biolink:QuantityValue a owl:Class ;
rdfs:label "quantity value" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom ;
owl:onProperty biolink:has_unit ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:double ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:has_numeric_value ],
[ a owl:Restriction ;
- owl:allValuesFrom ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:has_unit ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:has_numeric_value ],
+ owl:onProperty biolink:has_unit ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:double ;
owl:onProperty biolink:has_numeric_value ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_unit ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:has_numeric_value ],
biolink:Annotation ;
skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ;
skos:inScheme .
@@ -9461,8 +9559,14 @@ biolink:ResourceRoleEnum a owl:Class ;
biolink:SequenceFeatureRelationship a owl:Class ;
rdfs:label "sequence feature relationship" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:allValuesFrom biolink:NucleicAcidEntity ;
+ owl:onProperty biolink:subject ],
+ [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:NucleicAcidEntity ;
owl:onProperty biolink:object ],
@@ -9472,12 +9576,6 @@ biolink:SequenceFeatureRelationship a owl:Class ;
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:NucleicAcidEntity ;
- owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "For example, a particular exon is part of a particular transcript or gene" ;
skos:exactMatch CHADO:feature_relationship ;
@@ -9596,31 +9694,31 @@ biolink:ClinicalAttribute a owl:Class ;
biolink:DatasetVersion a owl:Class ;
rdfs:label "dataset version" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Dataset ;
- owl:onProperty biolink:has_dataset ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:has_distribution ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_dataset ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:ingest_date ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:ingest_date ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:ingest_date ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_distribution ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:has_dataset ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Dataset ;
+ owl:onProperty biolink:has_dataset ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:ingest_date ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DatasetDistribution ;
- owl:onProperty biolink:has_distribution ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_dataset ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:DatasetDistribution ;
owl:onProperty biolink:has_distribution ],
biolink:InformationContentEntity ;
skos:definition "an item that holds version level information about a dataset." ;
@@ -9650,23 +9748,23 @@ biolink:FDAIDAAdverseEventEnum a owl:Class ;
biolink:FunctionalAssociation a owl:Class ;
rdfs:label "functional association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:MacromolecularMachineMixin ;
- owl:onProperty biolink:subject ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:OntologyClass ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:object ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:OntologyClass ;
- owl:onProperty biolink:object ],
+ owl:allValuesFrom biolink:MacromolecularMachineMixin ;
+ owl:onProperty biolink:subject ],
biolink:Association ;
skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ;
skos:inScheme .
@@ -10047,38 +10145,38 @@ biolink:CellularOrganism a owl:Class ;
biolink:ChemicalMixture a owl:Class ;
rdfs:label "chemical mixture" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:drug_regulatory_status_world_wide ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:is_supplement ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:highest_FDA_approval_status ],
+ owl:onProperty biolink:routes_of_delivery ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:highest_FDA_approval_status ],
+ owl:allValuesFrom biolink:DrugDeliveryEnum ;
+ owl:onProperty biolink:routes_of_delivery ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:drug_regulatory_status_world_wide ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:highest_FDA_approval_status ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:is_supplement ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:highest_FDA_approval_status ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:drug_regulatory_status_world_wide ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:ApprovalStatusEnum ;
+ owl:onProperty biolink:highest_FDA_approval_status ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:is_supplement ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DrugDeliveryEnum ;
- owl:onProperty biolink:routes_of_delivery ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:drug_regulatory_status_world_wide ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:is_supplement ],
+ owl:allValuesFrom biolink:ApprovalStatusEnum ;
+ owl:onProperty biolink:drug_regulatory_status_world_wide ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:routes_of_delivery ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:highest_FDA_approval_status ],
biolink:ChemicalEntity ;
skos:closeMatch dcid:ChemicalCompound ;
skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ;
@@ -10104,20 +10202,17 @@ biolink:GeneProductMixin a owl:Class ;
biolink:GeneToDiseaseAssociation a owl:Class ;
rdfs:label "gene to disease association" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
owl:allValuesFrom biolink:GeneOrGeneProduct ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:object ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
+ owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GeneToEntityAssociationMixin ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:Disease ;
owl:onProperty biolink:object ],
@@ -10125,8 +10220,11 @@ biolink:GeneToDiseaseAssociation a owl:Class ;
owl:maxCardinality 1 ;
owl:onProperty biolink:subject ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:object ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:subject ],
biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ;
skos:closeMatch dcid:DiseaseGeneAssociation ;
skos:exactMatch SIO:000983 ;
@@ -10142,38 +10240,38 @@ biolink:MacromolecularMachineMixin a owl:Class ;
biolink:MolecularActivity a owl:Class ;
rdfs:label "molecular activity" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:OntologyClass ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:enabled_by ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:has_output ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:MolecularEntity ;
owl:onProperty biolink:has_output ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:has_input ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_input ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:Occurrent ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:MacromolecularMachineMixin ;
owl:onProperty biolink:enabled_by ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:MolecularEntity ;
- owl:onProperty biolink:has_output ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:enabled_by ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_input ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:MolecularEntity ;
owl:onProperty biolink:has_input ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:enabled_by ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_output ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Occurrent ],
biolink:BiologicalProcessOrActivity ;
skos:altLabel "molecular event",
"molecular function",
@@ -10193,38 +10291,38 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ;
biolink:RetrievalSource a owl:Class ;
rdfs:label "retrieval source" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:upstream_resource_ids ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:xref ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:resource_role ],
- [ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:upstream_resource_ids ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:resource_role ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:resource_id ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:xref ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:anyURI ;
owl:onProperty biolink:resource_id ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:xref ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:resource_id ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:resource_role ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:upstream_resource_ids ],
+ owl:onProperty biolink:xref ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:resource_id ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:ResourceRoleEnum ;
owl:onProperty biolink:resource_role ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:upstream_resource_ids ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:anyURI ;
+ owl:onProperty biolink:upstream_resource_ids ],
biolink:InformationContentEntity ;
skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ;
skos:inScheme .
@@ -10307,8 +10405,8 @@ biolink:has_sequence_variant a owl:ObjectProperty ;
biolink:treats_or_applied_or_studied_to_treat a owl:ObjectProperty ;
rdfs:label "treats or applied or studied to treat" ;
- rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
- rdfs:range biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:domain biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:range biolink:DiseaseOrPhenotypicFeature ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
skos:definition "Holds between an substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to treat the condition, has been observed to be taken/prescribed in practice with the intent of treating the condition, or has been interrogated in a scientific study that hypothesized an ability to treat the condition (in humans or other biological systems/organisms)." ;
skos:editorialNote "This predicate is helpful both as a grouping predicate to aid in searching for broader senses of treating a condition, and as a catch-all for representing sources that are not clear about the sense of treats that is being reported. For example, text-mined statements concerning treatments for disease are based on sentences that can report treatment in any of these different senses and thus require a broader predicate such as this to safely report statement semantics." ;
@@ -10583,34 +10681,26 @@ biolink:Drug a owl:Class ;
skos:narrowMatch STY:T195 ;
skos:note "The CHEBI ID represents a role rather than a substance" .
-biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ;
- rdfs:label "entity to phenotypic feature association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:FrequencyQuantifier ],
- biolink:EntityToFeatureOrDiseaseQualifiersMixin ;
- skos:inScheme .
-
biolink:Genotype a owl:Class ;
rdfs:label "genotype" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:has_zygosity ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenomicEntity ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Zygosity ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:has_zygosity ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:has_zygosity ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:GenomicEntity ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Zygosity ;
+ owl:onProperty biolink:has_zygosity ],
biolink:BiologicalEntity ;
skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ;
skos:exactMatch ,
@@ -10712,72 +10802,80 @@ biolink:AgentTypeEnum a owl:Class ;
biolink:Entity a owl:Class ;
rdfs:label "entity" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:type ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:type ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:description ],
+ owl:allValuesFrom biolink:label_type ;
+ owl:onProperty biolink:name ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:iri ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:deprecated ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:description ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:boolean ;
+ owl:onProperty biolink:deprecated ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:narrative_text ;
owl:onProperty biolink:description ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:deprecated ],
+ owl:onProperty biolink:name ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:Attribute ;
+ owl:onProperty biolink:has_attribute ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:iri_type ;
owl:onProperty biolink:iri ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:name ],
+ owl:onProperty biolink:type ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:label_type ;
- owl:onProperty biolink:name ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:id ],
+ owl:onProperty biolink:name ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:Attribute ;
- owl:onProperty biolink:has_attribute ],
+ owl:allValuesFrom xsd:anyURI ;
+ owl:onProperty biolink:category ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:category ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:deprecated ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_attribute ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:description ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:boolean ;
- owl:onProperty biolink:deprecated ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:iri ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:category ],
+ owl:onProperty biolink:type ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:name ],
+ owl:onProperty biolink:deprecated ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:category ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_attribute ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:iri_type ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:iri ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:id ],
linkml:ClassDefinition ;
skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ;
skos:inScheme .
+biolink:EntityToPhenotypicFeatureAssociationMixin a owl:Class ;
+ rdfs:label "entity to phenotypic feature association mixin" ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:FrequencyQuantifier ],
+ biolink:EntityToFeatureOrDiseaseQualifiersMixin ;
+ skos:inScheme .
+
biolink:MaxResearchPhaseEnum a owl:Class ;
rdfs:subClassOf linkml:EnumDefinition ;
owl:unionOf ( ) ;
@@ -10845,14 +10943,14 @@ biolink:xref a owl:DatatypeProperty ;
biolink:NucleicAcidEntity a owl:Class ;
rdfs:label "nucleic acid entity" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GenomicEntity ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:ThingWithTaxon ],
@@ -10874,10 +10972,10 @@ biolink:OrganismalEntity a owl:Class ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:SubjectOfInvestigation ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom owl:Thing ;
owl:onProperty biolink:has_attribute ],
[ a owl:Restriction ;
- owl:allValuesFrom owl:Thing ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:has_attribute ],
biolink:BiologicalEntity ;
skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ;
@@ -10980,18 +11078,6 @@ biolink:BiologicalProcessOrActivity a owl:Class ;
rdfs:subClassOf [ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:enabled_by ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_input ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:has_output ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:Occurrent ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:NamedThing ;
- owl:onProperty biolink:has_input ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:OntologyClass ],
@@ -10999,17 +11085,29 @@ biolink:BiologicalProcessOrActivity a owl:Class ;
owl:allValuesFrom biolink:PhysicalEntity ;
owl:onProperty biolink:enabled_by ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:NamedThing ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:has_output ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:has_output ],
+ owl:onProperty biolink:enabled_by ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_input ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:has_input ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:enabled_by ],
+ owl:onProperty biolink:has_output ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:NamedThing ;
+ owl:onProperty biolink:has_input ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:NamedThing ;
+ owl:onProperty biolink:has_output ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Occurrent ],
biolink:BiologicalEntity ;
skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ;
skos:inScheme .
@@ -11017,38 +11115,38 @@ biolink:BiologicalProcessOrActivity a owl:Class ;
biolink:Agent a owl:Class ;
rdfs:label "agent" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:address ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:affiliation ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:address ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:id ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:name ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:address ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:address ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:anyURI ;
+ owl:onProperty biolink:affiliation ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:name ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:affiliation ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:name ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:name ],
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:affiliation ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:name ],
biolink:AdministrativeEntity ;
skos:altLabel "group" ;
skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ;
@@ -11148,6 +11246,25 @@ biolink:object_aspect_qualifier a owl:DatatypeProperty ;
skos:definition "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)." ;
skos:inScheme .
+biolink:ApprovalStatusEnum a owl:Class ;
+ rdfs:subClassOf linkml:EnumDefinition ;
+ owl:unionOf ( ) ;
+ linkml:permissible_values ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ ,
+ .
+
biolink:BiologicalProcess a owl:Class ;
rdfs:label "biological process" ;
rdfs:subClassOf [ a owl:Restriction ;
@@ -11167,13 +11284,13 @@ biolink:BiologicalProcess a owl:Class ;
biolink:MolecularEntity a owl:Class ;
rdfs:label "molecular entity" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:is_metabolite ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:boolean ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:is_metabolite ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom xsd:boolean ;
owl:onProperty biolink:is_metabolite ],
biolink:ChemicalEntity ;
skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ;
@@ -11186,14 +11303,14 @@ biolink:MolecularEntity a owl:Class ;
biolink:OrganismTaxon a owl:Class ;
rdfs:label "organism taxon" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:has_taxonomic_rank ],
- [ a owl:Restriction ;
owl:allValuesFrom biolink:TaxonomicRank ;
owl:onProperty biolink:has_taxonomic_rank ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:has_taxonomic_rank ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:has_taxonomic_rank ],
biolink:NamedThing ;
skos:altLabel "taxon",
"taxonomic classification" ;
@@ -11207,41 +11324,41 @@ biolink:OrganismTaxon a owl:Class ;
biolink:InformationContentEntity a owl:Class ;
rdfs:label "information content entity" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:license ],
+ [ a owl:Restriction ;
owl:allValuesFrom xsd:date ;
owl:onProperty biolink:creation_date ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:rights ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:license ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:format ],
+ owl:onProperty biolink:license ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:license ],
+ owl:onProperty biolink:rights ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:license ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:rights ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:creation_date ],
+ owl:onProperty biolink:format ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:format ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:creation_date ],
+ owl:onProperty biolink:format ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:rights ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:rights ],
+ owl:onProperty biolink:creation_date ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
- owl:onProperty biolink:format ],
+ owl:onProperty biolink:creation_date ],
biolink:NamedThing ;
skos:altLabel "information",
"information artefact",
@@ -11301,89 +11418,98 @@ biolink:Attribute a owl:Class ;
rdfs:label "attribute" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:name ],
+ owl:onProperty biolink:has_qualitative_value ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:has_attribute_type ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
+ owl:onProperty biolink:has_attribute_type ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:name ],
[ a owl:Restriction ;
owl:allValuesFrom biolink:NamedThing ;
owl:onProperty biolink:has_qualitative_value ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:QuantityValue ;
- owl:onProperty biolink:has_quantitative_value ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_qualitative_value ],
+ owl:allValuesFrom biolink:OntologyClass ;
+ owl:onProperty biolink:has_attribute_type ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:has_quantitative_value ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:label_type ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:name ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:has_attribute_type ],
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:iri_type ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:iri ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:has_qualitative_value ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:OntologyClass ;
- owl:onProperty biolink:has_attribute_type ],
+ owl:allValuesFrom biolink:label_type ;
+ owl:onProperty biolink:name ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom biolink:QuantityValue ;
+ owl:onProperty biolink:has_quantitative_value ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:iri ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:has_attribute_type ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom biolink:iri_type ;
owl:onProperty biolink:iri ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:has_qualitative_value ],
biolink:NamedThing ;
skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ;
skos:exactMatch SIO:000614 ;
skos:inScheme .
+biolink:id a owl:DatatypeProperty ;
+ rdfs:label "id" ;
+ rdfs:domain biolink:Entity ;
+ skos:definition "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ;
+ skos:exactMatch gff3:ID,
+ gpi:DB_Object_ID,
+ AGRKB:primaryId ;
+ skos:inScheme .
+
biolink:predicate_type a rdfs:Datatype ;
owl:equivalentClass xsd:anyURI .
biolink:Gene a owl:Class ;
rdfs:label "gene" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom xsd:anyURI ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:xref ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:symbol ],
[ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:allValuesFrom xsd:anyURI ;
+ owl:onProperty biolink:xref ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:symbol ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:xref ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GeneOrGeneProduct ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:PhysicalEssence ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
owl:someValuesFrom biolink:GenomicEntity ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:symbol ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
biolink:BiologicalEntity ;
skos:broadMatch ;
skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ;
@@ -11397,38 +11523,38 @@ biolink:Gene a owl:Class ;
biolink:SequenceVariant a owl:Class ;
rdfs:label "sequence variant" ;
rdfs:subClassOf [ a owl:Restriction ;
+ owl:allValuesFrom biolink:Gene ;
+ owl:onProperty biolink:has_gene ],
+ [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:GenomicEntity ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:id ],
+ [ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:has_biological_sequence ],
+ owl:onProperty biolink:id ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:has_biological_sequence ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Gene ;
- owl:onProperty biolink:has_gene ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
+ owl:onProperty biolink:has_biological_sequence ],
[ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:id ],
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:has_gene ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:has_biological_sequence ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:OntologyClass ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:OntologyClass ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_gene ],
- [ a owl:Restriction ;
- owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:GenomicEntity ],
biolink:BiologicalEntity ;
skos:altLabel "allele" ;
skos:closeMatch ,
@@ -11473,58 +11599,43 @@ biolink:Publication a owl:Class ;
rdfs:label "publication" ;
rdfs:subClassOf [ a owl:Restriction ;
owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:xref ],
+ owl:onProperty biolink:mesh_terms ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:summary ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:id ],
+ owl:onProperty biolink:pages ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
owl:onProperty biolink:keywords ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:name ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:summary ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:pages ],
+ owl:onProperty biolink:name ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:anyURI ;
- owl:onProperty biolink:mesh_terms ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:Agent ;
- owl:onProperty biolink:authors ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
owl:onProperty biolink:xref ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
- owl:onProperty biolink:name ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:publication_type ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:id ],
- [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:authors ],
+ owl:onProperty biolink:summary ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
owl:onProperty biolink:summary ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:summary ],
+ owl:onProperty biolink:name ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:publication_type ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:name ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:pages ],
+ owl:allValuesFrom biolink:Agent ;
+ owl:onProperty biolink:authors ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:xref ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
owl:onProperty biolink:keywords ],
@@ -11533,7 +11644,22 @@ biolink:Publication a owl:Class ;
owl:onProperty biolink:mesh_terms ],
[ a owl:Restriction ;
owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:pages ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
owl:onProperty biolink:publication_type ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:id ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:authors ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:id ],
+ [ a owl:Restriction ;
+ owl:minCardinality 1 ;
+ owl:onProperty biolink:id ],
biolink:InformationContentEntity ;
skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ;
skos:exactMatch IAO:0000311 ;
@@ -11541,15 +11667,6 @@ biolink:Publication a owl:Class ;
skos:narrowMatch STY:T170,
IAO:0000013 .
-biolink:id a owl:DatatypeProperty ;
- rdfs:label "id" ;
- rdfs:domain biolink:Entity ;
- skos:definition "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ;
- skos:exactMatch gff3:ID,
- gpi:DB_Object_ID,
- AGRKB:primaryId ;
- skos:inScheme .
-
biolink:BiologicalEntity a owl:Class ;
rdfs:label "biological entity" ;
rdfs:subClassOf [ a owl:Restriction ;
@@ -11566,22 +11683,13 @@ biolink:BiologicalEntity a owl:Class ;
biolink:ChemicalEntity a owl:Class ;
rdfs:label "chemical entity" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:is_toxic ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:trade_name ],
- [ a owl:Restriction ;
- owl:allValuesFrom xsd:string ;
- owl:onProperty biolink:max_tolerated_dose ],
- [ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ],
+ owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:DrugAvailabilityEnum ;
- owl:onProperty biolink:available_from ],
+ owl:allValuesFrom biolink:ChemicalRole ;
+ owl:onProperty biolink:has_chemical_role ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:DrugAvailabilityEnum ;
owl:onProperty biolink:available_from ],
[ a owl:Restriction ;
owl:maxCardinality 1 ;
@@ -11591,31 +11699,40 @@ biolink:ChemicalEntity a owl:Class ;
owl:onProperty biolink:trade_name ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:PhysicalEssence ],
+ owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:boolean ;
+ owl:onProperty biolink:is_toxic ],
+ [ a owl:Restriction ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:available_from ],
[ a owl:Restriction ;
owl:minCardinality 0 ;
+ owl:onProperty biolink:has_chemical_role ],
+ [ a owl:Restriction ;
+ owl:allValuesFrom xsd:string ;
owl:onProperty biolink:max_tolerated_dose ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:max_tolerated_dose ],
[ a owl:Restriction ;
- owl:maxCardinality 1 ;
+ owl:minCardinality 0 ;
owl:onProperty biolink:is_toxic ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ],
+ owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ],
[ a owl:Restriction ;
- owl:allValuesFrom xsd:boolean ;
+ owl:maxCardinality 1 ;
owl:onProperty biolink:is_toxic ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ChemicalRole ;
- owl:onProperty biolink:has_chemical_role ],
[ a owl:Restriction ;
owl:onProperty linkml:mixins ;
- owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ],
+ owl:someValuesFrom biolink:PhysicalEssence ],
[ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_chemical_role ],
+ owl:allValuesFrom xsd:string ;
+ owl:onProperty biolink:trade_name ],
+ [ a owl:Restriction ;
+ owl:maxCardinality 1 ;
+ owl:onProperty biolink:max_tolerated_dose ],
biolink:NamedThing ;
skos:broadMatch STY:T167 ;
skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ;
@@ -11678,13 +11795,15 @@ biolink:OntologyClass a owl:Class ;
biolink:GeneOrGeneProductOrChemicalEntityAspectEnum a owl:Class ;
rdfs:subClassOf linkml:EnumDefinition ;
- owl:unionOf ( ) ;
+ owl:unionOf (