provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
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, 'FDA 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.'
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
diff --git a/prevented_by/index.html b/ClinicalApprovalStatusEnum/index.html
similarity index 90%
rename from prevented_by/index.html
rename to ClinicalApprovalStatusEnum/index.html
index 943536f856..e611b5d8a6 100644
--- a/prevented_by/index.html
+++ b/ClinicalApprovalStatusEnum/index.html
@@ -8,7 +8,7 @@
-
+
@@ -18,7 +18,7 @@
- Slot: prevented_by (multivalued) - Biolink Model Documentation
+ Enum: ClinicalApprovalStatusEnum - Biolink Model Documentation
@@ -81,7 +81,7 @@
name: prevented by
-annotations:
- opposite_of:
- tag: opposite_of
- value: enabled by
-description: holds between a potential outcome of which the likelihood was reduced
- by the application or use of an entity.
+
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
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, 'FDA 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.'
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
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, 'FDA 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.'
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
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: FDAApprovalStatusEnum
-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/Food/index.html b/Food/index.html
index 83f2b871d1..c0c9510df2 100644
--- a/Food/index.html
+++ b/Food/index.html
@@ -347,7 +347,7 @@
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, 'FDA 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.'
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -395,7 +395,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
name: The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
Biolink 'pre_clinical_research' is the union of both the FDA discovery and development phase and FDA preclinical research 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. 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.
+
+
+
clinical_trial_phase
+
None
+
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.
+
+
+
clinical_trial_phase_1
+
None
+
In the FDA Clinical Trial Phase, the Clinical Trial 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.
+
+
+
clinical_trial_phase_2
+
None
+
In the FDA Clinical Trial Phase, the Clinical Trial 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.
+
+
+
clinical_trial_phase_3
+
None
+
In the FDA Clinical Trial Phase, the Clinical Trial 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.
+
+
+
clinical_trial_phase_4
+
None
+
In the FDA Clinical Trial Phase, the Clinical Trial 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.
name: MaxResearchPhaseEnum
+from_schema: https://w3id.org/biolink/biolink-model
+permissible_values:
+ pre_clinical_research_phase:
+ text: pre_clinical_research_phase
+ description: 'Biolink ''pre_clinical_research'' is the union of both the `FDA
+ discovery and development phase` and `FDA preclinical research 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. 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.'
+ notes:
+ - DrugBank calls this 'experimental'.
+ clinical_trial_phase:
+ text: clinical_trial_phase
+ description: 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.
+ clinical_trial_phase_1:
+ text: clinical_trial_phase_1
+ description: In the FDA Clinical Trial Phase, the Clinical Trial 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.
+ is_a: clinical_trial_phase
+ clinical_trial_phase_2:
+ text: clinical_trial_phase_2
+ description: In the FDA Clinical Trial Phase, the Clinical Trial 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.
+ is_a: clinical_trial_phase
+ clinical_trial_phase_3:
+ text: clinical_trial_phase_3
+ description: In the FDA Clinical Trial Phase, the Clinical Trial 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.
+ is_a: clinical_trial_phase
+ clinical_trial_phase_4:
+ text: clinical_trial_phase_4
+ description: In the FDA Clinical Trial Phase, the Clinical Trial 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.
+ is_a: clinical_trial_phase
+ not_provided:
+ text: not_provided
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/MicroRNA/index.html b/MicroRNA/index.html
index c113ccafcc..1500a949dc 100644
--- a/MicroRNA/index.html
+++ b/MicroRNA/index.html
@@ -325,12 +325,12 @@
Slots
synonym: Alternate human-readable names for a thing
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -375,7 +375,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
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, 'FDA 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.'
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -381,7 +381,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -372,7 +372,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
@@ -560,6 +560,7 @@
LinkML Source
name: onset
description: The age group in which (disease) symptom manifestations appear
+deprecated: 'True'
from_schema: https://w3id.org/biolink/biolink-model
exact_mappings:
- HP:0003674
diff --git a/OrganismAttribute/index.html b/OrganismAttribute/index.html
index 20f51064aa..a87030369b 100644
--- a/OrganismAttribute/index.html
+++ b/OrganismAttribute/index.html
@@ -350,7 +350,7 @@
Slots
id: A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
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, 'FDA 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.'
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -380,7 +380,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -377,7 +377,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -379,7 +379,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -376,7 +376,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
@@ -554,6 +554,7 @@
LinkML Source
name: severity value
description: describes the severity of a phenotypic feature or disease
+deprecated: 'True'
from_schema: https://w3id.org/biolink/biolink-model
is_a: attribute
diff --git a/SiRNA/index.html b/SiRNA/index.html
index 37b01a65f3..7b158ff23e 100644
--- a/SiRNA/index.html
+++ b/SiRNA/index.html
@@ -329,12 +329,12 @@
Slots
synonym: Alternate human-readable names for a thing
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.
in_taxon: connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'
@@ -379,7 +379,7 @@
Slots
name: genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
describes an entity that has a direct affect on the state or quality of another existing entity. Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.
+
Describes an entity that has an effect on the state or quality of another existing entity.
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.
Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).
holds between a measurable chemical entity and a disease or phenotypic feature, where the entity is used as an indicator of the presence or state of the disease or feature.
@@ -669,6 +673,14 @@
Slots in subset:
holds between a gene and a disease or phenotypic feature that may be influenced, contribute to, or be correlated with the gene or its alleles/products
Restricts the setting/context/location where the core concept (or qualified core concept) resides or occurs.
@@ -833,10 +845,6 @@
Slots in subset:
Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.
Holds between an intervention and a medical condition, and reports that a clinical trial is being or has been performed in human patients to test the potential of the intervention to treat the medical condition (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).
Holds between an substance, procedure, or activity and a medical condition, and reports that a pre-clinical study has been performed specifically to test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).
holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical entity, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.
Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to prevent it manifesting in the first place.
Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place.
holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat
+
Holds between an intervention (substance, procedure, or activity) and a medical condition (disease or phenotypic feature), and states that the intervention is able to ameliorate, stabilize, or cure the condition or delay, prevent, or reduce the risk of it manifesting in the first place. ‘Treats’ edges should be asserted (knowledge_level: assertion) only in cases where there is strong supporting evidence - i.e. the intervention is approved or in phase 4 trials for the condition, or is an otherwise established treatment in the medical community (e.g. a widely-accepted or formally recommended off-label use). In the absence of such evidence, weaker predicates should be used in asserted edges (e.g. ‘in clinical trials for’ or ‘beneficial in models of’). ‘Treats’ edges based on weaker or indirect forms of evidence can however be created as predictions (knowledge_level: prediction) and should point to the more foundational asserted edges that support them.
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).
Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition.
provided_by: The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph.
Description: describes an entity that has a direct affect on the state or quality of another existing entity. Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.
-
+
Description: Describes an entity that has an effect on the state or quality of another existing entity.
+ Notes: Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects likelihood of' and 'prevents' where the effect concerns whether or when something may or may not come into existence.
canonical_predicate:
tag: canonical_predicate
value: true
-description: describes an entity that has a direct affect on the state or quality
- of another existing entity. Use of the 'affects' predicate implies that the affected
- entity already exists, unlike predicates such as 'affects risk for' and 'prevents,
- where the outcome is something that may or may not come to be.
+description: Describes an entity that has an effect on the state or quality of another
+ existing entity.
+notes:
+- Use of the 'affects' predicate implies that the affected entity already exists,
+ unlike predicates such as 'affects likelihood of' and 'prevents' where the effect
+ concerns whether or when something may or may not come into existence.
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
diff --git a/affects_risk_for/index.html b/affects_likelihood_of/index.html
similarity index 89%
rename from affects_risk_for/index.html
rename to affects_likelihood_of/index.html
index fb3b621f5e..c357161a02 100644
--- a/affects_risk_for/index.html
+++ b/affects_likelihood_of/index.html
@@ -8,7 +8,7 @@
-
+
@@ -18,7 +18,7 @@
- Slot: affects_risk_for (multivalued) - Biolink Model Documentation
+ Slot: affects_likelihood_of (multivalued) - Biolink Model Documentation
@@ -81,7 +81,7 @@
Description: holds between two entities where exposure to one entity alters the chance of developing the other
-
+
Slot: affects_likelihood_of (multivalued)
+
Description: Holds between two entities where the presence or application of one alters the chance that the other will come to be.
+ Notes: This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.)
name: affects likelihood of
annotations:
canonical_predicate:
tag: canonical_predicate
value: true
-description: holds between two entities where exposure to one entity alters the chance
- of developing the other
+description: Holds between two entities where the presence or application of one alters
+ the chance that the other will come to be.
+notes:
+- This predicate implies causation, where the 'affected' entity is something that
+ does not yet exist, and the actions/execution of effector impact the likelihood
+ that this entity may come to be. It is NOT to be used for a statistical associations
+ that describe correlations between two feature variables (use predicates in the
+ 'associated with likelihood of' hierarchy here.)
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
@@ -590,7 +596,7 @@
LinkML Source
domain: named thing
multivalued: true
inherited: true
-alias: affects_risk_for
+alias: affects_likelihood_of
range: named thing
diff --git a/predisposes/index.html b/ameliorates_condition/index.html
similarity index 88%
rename from predisposes/index.html
rename to ameliorates_condition/index.html
index 090743786c..59292381b9 100644
--- a/predisposes/index.html
+++ b/ameliorates_condition/index.html
@@ -8,7 +8,7 @@
-
+
@@ -18,7 +18,7 @@
- Slot: predisposes (multivalued) - Biolink Model Documentation
+ Slot: ameliorates_condition (multivalued) - Biolink Model Documentation
@@ -81,7 +81,7 @@
Description: holds between two entities where exposure to one entity increases the chance of developing the other
-
-
+
Slot: ameliorates_condition (multivalued)
+
Description: Holds between an entity and an existing medical condition (disease or phenotypic feature) where the entity is able to ameliorate symptoms, stabilize progression, or cure the condition.
+ Aliases: ameliorates, beneficial for condition, therapeutic for condition
+ Notes: This predicate describes a narrower view of 'treats' - that covers interventions that are beneficial for existing disease, and excludes interventions that prevent/reduce risk of developing a condition in the future.
name: ameliorates condition
annotations:
canonical_predicate:
tag: canonical_predicate
value: true
opposite_of:
tag: opposite_of
- value: prevents
-description: holds between two entities where exposure to one entity increases the
- chance of developing the other
-in_subset:
-- translator_minimal
+ value: exacerbates condition
+description: Holds between an entity and an existing medical condition (disease or
+ phenotypic feature) where the entity is able to ameliorate symptoms, stabilize
+ progression, or cure the condition.
+notes:
+- This predicate describes a narrower view of 'treats' - that covers interventions
+ that are beneficial for existing disease, and excludes interventions that prevent/reduce
+ risk of developing a condition in the future.
from_schema: https://w3id.org/biolink/biolink-model
+aliases:
+- ameliorates
+- beneficial for condition
+- therapeutic for condition
exact_mappings:
-- SEMMEDDB:PREDISPOSES
-is_a: affects risk for
-domain: named thing
+- RO:0003307
+is_a: affects
+mixins:
+- treats
+domain: chemical or drug or treatment
multivalued: true
inherited: true
-alias: predisposes
-range: named thing
+alias: ameliorates_condition
+range: disease or phenotypic feature
Description: Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).
+
+
+ Notes: This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) . A knowledge level of Assertion should be used with this predicate, because it requires interpretation of results to conclude an intervention to be 'beneficial', and thus goes beyond merely reporting the occurrence of a study).
+
name: beneficial in models for
+annotations:
+ canonical_predicate:
+ tag: canonical_predicate
+ value: true
+description: Holds between an substance, procedure, or activity and a medical condition,
+ and reports that the substance, procedure, or activity has been shown to be effective
+ in alleviating, preventing, or delaying symptoms/ phenotypes associated with a
+ disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).
+notes:
+- This predicate would be used to represent Model Organism Database (MOD) records
+ reporting that an intervention alleviated phenotypes associated with a human disease
+ in a model organism designated as a model of that disease. (e.g. a ZFIN record
+ reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype
+ of zebrafish used to model the human disease Kabuki Syndrome) . A knowledge level
+ of Assertion should be used with this predicate, because it requires interpretation
+ of results to conclude an intervention to be 'beneficial', and thus goes beyond
+ merely reporting the occurrence of a study).
+in_subset:
+- translator_minimal
+from_schema: https://w3id.org/biolink/biolink-model
+is_a: in preclinical trials for
+mixins:
+- treats or taken to treat or studied to treat
+domain: chemical or drug or treatment
+multivalued: true
+inherited: true
+alias: beneficial_in_models_for
+range: disease or phenotypic feature
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/biolink-model.context.jsonld b/biolink-model.context.jsonld
index 5f01115d93..1bf7ee1bec 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": "2023-12-04T21:37:38",
+ "generation_date": "2023-12-14T13:52:16",
"source": "biolink_model.yaml"
},
"@context": {
@@ -619,17 +619,17 @@
"affects": {
"@type": "@id"
},
- "affects_response_to": {
+ "affects_likelihood_of": {
"@type": "@id"
},
- "affects_risk_for": {
+ "affects_response_to": {
"@type": "@id"
},
"affiliation": {
"@type": "@id"
},
"id": "@id",
- "ameliorates": {
+ "ameliorates_condition": {
"@type": "@id"
},
"amount_or_activity_decreased_by": {
@@ -679,6 +679,9 @@
"base_coordinate": {
"@type": "xsd:integer"
},
+ "beneficial_in_models_for": {
+ "@type": "@id"
+ },
"binds": {
"@type": "@id"
},
@@ -726,6 +729,14 @@
"chi_squared_statistic": {
"@type": "xsd:float"
},
+ "clinical_approval_status": {
+ "@context": {
+ "@vocab": "@null",
+ "text": "skos:notation",
+ "description": "skos:prefLabel",
+ "meaning": "@id"
+ }
+ },
"clinical_modifier_qualifier": {
"@type": "@id"
},
@@ -756,9 +767,21 @@
"concept_pair_count": {
"@type": "xsd:integer"
},
+ "condition_ameliorated_by": {
+ "@type": "@id"
+ },
"condition_associated_with_gene": {
"@type": "@id"
},
+ "condition_exacerbated_by": {
+ "@type": "@id"
+ },
+ "condition_predisposed_by": {
+ "@type": "@id"
+ },
+ "condition_prevented_by": {
+ "@type": "@id"
+ },
"consumed_by": {
"@type": "@id"
},
@@ -768,7 +791,7 @@
"contains_process": {
"@type": "@id"
},
- "contraindicated_for": {
+ "contraindicated_in": {
"@type": "@id"
},
"contributes_to": {
@@ -861,7 +884,7 @@
"evidence_count": {
"@type": "xsd:integer"
},
- "exacerbates": {
+ "exacerbates_condition": {
"@type": "@id"
},
"exact_match": {
@@ -887,14 +910,6 @@
"meaning": "@id"
}
},
- "FDA_approval_status": {
- "@context": {
- "@vocab": "@null",
- "text": "skos:notation",
- "description": "skos:prefLabel",
- "meaning": "@id"
- }
- },
"food_component_of": {
"@type": "@id"
},
@@ -1087,9 +1102,6 @@
"has_positive_upstream_or_within_actor": {
"@type": "@id"
},
- "has_predisposing_factor": {
- "@type": "@id"
- },
"has_procedure": {
"@type": "@id"
},
@@ -1162,6 +1174,9 @@
"in_cell_population_with": {
"@type": "@id"
},
+ "in_clinical_trials_for": {
+ "@type": "@id"
+ },
"in_complex_with": {
"@type": "@id"
},
@@ -1171,6 +1186,9 @@
"in_pathway_with": {
"@type": "@id"
},
+ "in_preclinical_trials_for": {
+ "@type": "@id"
+ },
"in_taxon": {
"@type": "@id"
},
@@ -1207,18 +1225,12 @@
"is_active_ingredient_of": {
"@type": "@id"
},
- "is_ameliorated_by": {
- "@type": "@id"
- },
"is_assessed_by": {
"@type": "@id"
},
"is_diagnosed_by": {
"@type": "@id"
},
- "is_exacerbated_by": {
- "@type": "@id"
- },
"is_excipient_of": {
"@type": "@id"
},
@@ -1279,6 +1291,9 @@
"latitude": {
"@type": "xsd:float"
},
+ "likelihood_affected_by": {
+ "@type": "@id"
+ },
"likelihood_associated_with": {
"@type": "@id"
},
@@ -1317,6 +1332,14 @@
"manifestation_of": {
"@type": "@id"
},
+ "max_research_phase": {
+ "@context": {
+ "@vocab": "@null",
+ "text": "skos:notation",
+ "description": "skos:prefLabel",
+ "meaning": "@id"
+ }
+ },
"mechanism_of_action": {
"@type": "xsd:boolean"
},
@@ -1458,13 +1481,10 @@
"predicate_mappings": {
"@type": "@id"
},
- "predisposes": {
- "@type": "@id"
- },
- "prevented_by": {
+ "predisposes_to_condition": {
"@type": "@id"
},
- "prevents": {
+ "preventative_for_condition": {
"@type": "@id"
},
"primarily_composed_of": {
@@ -1476,6 +1496,9 @@
"produces": {
"@type": "@id"
},
+ "promotes_condition": {
+ "@type": "@id"
+ },
"provider": {
"@type": "@id"
},
@@ -1566,9 +1589,6 @@
"retrieved_on": {
"@type": "xsd:date"
},
- "risk_affected_by": {
- "@type": "@id"
- },
"routes_of_delivery": {
"@context": {
"@vocab": "@null",
@@ -1627,6 +1647,12 @@
"meaning": "@id"
}
},
+ "studied_for_treatment_with": {
+ "@type": "@id"
+ },
+ "studied_to_treat": {
+ "@type": "@id"
+ },
"subclass_of": {
"@type": "@id"
},
@@ -1729,6 +1755,9 @@
"version_of": {
"@type": "@id"
},
+ "was_applied_to_treat": {
+ "@type": "@id"
+ },
"xenologous_to": {
"@type": "@id"
},
diff --git a/biolink-model.graphql b/biolink-model.graphql
index 7787c36624..b67b2293f6 100644
--- a/biolink-model.graphql
+++ b/biolink-model.graphql
@@ -2330,7 +2330,8 @@ type EntityToDiseaseAssociation
retrievalSourceIds: [RetrievalSource]
type: [String]
category: [CategoryType]
- fDAApprovalStatus: FDAApprovalStatusEnum
+ clinicalApprovalStatus: ClinicalApprovalStatusEnum
+ maxResearchPhase: MaxResearchPhaseEnum
}
interface EntityToDiseaseAssociationMixin
@@ -2399,7 +2400,8 @@ type EntityToPhenotypicFeatureAssociation
retrievalSourceIds: [RetrievalSource]
type: [String]
category: [CategoryType]
- fDAApprovalStatus: FDAApprovalStatusEnum
+ clinicalApprovalStatus: ClinicalApprovalStatusEnum
+ maxResearchPhase: MaxResearchPhaseEnum
}
type EntityToPhenotypicFeatureAssociationMixin implements FrequencyQuantifier
diff --git a/biolink-model.json b/biolink-model.json
index cbad81542a..0956e92743 100644
--- a/biolink-model.json
+++ b/biolink-model.json
@@ -4988,7 +4988,7 @@
"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, '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"
},
"id": {
@@ -6458,6 +6458,19 @@
"title": "ChiSquaredAnalysisResult",
"type": "object"
},
+ "ClinicalApprovalStatusEnum": {
+ "description": "",
+ "enum": [
+ "approved_for_condition",
+ "fda_approved_for_condition",
+ "not_approved_for_condition",
+ "post_approval_withdrawal",
+ "off_label_use",
+ "not_provided"
+ ],
+ "title": "ClinicalApprovalStatusEnum",
+ "type": "string"
+ },
"ClinicalAttribute": {
"additionalProperties": false,
"description": "Attributes relating to a clinical manifestation",
@@ -7614,7 +7627,7 @@
"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, '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"
},
"id": {
@@ -10037,7 +10050,7 @@
"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, '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"
},
"id": {
@@ -10912,10 +10925,6 @@
"additionalProperties": false,
"description": "",
"properties": {
- "FDA_approval_status": {
- "$ref": "#/$defs/FDAApprovalStatusEnum",
- "description": ""
- },
"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": {
@@ -10933,6 +10942,10 @@
},
"type": "array"
},
+ "clinical_approval_status": {
+ "$ref": "#/$defs/ClinicalApprovalStatusEnum",
+ "description": ""
+ },
"deprecated": {
"description": "A boolean flag indicating that an entity is no longer considered current or valid.",
"type": "boolean"
@@ -10967,6 +10980,9 @@
"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"
},
+ "max_research_phase": {
+ "$ref": "#/$defs/MaxResearchPhaseEnum"
+ },
"name": {
"description": "A human-readable name for an attribute or entity.",
"type": "string"
@@ -11112,10 +11128,6 @@
"additionalProperties": false,
"description": "",
"properties": {
- "FDA_approval_status": {
- "$ref": "#/$defs/FDAApprovalStatusEnum",
- "description": ""
- },
"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": {
@@ -11133,6 +11145,10 @@
},
"type": "array"
},
+ "clinical_approval_status": {
+ "$ref": "#/$defs/ClinicalApprovalStatusEnum",
+ "description": ""
+ },
"deprecated": {
"description": "A boolean flag indicating that an entity is no longer considered current or valid.",
"type": "boolean"
@@ -11167,6 +11183,9 @@
"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"
},
+ "max_research_phase": {
+ "$ref": "#/$defs/MaxResearchPhaseEnum"
+ },
"name": {
"description": "A human-readable name for an attribute or entity.",
"type": "string"
@@ -12581,28 +12600,6 @@
"title": "ExposureEventToPhenotypicFeatureAssociation",
"type": "object"
},
- "FDAApprovalStatusEnum": {
- "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": "FDAApprovalStatusEnum",
- "type": "string"
- },
"FDAIDAAdverseEventEnum": {
"description": "please consult with the FDA guidelines as proposed in this document: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/cfrsearch.cfm?fr=312.32",
"enum": [
@@ -12667,7 +12664,7 @@
"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, '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"
},
"id": {
@@ -20780,6 +20777,20 @@
"title": "MaterialSampleToDiseaseOrPhenotypicFeatureAssociation",
"type": "object"
},
+ "MaxResearchPhaseEnum": {
+ "description": "",
+ "enum": [
+ "pre_clinical_research_phase",
+ "clinical_trial_phase",
+ "clinical_trial_phase_1",
+ "clinical_trial_phase_2",
+ "clinical_trial_phase_3",
+ "clinical_trial_phase_4",
+ "not_provided"
+ ],
+ "title": "MaxResearchPhaseEnum",
+ "type": "string"
+ },
"MicroRNA": {
"additionalProperties": false,
"description": "",
@@ -21737,7 +21748,7 @@
"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, '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"
},
"id": {
@@ -26294,7 +26305,7 @@
"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, '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"
},
"id": {
diff --git a/biolink-model.jsonld b/biolink-model.jsonld
index 2525f3924a..d209f16b8a 100644
--- a/biolink-model.jsonld
+++ b/biolink-model.jsonld
@@ -1021,6 +1021,75 @@
}
],
"enums": [
+ {
+ "name": "ClinicalApprovalStatusEnum",
+ "definition_uri": "https://w3id.org/biolink/vocab/ClinicalApprovalStatusEnum",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "permissible_values": [
+ {
+ "text": "approved_for_condition"
+ },
+ {
+ "text": "fda_approved_for_condition",
+ "is_a": "approved_for_condition"
+ },
+ {
+ "text": "not_approved_for_condition"
+ },
+ {
+ "text": "post_approval_withdrawal",
+ "is_a": "not_approved_for_condition"
+ },
+ {
+ "text": "off_label_use",
+ "is_a": "not_approved_for_condition"
+ },
+ {
+ "text": "not_provided"
+ }
+ ]
+ },
+ {
+ "name": "MaxResearchPhaseEnum",
+ "definition_uri": "https://w3id.org/biolink/vocab/MaxResearchPhaseEnum",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "permissible_values": [
+ {
+ "text": "pre_clinical_research_phase",
+ "description": "Biolink 'pre_clinical_research' is the union of both the `FDA discovery and development phase` and `FDA preclinical research 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. 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.",
+ "notes": [
+ "DrugBank calls this 'experimental'."
+ ]
+ },
+ {
+ "text": "clinical_trial_phase",
+ "description": "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": "clinical_trial_phase_1",
+ "description": "In the FDA Clinical Trial Phase, the Clinical Trial 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.",
+ "is_a": "clinical_trial_phase"
+ },
+ {
+ "text": "clinical_trial_phase_2",
+ "description": "In the FDA Clinical Trial Phase, the Clinical Trial 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.",
+ "is_a": "clinical_trial_phase"
+ },
+ {
+ "text": "clinical_trial_phase_3",
+ "description": "In the FDA Clinical Trial Phase, the Clinical Trial 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.",
+ "is_a": "clinical_trial_phase"
+ },
+ {
+ "text": "clinical_trial_phase_4",
+ "description": "In the FDA Clinical Trial Phase, the Clinical Trial 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.",
+ "is_a": "clinical_trial_phase"
+ },
+ {
+ "text": "not_provided"
+ }
+ ]
+ },
{
"name": "DirectionQualifierEnum",
"definition_uri": "https://w3id.org/biolink/vocab/DirectionQualifierEnum",
@@ -1681,73 +1750,6 @@
}
]
},
- {
- "name": "FDAApprovalStatusEnum",
- "definition_uri": "https://w3id.org/biolink/vocab/FDAApprovalStatusEnum",
- "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": "FDAIDAAdverseEventEnum",
"definition_uri": "https://w3id.org/biolink/vocab/FDAIDAAdverseEventEnum",
@@ -3586,7 +3588,7 @@
{
"name": "highest_FDA_approval_status",
"definition_uri": "https://w3id.org/biolink/vocab/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, '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.'",
"from_schema": "https://w3id.org/biolink/biolink-model",
"slot_uri": "https://w3id.org/biolink/vocab/highest_FDA_approval_status",
"owner": "ChemicalMixture",
@@ -4283,6 +4285,7 @@
"name": "severity_qualifier",
"definition_uri": "https://w3id.org/biolink/vocab/severity_qualifier",
"description": "a qualifier used in a phenotypic association to state how severe the phenotype is in the subject",
+ "deprecated": "True",
"in_subset": [
"translator_minimal"
],
@@ -4319,6 +4322,7 @@
"name": "onset_qualifier",
"definition_uri": "https://w3id.org/biolink/vocab/onset_qualifier",
"description": "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject",
+ "deprecated": "True",
"in_subset": [
"translator_minimal"
],
@@ -4660,6 +4664,7 @@
"multivalued": true,
"inherited": true,
"owner": "superclass_of",
+ "inverse": "subclass_of",
"range": "OntologyClass",
"@type": "SlotDefinition"
},
@@ -4717,6 +4722,7 @@
"multivalued": true,
"inherited": true,
"owner": "subclass_of",
+ "inverse": "superclass_of",
"range": "OntologyClass",
"@type": "SlotDefinition"
},
@@ -4972,6 +4978,48 @@
"range": "NamedThing",
"@type": "SlotDefinition"
},
+ {
+ "name": "affects_likelihood_of",
+ "definition_uri": "https://w3id.org/biolink/vocab/affects_likelihood_of",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ }
+ ],
+ "description": "Holds between two entities where the presence or application of one alters the chance that the other will come to be.",
+ "notes": [
+ "This predicate implies causation, where the 'affected' entity is something that does not yet exist, and the actions/execution of effector impact the likelihood that this entity may come to be. It is NOT to be used for a statistical associations that describe correlations between two feature variables (use predicates in the 'associated with likelihood of' hierarchy here.)"
+ ],
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "related_to_at_instance_level",
+ "domain": "NamedThing",
+ "slot_uri": "https://w3id.org/biolink/vocab/affects_likelihood_of",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "affects_likelihood_of",
+ "inverse": "likelihood_affected_by",
+ "range": "NamedThing",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "likelihood_affected_by",
+ "definition_uri": "https://w3id.org/biolink/vocab/likelihood_affected_by",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "related_to_at_instance_level",
+ "domain": "NamedThing",
+ "slot_uri": "https://w3id.org/biolink/vocab/likelihood_affected_by",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "likelihood_affected_by",
+ "inverse": "affects_likelihood_of",
+ "range": "NamedThing",
+ "@type": "SlotDefinition"
+ },
{
"name": "associated_with_likelihood_of",
"definition_uri": "https://w3id.org/biolink/vocab/associated_with_likelihood_of",
@@ -5870,7 +5918,10 @@
"@type": "Annotation"
}
],
- "description": "describes an entity that has a direct affect on the state or quality of another existing entity. Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects risk for' and 'prevents, where the outcome is something that may or may not come to be.",
+ "description": "Describes an entity that has an effect on the state or quality of another existing entity.",
+ "notes": [
+ "Use of the 'affects' predicate implies that the affected entity already exists, unlike predicates such as 'affects likelihood of' and 'prevents' where the effect concerns whether or when something may or may not come into existence."
+ ],
"in_subset": [
"translator_minimal"
],
@@ -7104,95 +7155,6 @@
"range": "Gene",
"@type": "SlotDefinition"
},
- {
- "name": "affects_risk_for",
- "definition_uri": "https://w3id.org/biolink/vocab/affects_risk_for",
- "annotations": [
- {
- "tag": "canonical_predicate",
- "value": true,
- "@type": "Annotation"
- }
- ],
- "description": "holds between two entities where exposure to one entity alters the chance of developing the other",
- "in_subset": [
- "translator_minimal"
- ],
- "from_schema": "https://w3id.org/biolink/biolink-model",
- "is_a": "related_to_at_instance_level",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/affects_risk_for",
- "multivalued": true,
- "inherited": true,
- "owner": "affects_risk_for",
- "inverse": "risk_affected_by",
- "range": "NamedThing",
- "@type": "SlotDefinition"
- },
- {
- "name": "risk_affected_by",
- "definition_uri": "https://w3id.org/biolink/vocab/risk_affected_by",
- "from_schema": "https://w3id.org/biolink/biolink-model",
- "is_a": "related_to_at_instance_level",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/risk_affected_by",
- "multivalued": true,
- "inherited": true,
- "owner": "risk_affected_by",
- "inverse": "affects_risk_for",
- "range": "NamedThing",
- "@type": "SlotDefinition"
- },
- {
- "name": "predisposes",
- "definition_uri": "https://w3id.org/biolink/vocab/predisposes",
- "annotations": [
- {
- "tag": "canonical_predicate",
- "value": true,
- "@type": "Annotation"
- },
- {
- "tag": "opposite_of",
- "value": "prevents",
- "@type": "Annotation"
- }
- ],
- "description": "holds between two entities where exposure to one entity increases the chance of developing the other",
- "in_subset": [
- "translator_minimal"
- ],
- "from_schema": "https://w3id.org/biolink/biolink-model",
- "exact_mappings": [
- "https://skr3.nlm.nih.gov/SemMedDBPREDISPOSES"
- ],
- "is_a": "affects_risk_for",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/predisposes",
- "multivalued": true,
- "inherited": true,
- "owner": "predisposes",
- "inverse": "has_predisposing_factor",
- "range": "NamedThing",
- "@type": "SlotDefinition"
- },
- {
- "name": "has_predisposing_factor",
- "definition_uri": "https://w3id.org/biolink/vocab/has_predisposing_factor",
- "in_subset": [
- "translator_minimal"
- ],
- "from_schema": "https://w3id.org/biolink/biolink-model",
- "is_a": "risk_affected_by",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/has_predisposing_factor",
- "multivalued": true,
- "inherited": true,
- "owner": "has_predisposing_factor",
- "inverse": "predisposes",
- "range": "NamedThing",
- "@type": "SlotDefinition"
- },
{
"name": "contributes_to",
"definition_uri": "https://w3id.org/biolink/vocab/contributes_to",
@@ -7350,8 +7312,8 @@
"@type": "SlotDefinition"
},
{
- "name": "ameliorates",
- "definition_uri": "https://w3id.org/biolink/vocab/ameliorates",
+ "name": "ameliorates_condition",
+ "definition_uri": "https://w3id.org/biolink/vocab/ameliorates_condition",
"annotations": [
{
"tag": "canonical_predicate",
@@ -7360,51 +7322,203 @@
},
{
"tag": "opposite_of",
- "value": "exacerbates",
+ "value": "exacerbates condition",
"@type": "Annotation"
}
],
- "description": "A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure, clinical intervention) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.",
+ "description": "Holds between an entity and an existing medical condition (disease or phenotypic feature) where the entity is able to ameliorate symptoms, stabilize progression, or cure the condition.",
+ "notes": [
+ "This predicate describes a narrower view of 'treats' - that covers interventions that are beneficial for existing disease, and excludes interventions that prevent/reduce risk of developing a condition in the future."
+ ],
"from_schema": "https://w3id.org/biolink/biolink-model",
+ "aliases": [
+ "ameliorates",
+ "beneficial for condition",
+ "therapeutic for condition"
+ ],
"exact_mappings": [
"http://purl.obolibrary.org/obo/RO_0003307"
],
"is_a": "affects",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/ameliorates",
+ "mixins": [
+ "treats"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/ameliorates_condition",
"multivalued": true,
"inherited": true,
- "owner": "ameliorates",
- "inverse": "is_ameliorated_by",
+ "owner": "ameliorates_condition",
+ "inverse": "condition_ameliorated_by",
"range": "DiseaseOrPhenotypicFeature",
"@type": "SlotDefinition"
},
{
- "name": "is_ameliorated_by",
- "definition_uri": "https://w3id.org/biolink/vocab/is_ameliorated_by",
+ "name": "condition_ameliorated_by",
+ "definition_uri": "https://w3id.org/biolink/vocab/condition_ameliorated_by",
"from_schema": "https://w3id.org/biolink/biolink-model",
"is_a": "affected_by",
"domain": "DiseaseOrPhenotypicFeature",
- "slot_uri": "https://w3id.org/biolink/vocab/is_ameliorated_by",
+ "slot_uri": "https://w3id.org/biolink/vocab/condition_ameliorated_by",
"multivalued": true,
"inherited": true,
- "owner": "is_ameliorated_by",
- "inverse": "ameliorates",
- "range": "NamedThing",
+ "owner": "condition_ameliorated_by",
+ "inverse": "ameliorates_condition",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
"@type": "SlotDefinition"
},
{
- "name": "exacerbates",
- "definition_uri": "https://w3id.org/biolink/vocab/exacerbates",
+ "name": "preventative_for_condition",
+ "definition_uri": "https://w3id.org/biolink/vocab/preventative_for_condition",
"annotations": [
{
"tag": "canonical_predicate",
"value": true,
"@type": "Annotation"
+ },
+ {
+ "tag": "opposite_of",
+ "value": "promotes condition",
+ "@type": "Annotation"
}
],
- "description": "A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.",
+ "description": "Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to prevent it manifesting in the first place.",
+ "in_subset": [
+ "translator_minimal"
+ ],
"from_schema": "https://w3id.org/biolink/biolink-model",
+ "aliases": [
+ "prophylactic for",
+ "prevents"
+ ],
+ "is_a": "affects_likelihood_of",
+ "mixins": [
+ "treats"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/preventative_for_condition",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "preventative_for_condition",
+ "inverse": "condition_prevented_by",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "condition_prevented_by",
+ "definition_uri": "https://w3id.org/biolink/vocab/condition_prevented_by",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "affected_by",
+ "domain": "DiseaseOrPhenotypicFeature",
+ "slot_uri": "https://w3id.org/biolink/vocab/condition_prevented_by",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "condition_prevented_by",
+ "inverse": "preventative_for_condition",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "promotes_condition",
+ "definition_uri": "https://w3id.org/biolink/vocab/promotes_condition",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ },
+ {
+ "tag": "opposite_of",
+ "value": "preventative for condition",
+ "@type": "Annotation"
+ }
+ ],
+ "description": "Holds between a substance, procedure, or activity and a medical condition (disease or phenotypic feature), and states that the substance, procedure, or activity is able to promote it manifesting in the first place.",
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "related_to_at_instance_level",
+ "mixin": true,
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/promotes_condition",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "promotes_condition",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "predisposes_to_condition",
+ "definition_uri": "https://w3id.org/biolink/vocab/predisposes_to_condition",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ }
+ ],
+ "description": "Holds between two entities where the presence or application of one increases the chance that the other will come to be.",
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "aliases": [
+ "risk factor for"
+ ],
+ "is_a": "affects_likelihood_of",
+ "mixins": [
+ "promotes_condition"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/predisposes_to_condition",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "predisposes_to_condition",
+ "inverse": "condition_predisposed_by",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "condition_predisposed_by",
+ "definition_uri": "https://w3id.org/biolink/vocab/condition_predisposed_by",
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "related_to_at_instance_level",
+ "domain": "DiseaseOrPhenotypicFeature",
+ "slot_uri": "https://w3id.org/biolink/vocab/condition_predisposed_by",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "condition_predisposed_by",
+ "inverse": "predisposes_to_condition",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "exacerbates_condition",
+ "definition_uri": "https://w3id.org/biolink/vocab/exacerbates_condition",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ },
+ {
+ "tag": "opposite_of",
+ "value": "ameliorates condition",
+ "@type": "Annotation"
+ }
+ ],
+ "description": "Holds between a substance, procedure, or activity and an existing medical condition (disease or phenotypic \n feature) where the substance, procedure, or activity worsens some or all aspects of the condition.",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "aliases": [
+ "exacerbates",
+ "detrimental for condition"
+ ],
"exact_mappings": [
"http://purl.obolibrary.org/obo/RO_0003309"
],
@@ -7412,30 +7526,34 @@
"https://skr3.nlm.nih.gov/SemMedDBCOMPLICATES"
],
"is_a": "affects",
- "domain": "BiologicalEntity",
- "slot_uri": "https://w3id.org/biolink/vocab/exacerbates",
+ "mixins": [
+ "promotes_condition"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/exacerbates_condition",
"multivalued": true,
"inherited": true,
- "owner": "exacerbates",
- "inverse": "is_exacerbated_by",
+ "owner": "exacerbates_condition",
+ "inverse": "condition_exacerbated_by",
"range": "DiseaseOrPhenotypicFeature",
"@type": "SlotDefinition"
},
{
- "name": "is_exacerbated_by",
- "definition_uri": "https://w3id.org/biolink/vocab/is_exacerbated_by",
+ "name": "condition_exacerbated_by",
+ "definition_uri": "https://w3id.org/biolink/vocab/condition_exacerbated_by",
"in_subset": [
"translator_minimal"
],
"from_schema": "https://w3id.org/biolink/biolink-model",
"is_a": "affected_by",
"domain": "DiseaseOrPhenotypicFeature",
- "slot_uri": "https://w3id.org/biolink/vocab/is_exacerbated_by",
+ "slot_uri": "https://w3id.org/biolink/vocab/condition_exacerbated_by",
"multivalued": true,
"inherited": true,
- "owner": "is_exacerbated_by",
- "inverse": "exacerbates",
- "range": "BiologicalEntity",
+ "owner": "condition_exacerbated_by",
+ "inverse": "exacerbates_condition",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
"@type": "SlotDefinition"
},
{
@@ -7446,21 +7564,17 @@
"tag": "canonical_predicate",
"value": true,
"@type": "Annotation"
- },
- {
- "tag": "opposite_of",
- "value": "contraindicated for",
- "@type": "Annotation"
}
],
- "description": "holds between a therapeutic procedure or chemical entity and a disease or phenotypic feature that it is used to treat",
+ "description": "Holds between an intervention (substance, procedure, or activity) and a medical condition (disease or phenotypic feature), and states that the intervention is able to ameliorate, stabilize, or cure the condition or delay, prevent, or reduce the risk of it manifesting in the first place. \u2018Treats\u2019 edges should be asserted (knowledge_level: assertion) only in cases where there is strong supporting evidence - i.e. the intervention is approved or in phase 4 trials for the condition, or is an otherwise established treatment in the medical community (e.g. a widely-accepted or formally recommended off-label use). In the absence of such evidence, weaker predicates should be used in asserted edges (e.g. \u2018in clinical trials for\u2019 or \u2018beneficial in models of\u2019). \u2018Treats\u2019 edges based on weaker or indirect forms of evidence can however be created as predictions (knowledge_level: prediction) and should point to the more foundational asserted edges that support them.",
"in_subset": [
"translator_minimal"
],
"from_schema": "https://w3id.org/biolink/biolink-model",
"aliases": [
"is substance that treats",
- "indicated for"
+ "indicated for",
+ "ameliorates or prevents condition"
],
"exact_mappings": [
"http://identifiers.org/drugbank/treats",
@@ -7494,11 +7608,16 @@
"http://apps.chiragjpgroup.org/repoDB/clinically_tested_withdrawn_phase_3",
"http://purl.obolibrary.org/obo/SNOMED_plays_role"
],
- "is_a": "ameliorates",
+ "broad_mappings": [
+ "http://identifiers.org/drugbank/treats",
+ "https://skr3.nlm.nih.gov/SemMedDBTREATS",
+ "https://www.wikidata.org/prop/P2175",
+ "http://purl.obolibrary.org/obo/MONDO_disease_responds_to"
+ ],
+ "is_a": "treats_or_taken_to_treat_or_studied_to_treat",
+ "mixin": true,
"domain": "ChemicalOrDrugOrTreatment",
"slot_uri": "https://w3id.org/biolink/vocab/treats",
- "multivalued": true,
- "inherited": true,
"owner": "treats",
"inverse": "treated_by",
"range": "DiseaseOrPhenotypicFeature",
@@ -7507,7 +7626,6 @@
{
"name": "treated_by",
"definition_uri": "https://w3id.org/biolink/vocab/treated_by",
- "description": "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition",
"in_subset": [
"translator_minimal"
],
@@ -7519,11 +7637,9 @@
"narrow_mappings": [
"http://purl.obolibrary.org/obo/RO_0002302"
],
- "is_a": "is_ameliorated_by",
+ "mixin": true,
"domain": "DiseaseOrPhenotypicFeature",
"slot_uri": "https://w3id.org/biolink/vocab/treated_by",
- "multivalued": true,
- "inherited": true,
"owner": "treated_by",
"inverse": "treats",
"range": "ChemicalOrDrugOrTreatment",
@@ -7531,61 +7647,191 @@
"@type": "SlotDefinition"
},
{
- "name": "prevents",
- "definition_uri": "https://w3id.org/biolink/vocab/prevents",
+ "name": "studied_to_treat",
+ "definition_uri": "https://w3id.org/biolink/vocab/studied_to_treat",
"annotations": [
{
"tag": "canonical_predicate",
"value": true,
"@type": "Annotation"
- },
+ }
+ ],
+ "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that one or more scientific study has been performed to specifically test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).",
+ "notes": [
+ "Predicates in this hierarchy are used in practice when a source reports performance of a study, but there is not sufficient evidence or demonstrated efficacy against the condition to warrant creating a \u2018treats\u2019 assertion edge. Note however that a 'studied to treat' edge may be used as evidence to support creation of a separate 'treats' prediction edge. A knowledge level of Observation MUST be used with this predicate (because it is merely reporting that a study was observed to have been performed)."
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "related_to_at_instance_level",
+ "mixins": [
+ "treats_or_taken_to_treat_or_studied_to_treat"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/studied_to_treat",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "studied_to_treat",
+ "inverse": "studied_for_treatment_with",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "studied_for_treatment_with",
+ "definition_uri": "https://w3id.org/biolink/vocab/studied_for_treatment_with",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "domain": "DiseaseOrPhenotypicFeature",
+ "slot_uri": "https://w3id.org/biolink/vocab/studied_for_treatment_with",
+ "owner": "studied_for_treatment_with",
+ "inverse": "studied_to_treat",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "in_clinical_trials_for",
+ "definition_uri": "https://w3id.org/biolink/vocab/in_clinical_trials_for",
+ "annotations": [
{
- "tag": "opposite_of",
- "value": "predisposes",
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ }
+ ],
+ "description": "Holds between an intervention and a medical condition, and reports that a clinical trial is being or has been performed in human patients to test the potential of the intervention to treat the medical condition (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).",
+ "notes": [
+ "This predicate should be used when a source reports a clinical trial where the intervention is being or was interrogated, regardless of the phase of the trial, or its ultimate outcome. Information about phase and outcome can be capture using other modeling elements. A knowledge level of \"\"Observation\"\" MUST be used with this predicate (because it is merely reporting that a study was observed to have been performed). Note that if the source reports an intervention to be in a phase 4 trial, or a completed phase 3 trial where clinical benefit was demonstrated, a separate 'treats' edge SHOULD also be created (with knowledge_level = Assertion)."
+ ],
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "studied_to_treat",
+ "mixins": [
+ "treats_or_taken_to_treat_or_studied_to_treat"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/in_clinical_trials_for",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "in_clinical_trials_for",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "in_preclinical_trials_for",
+ "definition_uri": "https://w3id.org/biolink/vocab/in_preclinical_trials_for",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
"@type": "Annotation"
}
],
- "description": "holds between an entity whose application or use reduces the likelihood of a potential outcome. Typically used to associate a chemical entity, exposure, activity, or medical intervention that can prevent the onset a disease or phenotypic feature.",
+ "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that a pre-clinical study has been performed specifically to test the potential of the substance, procedure, or activity to treat the medical condition (i.e. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place).",
+ "notes": [
+ "A knowledge level of Observation MUST be used with this predicate (because it is merely reporting that a study was observed to have been performed)."
+ ],
"in_subset": [
"translator_minimal"
],
"from_schema": "https://w3id.org/biolink/biolink-model",
- "exact_mappings": [
- "https://skr3.nlm.nih.gov/SemMedDBPREVENTS"
+ "is_a": "studied_to_treat",
+ "mixins": [
+ "treats_or_taken_to_treat_or_studied_to_treat"
],
- "narrow_mappings": [
- "http://purl.obolibrary.org/obo/RO_0002599"
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/in_preclinical_trials_for",
+ "multivalued": true,
+ "inherited": true,
+ "owner": "in_preclinical_trials_for",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "beneficial_in_models_for",
+ "definition_uri": "https://w3id.org/biolink/vocab/beneficial_in_models_for",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ }
],
- "is_a": "affects_risk_for",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/prevents",
+ "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc).",
+ "notes": [
+ "This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) . A knowledge level of Assertion should be used with this predicate, because it requires interpretation of results to conclude an intervention to be 'beneficial', and thus goes beyond merely reporting the occurrence of a study)."
+ ],
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "in_preclinical_trials_for",
+ "mixins": [
+ "treats_or_taken_to_treat_or_studied_to_treat"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/beneficial_in_models_for",
"multivalued": true,
"inherited": true,
- "owner": "prevents",
- "inverse": "prevented_by",
- "range": "NamedThing",
+ "owner": "beneficial_in_models_for",
+ "range": "DiseaseOrPhenotypicFeature",
"@type": "SlotDefinition"
},
{
- "name": "prevented_by",
- "definition_uri": "https://w3id.org/biolink/vocab/prevented_by",
+ "name": "was_applied_to_treat",
+ "definition_uri": "https://w3id.org/biolink/vocab/was_applied_to_treat",
"annotations": [
{
- "tag": "opposite_of",
- "value": "enabled by",
+ "tag": "canonical_predicate",
+ "value": true,
"@type": "Annotation"
}
],
- "description": "holds between a potential outcome of which the likelihood was reduced by the application or use of an entity.",
+ "description": "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition.",
+ "notes": [
+ "This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here). A knowledge level of Observation MUST be used with this predicate (because it is merely reporting that an intervention was used / prescribed for use at some point in time)."
+ ],
+ "in_subset": [
+ "translator_minimal"
+ ],
"from_schema": "https://w3id.org/biolink/biolink-model",
- "is_a": "risk_affected_by",
- "domain": "NamedThing",
- "slot_uri": "https://w3id.org/biolink/vocab/prevented_by",
+ "aliases": [
+ "administered to treat",
+ "used to treat",
+ "given to treat"
+ ],
+ "is_a": "related_to_at_instance_level",
+ "mixins": [
+ "treats_or_taken_to_treat_or_studied_to_treat"
+ ],
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/was_applied_to_treat",
"multivalued": true,
"inherited": true,
- "owner": "prevented_by",
- "inverse": "prevents",
- "range": "NamedThing",
+ "owner": "was_applied_to_treat",
+ "range": "DiseaseOrPhenotypicFeature",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "treats_or_taken_to_treat_or_studied_to_treat",
+ "definition_uri": "https://w3id.org/biolink/vocab/treats_or_taken_to_treat_or_studied_to_treat",
+ "annotations": [
+ {
+ "tag": "canonical_predicate",
+ "value": true,
+ "@type": "Annotation"
+ }
+ ],
+ "description": "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).",
+ "notes": [
+ "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."
+ ],
+ "in_subset": [
+ "translator_minimal"
+ ],
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "mixin": true,
+ "slot_uri": "https://w3id.org/biolink/vocab/treats_or_taken_to_treat_or_studied_to_treat",
+ "range": "string",
"@type": "SlotDefinition"
},
{
@@ -10135,8 +10381,8 @@
"@type": "SlotDefinition"
},
{
- "name": "contraindicated_for",
- "definition_uri": "https://w3id.org/biolink/vocab/contraindicated_for",
+ "name": "contraindicated_in",
+ "definition_uri": "https://w3id.org/biolink/vocab/contraindicated_in",
"annotations": [
{
"tag": "canonical_predicate",
@@ -10149,21 +10395,34 @@
"@type": "Annotation"
}
],
- "description": "Holds between a drug and a disease or phenotype, such that a person with that disease should not be treated with the drug.",
+ "description": "Holds between a substance, procedure, or activity and a medical condition or circumstance, where an authority has established that the substance, procedure, or activity should not be applied as an intervention in patients with the condition or circumstance because it can result in detrimental outcomes.",
+ "notes": [
+ "This predicate relates the intervention with a specific disease, phenotype, or other medical circumstance that puts patients at high risk for detrimental outcomes. This may be a different condition from the one that the drug would be used to treat (e.g. pseudoephedrine is contraindicated in people with high-blood pressure as a treatment for nasal congestion), a biological state (e.g. isotretinoin is contraindicated in people who are pregnant as a treatment for acne), or being on a different medication (e.g. aspirin is contraindicated in people taking warfarin as a preventative treatment for stroke)."
+ ],
"from_schema": "https://w3id.org/biolink/biolink-model",
"exact_mappings": [
"http://purl.obolibrary.org/obo/NCIT_C37933"
],
"is_a": "related_to_at_instance_level",
- "domain": "Drug",
- "slot_uri": "https://w3id.org/biolink/vocab/contraindicated_for",
+ "domain": "ChemicalOrDrugOrTreatment",
+ "slot_uri": "https://w3id.org/biolink/vocab/contraindicated_in",
"multivalued": true,
"inherited": true,
- "owner": "contraindicated_for",
+ "owner": "contraindicated_in",
"inverse": "has_contraindication",
"range": "DiseaseOrPhenotypicFeature",
"@type": "SlotDefinition"
},
+ {
+ "name": "chemical_entity_or_drug_or_treatment",
+ "definition_uri": "https://w3id.org/biolink/vocab/chemical_entity_or_drug_or_treatment",
+ "description": "A union of chemical entities and children, and drug or treatment.",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "mixin": true,
+ "slot_uri": "https://w3id.org/biolink/vocab/chemical_entity_or_drug_or_treatment",
+ "range": "string",
+ "@type": "SlotDefinition"
+ },
{
"name": "has_contraindication",
"definition_uri": "https://w3id.org/biolink/vocab/has_contraindication",
@@ -10174,8 +10433,9 @@
"multivalued": true,
"inherited": true,
"owner": "has_contraindication",
- "inverse": "contraindicated_for",
- "range": "Drug",
+ "inverse": "contraindicated_in",
+ "range": "ChemicalOrDrugOrTreatment",
+ "inlined": true,
"@type": "SlotDefinition"
},
{
@@ -12005,19 +12265,34 @@
"@type": "SlotDefinition"
},
{
- "name": "FDA_approval_status",
- "definition_uri": "https://w3id.org/biolink/vocab/FDA_approval_status",
+ "name": "clinical_approval_status",
+ "definition_uri": "https://w3id.org/biolink/vocab/clinical_approval_status",
"description": "",
"from_schema": "https://w3id.org/biolink/biolink-model",
"is_a": "association_slot",
"domain": "Association",
- "slot_uri": "https://w3id.org/biolink/vocab/FDA_approval_status",
+ "slot_uri": "https://w3id.org/biolink/vocab/clinical_approval_status",
"owner": "EntityToPhenotypicFeatureAssociation",
"domain_of": [
"EntityToDiseaseAssociation",
"EntityToPhenotypicFeatureAssociation"
],
- "range": "FDAApprovalStatusEnum",
+ "range": "ClinicalApprovalStatusEnum",
+ "@type": "SlotDefinition"
+ },
+ {
+ "name": "max_research_phase",
+ "definition_uri": "https://w3id.org/biolink/vocab/max_research_phase",
+ "from_schema": "https://w3id.org/biolink/biolink-model",
+ "is_a": "association_slot",
+ "domain": "Association",
+ "slot_uri": "https://w3id.org/biolink/vocab/max_research_phase",
+ "owner": "EntityToPhenotypicFeatureAssociation",
+ "domain_of": [
+ "EntityToDiseaseAssociation",
+ "EntityToPhenotypicFeatureAssociation"
+ ],
+ "range": "MaxResearchPhaseEnum",
"@type": "SlotDefinition"
},
{
@@ -21796,6 +22071,7 @@
"name": "SeverityValue",
"definition_uri": "https://w3id.org/biolink/vocab/SeverityValue",
"description": "describes the severity of a phenotypic feature or disease",
+ "deprecated": "True",
"from_schema": "https://w3id.org/biolink/biolink-model",
"is_a": "Attribute",
"slots": [
@@ -27252,6 +27528,7 @@
"name": "Onset",
"definition_uri": "https://w3id.org/biolink/vocab/Onset",
"description": "The age group in which (disease) symptom manifestations appear",
+ "deprecated": "True",
"from_schema": "https://w3id.org/biolink/biolink-model",
"exact_mappings": [
"HP:0003674"
@@ -32490,7 +32767,8 @@
"retrieval_source_ids",
"association_type",
"association_category",
- "FDA_approval_status"
+ "clinical_approval_status",
+ "max_research_phase"
],
"slot_usage": {},
"class_uri": "https://w3id.org/biolink/vocab/EntityToDiseaseAssociation",
@@ -32540,7 +32818,8 @@
"retrieval_source_ids",
"association_type",
"association_category",
- "FDA_approval_status"
+ "clinical_approval_status",
+ "max_research_phase"
],
"slot_usage": {},
"class_uri": "https://w3id.org/biolink/vocab/EntityToPhenotypicFeatureAssociation",
@@ -33272,9 +33551,9 @@
],
"metamodel_version": "1.7.0",
"source_file": "biolink_model.yaml",
- "source_file_date": "2023-12-04T21:37:33",
- "source_file_size": 362227,
- "generation_date": "2023-12-04T21:37:41",
+ "source_file_date": "2023-12-14T13:52:09",
+ "source_file_size": 370258,
+ "generation_date": "2023-12-14T13:52:18",
"@type": "SchemaDefinition",
"@context": [
"project/jsonld/biolink_model.context.jsonld",
diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl
index 83e51a8c10..93f5efa26a 100644
--- a/biolink-model.owl.ttl
+++ b/biolink-model.owl.ttl
@@ -70,97 +70,110 @@
@prefix wgs: .
@prefix xsd: .
-biolink:BehavioralOutcome a owl:Class,
- linkml:ClassDefinition ;
+ a rdfs:Datatype ;
+ owl:equivalentClass xsd:double .
+
+ a rdfs:Datatype ;
+ owl:equivalentClass xsd:double .
+
+ a owl:Ontology ;
+ rdfs:label "Biolink-Model" ;
+ dct:license "https://creativecommons.org/publicdomain/zero/1.0/" ;
+ pav:version "4.0.0" ;
+ skos:definition "Entity and association taxonomy and datamodel for life-sciences data" .
+
+biolink:BehavioralOutcome a owl:Class ;
rdfs:label "behavioral outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "An outcome resulting from an exposure event which is the manifestation of human behavior." ;
skos:inScheme .
-biolink:DiseaseOrPhenotypicFeatureOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:DiseaseOrPhenotypicFeatureOutcome a owl:Class ;
rdfs:label "disease or phenotypic feature outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "Physiological outcomes resulting from an exposure event which is the manifestation of a disease or other characteristic phenotype." ;
skos:inScheme .
-biolink:EpidemiologicalOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:EpidemiologicalOutcome a owl:Class ;
rdfs:label "epidemiological outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "An epidemiological outcome, such as societal disease burden, resulting from an exposure event." ;
skos:inScheme ;
skos:relatedMatch .
-biolink:HospitalizationOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:HospitalizationOutcome a owl:Class ;
rdfs:label "hospitalization outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "An outcome resulting from an exposure event which is the increased manifestation of acute (e.g. emergency room visit) or chronic (inpatient) hospitalization." ;
skos:inScheme .
-biolink:MappingCollection a owl:Class,
- linkml:ClassDefinition ;
+biolink:MappingCollection a owl:Class ;
rdfs:label "mapping collection" ;
rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
+ owl:allValuesFrom biolink:PredicateMapping ;
owl:onProperty biolink:predicate_mappings ],
[ a owl:Restriction ;
- owl:allValuesFrom biolink:PredicateMapping ;
- owl:onProperty biolink:predicate_mappings ] ;
+ owl:minCardinality 0 ;
+ owl:onProperty biolink:predicate_mappings ],
+ linkml:ClassDefinition ;
skos:definition "A collection of deprecated mappings." ;
skos:inScheme .
-biolink:MortalityOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:MortalityOutcome a owl:Class ;
rdfs:label "mortality outcome" ;
- rdfs:subClassOf biolink:Outcome ;
- skos:definition "An outcome of death from resulting from an exposure event." ;
- skos:inScheme .
-
-biolink:PathognomonicityQuantifier a owl:Class,
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
linkml:ClassDefinition ;
- rdfs:label "pathognomonicity quantifier" ;
- rdfs:subClassOf biolink:SpecificityQuantifier ;
- skos:definition "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ;
+ skos:definition "An outcome of death from resulting from an exposure event." ;
skos:inScheme .
-biolink:PathologicalAnatomicalOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:PathologicalAnatomicalOutcome a owl:Class ;
rdfs:label "pathological anatomical outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "An outcome resulting from an exposure event which is the manifestation of an abnormal anatomical structure." ;
skos:inScheme .
-biolink:PathologicalProcessOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:PathologicalProcessOutcome a owl:Class ;
rdfs:label "pathological process outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "An outcome resulting from an exposure event which is the manifestation of a pathological process." ;
skos:inScheme .
-biolink:RelationshipType a owl:Class,
- linkml:ClassDefinition ;
+biolink:RelationshipType a owl:Class ;
rdfs:label "relationship type" ;
rdfs:subClassOf biolink:OntologyClass ;
skos:definition "An OWL property used as an edge label" ;
skos:inScheme .
-biolink:SensitivityQuantifier a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "sensitivity quantifier" ;
- rdfs:subClassOf biolink:RelationshipQuantifier ;
- skos:inScheme .
-
-biolink:SocioeconomicOutcome a owl:Class,
- linkml:ClassDefinition ;
+biolink:SocioeconomicOutcome a owl:Class ;
rdfs:label "socioeconomic outcome" ;
- rdfs:subClassOf biolink:Outcome ;
+ rdfs:subClassOf [ a owl:Restriction ;
+ owl:onProperty linkml:mixins ;
+ owl:someValuesFrom biolink:Outcome ],
+ linkml:ClassDefinition ;
skos:definition "An general social or economic outcome, such as healthcare costs, utilization, etc., resulting from an exposure event" ;
skos:inScheme .
-biolink:adverse_event_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:adverse_event_of a owl:ObjectProperty ;
rdfs:label "adverse event of" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
rdfs:range biolink:ChemicalOrDrugOrTreatment ;
@@ -168,30 +181,37 @@ biolink:adverse_event_of a owl:ObjectProperty,
owl:inverseOf biolink:has_adverse_event ;
skos:inScheme .
-biolink:amount_or_activity_decreased_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:amount_or_activity_decreased_by a owl:DatatypeProperty ;
rdfs:label "amount or activity decreased by" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:decreases_amount_or_activity_of ;
skos:inScheme .
-biolink:amount_or_activity_increased_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:amount_or_activity_increased_by a owl:DatatypeProperty ;
rdfs:label "amount or activity increased by" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:increases_amount_or_activity_of ;
skos:inScheme .
-biolink:animal_model_available_from a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:animal_model_available_from a owl:ObjectProperty ;
rdfs:label "animal model available from" ;
rdfs:range biolink:DiseaseOrPhenotypicFeature ;
rdfs:subPropertyOf biolink:node_property ;
skos:inScheme .
-biolink:binds a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:beneficial_in_models_for a owl:ObjectProperty ;
+ rdfs:label "beneficial in models for" ;
+ rdfs:domain biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:range biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:subPropertyOf biolink:in_preclinical_trials_for,
+ biolink:treats_or_taken_to_treat_or_studied_to_treat ;
+ skos:definition "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity has been shown to be effective in alleviating, preventing, or delaying symptoms/ phenotypes associated with a disease, in a model system for that disease (e.g. a mouse, fly, cell line, etc)." ;
+ skos:editorialNote "This predicate would be used to represent Model Organism Database (MOD) records reporting that an intervention alleviated phenotypes associated with a human disease in a model organism designated as a model of that disease. (e.g. a ZFIN record reporting that treatment with Braf Inhibitors reduced the abnormal brain cell proliferation phenotype of zebrafish used to model the human disease Kabuki Syndrome) . A knowledge level of Assertion should be used with this predicate, because it requires interpretation of results to conclude an intervention to be 'beneficial', and thus goes beyond merely reporting the occurrence of a study)." ;
+ skos:inScheme ;
+ biolink:canonical_predicate true .
+
+biolink:binds a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "binds" ;
rdfs:subPropertyOf biolink:directly_physically_interacts_with ;
skos:closeMatch DGIdb:binder ;
@@ -199,36 +219,31 @@ biolink:binds a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:biological_role_mixin a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:biological_role_mixin a owl:DatatypeProperty ;
rdfs:label "biological role mixin" ;
skos:definition "A role played by the chemical entity or part thereof within a biological context." ;
skos:inScheme ;
skos:narrowMatch .
-biolink:bonferonni_adjusted_p_value a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:bonferonni_adjusted_p_value a owl:DatatypeProperty ;
rdfs:label "bonferonni adjusted p value" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:adjusted_p_value ;
skos:definition "The Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made. 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<." ;
skos:inScheme .
-biolink:broad_matches a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:broad_matches a owl:DatatypeProperty ;
rdfs:label "broad matches" ;
skos:definition "A list of terms from different schemas or terminology systems that have a broader meaning. Such terms often describe a more general concept from different ontological perspectives." ;
skos:inScheme .
-biolink:broad_synonym a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:broad_synonym a owl:DatatypeProperty ;
rdfs:label "broad synonym" ;
rdfs:subPropertyOf biolink:synonym ;
skos:exactMatch OIO:hasBroadSynonym ;
skos:inScheme .
-biolink:can_be_carried_out_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:can_be_carried_out_by a owl:ObjectProperty ;
rdfs:label "can be carried out by" ;
rdfs:domain biolink:Occurrent ;
rdfs:range biolink:NamedThing ;
@@ -236,8 +251,7 @@ biolink:can_be_carried_out_by a owl:ObjectProperty,
owl:inverseOf biolink:capable_of ;
skos:inScheme .
-biolink:caused_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:caused_by a owl:DatatypeProperty ;
rdfs:label "caused by" ;
rdfs:subPropertyOf biolink:contribution_from ;
owl:inverseOf biolink:causes ;
@@ -255,16 +269,19 @@ biolink:caused_by a owl:ObjectProperty,
RO:0004028,
RO:0009501 .
-biolink:chemical_role_mixin a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:chemical_entity_or_drug_or_treatment a owl:DatatypeProperty ;
+ rdfs:label "chemical entity or drug or treatment" ;
+ skos:definition "A union of chemical entities and children, and drug or treatment." ;
+ skos:inScheme .
+
+biolink:chemical_role_mixin a owl:DatatypeProperty ;
rdfs:label "chemical role mixin" ;
skos:definition "A role played by the chemical entity or part thereof within a chemical context." ;
skos:exactMatch ;
skos:inScheme .
-biolink:chemically_similar_to a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:chemically_similar_to a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "chemically similar to" ;
rdfs:subPropertyOf biolink:similar_to ;
skos:definition "holds between one small molecule entity and another that it approximates for purposes of scientific study, in virtue of its exhibiting similar features of the studied entity." ;
@@ -278,17 +295,15 @@ biolink:chemically_similar_to a owl:ObjectProperty,
;
biolink:canonical_predicate true .
-biolink:chi_squared_statistic a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:chi_squared_statistic a owl:DatatypeProperty ;
rdfs:label "chi squared statistic" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "represents the chi-squared statistic computed from observations" ;
skos:exactMatch ;
skos:inScheme .
-biolink:clinical_modifier_qualifier a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:clinical_modifier_qualifier a owl:ObjectProperty ;
rdfs:label "clinical modifier qualifier" ;
rdfs:range biolink:ClinicalModifier ;
rdfs:subPropertyOf biolink:association_slot ;
@@ -296,8 +311,7 @@ biolink:clinical_modifier_qualifier a owl:ObjectProperty,
skos:inScheme .
biolink:coexpressed_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "coexpressed with" ;
rdfs:domain biolink:GeneOrGeneProduct ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -306,9 +320,8 @@ biolink:coexpressed_with a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:colocalizes_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:colocalizes_with a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "colocalizes with" ;
rdfs:subPropertyOf biolink:coexists_with ;
skos:definition "holds between two entities that are observed to be located in the same place." ;
@@ -316,39 +329,42 @@ biolink:colocalizes_with a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:completed_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:completed_by a owl:DatatypeProperty ;
rdfs:label "completed by" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:has_completed ;
skos:inScheme .
-biolink:concept_count_object a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:concept_count_object a owl:DatatypeProperty ;
rdfs:label "concept count object" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The number of instances in a dataset/cohort whose records contain the concept in the object slot of an association." ;
skos:inScheme .
-biolink:concept_count_subject a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:concept_count_subject a owl:DatatypeProperty ;
rdfs:label "concept count subject" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The number of instances in a dataset/cohort whose records contain the concept in the subject slot of an association." ;
skos:inScheme .
-biolink:concept_pair_count a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:concept_pair_count a owl:DatatypeProperty ;
rdfs:label "concept pair count" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The number of instances in a dataset/cohort whose records contain both the subject and object concept of an association." ;
skos:inScheme .
-biolink:condition_associated_with_gene a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:condition_ameliorated_by a owl:ObjectProperty ;
+ rdfs:label "condition ameliorated by" ;
+ rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:subPropertyOf biolink:affected_by ;
+ owl:inverseOf biolink:ameliorates_condition ;
+ skos:inScheme .
+
+biolink:condition_associated_with_gene a owl:ObjectProperty ;
rdfs:label "condition associated with gene" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
rdfs:range biolink:Gene ;
@@ -359,8 +375,31 @@ biolink:condition_associated_with_gene a owl:ObjectProperty,
skos:inScheme ;
skos:narrowMatch .
-biolink:consumed_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:condition_exacerbated_by a owl:ObjectProperty ;
+ rdfs:label "condition exacerbated by" ;
+ rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:subPropertyOf biolink:affected_by ;
+ owl:inverseOf biolink:exacerbates_condition ;
+ skos:inScheme .
+
+biolink:condition_predisposed_by a owl:ObjectProperty ;
+ rdfs:label "condition predisposed by" ;
+ rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:subPropertyOf biolink:related_to_at_instance_level ;
+ owl:inverseOf biolink:predisposes_to_condition ;
+ skos:inScheme .
+
+biolink:condition_prevented_by a owl:ObjectProperty ;
+ rdfs:label "condition prevented by" ;
+ rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:subPropertyOf biolink:affected_by ;
+ owl:inverseOf biolink:preventative_for_condition ;
+ skos:inScheme .
+
+biolink:consumed_by a owl:ObjectProperty ;
rdfs:label "consumed by" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:NamedThing ;
@@ -368,66 +407,57 @@ biolink:consumed_by a owl:ObjectProperty,
owl:inverseOf biolink:consumes ;
skos:inScheme .
-biolink:contains_process a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:contains_process a owl:DatatypeProperty ;
rdfs:label "contains process" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:occurs_in ;
skos:inScheme .
-biolink:created_with a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:created_with a owl:DatatypeProperty ;
rdfs:label "created with" ;
rdfs:domain biolink:Dataset ;
rdfs:subPropertyOf biolink:node_property ;
skos:exactMatch pav:createdWith ;
skos:inScheme .
-biolink:dataset_download_url a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:dataset_download_url a owl:DatatypeProperty ;
rdfs:label "dataset download url" ;
rdfs:domain biolink:Dataset ;
rdfs:subPropertyOf biolink:node_property ;
skos:inScheme .
-biolink:decreased_amount_in a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:decreased_amount_in a owl:DatatypeProperty ;
rdfs:label "decreased amount in" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:has_decreased_amount ;
skos:inScheme .
-biolink:decreased_likelihood_associated_with a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:decreased_likelihood_associated_with a owl:DatatypeProperty ;
rdfs:label "decreased likelihood associated with" ;
rdfs:subPropertyOf biolink:likelihood_associated_with ;
owl:inverseOf biolink:associated_with_decreased_likelihood_of ;
skos:inScheme .
-biolink:develops_into a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:develops_into a owl:DatatypeProperty ;
rdfs:label "develops into" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:develops_from ;
skos:inScheme .
-biolink:disrupted_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:disrupted_by a owl:DatatypeProperty ;
rdfs:label "disrupted by" ;
rdfs:subPropertyOf biolink:affected_by ;
owl:inverseOf biolink:disrupts ;
skos:definition "describes a relationship where the structure, function, or occurrence of one entity is degraded or interfered with by another." ;
skos:inScheme .
-biolink:download_url a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:download_url a owl:DatatypeProperty ;
rdfs:label "download url" ;
rdfs:domain biolink:InformationContentEntity ;
rdfs:subPropertyOf biolink:node_property ;
skos:inScheme .
-biolink:end_coordinate a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:end_coordinate a owl:DatatypeProperty ;
rdfs:label "end coordinate" ;
rdfs:subPropertyOf biolink:base_coordinate ;
skos:altLabel "end" ;
@@ -436,36 +466,31 @@ biolink:end_coordinate a owl:ObjectProperty,
skos:exactMatch gff3:end ;
skos:inScheme .
-biolink:evidence_count a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:evidence_count a owl:DatatypeProperty ;
rdfs:label "evidence count" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The number of evidence instances that are connected to an association." ;
skos:inScheme .
-biolink:exact_matches a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:exact_matches a owl:DatatypeProperty ;
rdfs:label "exact matches" ;
skos:definition "A list of terms from different schemas or terminology systems that have an identical meaning. Such terms often describe the same concept from different ontological perspectives." ;
skos:inScheme .
-biolink:exact_synonym a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:exact_synonym a owl:DatatypeProperty ;
rdfs:label "exact synonym" ;
rdfs:subPropertyOf biolink:synonym ;
skos:exactMatch OIO:hasExactSynonym ;
skos:inScheme .
-biolink:expected_count a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:expected_count a owl:DatatypeProperty ;
rdfs:label "expected count" ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The expected (calculated) number of instances in a dataset/cohort whose records contain both the subject and object concept of an association if the subject and object concepts are independent." ;
skos:inScheme .
-biolink:expresses a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:expresses a owl:ObjectProperty ;
rdfs:label "expresses" ;
rdfs:domain biolink:AnatomicalEntity ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -476,17 +501,15 @@ biolink:expresses a owl:ObjectProperty,
skos:exactMatch RO:0002292 ;
skos:inScheme .
-biolink:extraction_confidence_score a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:extraction_confidence_score a owl:DatatypeProperty ;
rdfs:label "extraction confidence score" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "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." ;
skos:inScheme .
biolink:gene_fusion_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "gene_fusion_with" ;
rdfs:domain biolink:Gene ;
rdfs:range biolink:Gene ;
@@ -495,16 +518,14 @@ biolink:gene_fusion_with a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:genetic_association a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:genetic_association a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "genetic association" ;
rdfs:subPropertyOf biolink:associated_with ;
skos:inScheme .
biolink:genetic_neighborhood_of a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "genetic_neighborhood_of" ;
rdfs:domain biolink:Gene ;
rdfs:range biolink:Gene ;
@@ -513,8 +534,7 @@ biolink:genetic_neighborhood_of a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:has_active_component a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_active_component a owl:ObjectProperty ;
rdfs:label "has active component" ;
rdfs:domain biolink:CellularComponent ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -522,8 +542,7 @@ biolink:has_active_component a owl:ObjectProperty,
owl:inverseOf biolink:active_in ;
skos:inScheme .
-biolink:has_author a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_author a owl:ObjectProperty ;
rdfs:label "has author" ;
rdfs:domain biolink:Publication ;
rdfs:range biolink:Agent ;
@@ -531,8 +550,7 @@ biolink:has_author a owl:ObjectProperty,
owl:inverseOf biolink:author ;
skos:inScheme .
-biolink:has_biomarker a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_biomarker a owl:ObjectProperty ;
rdfs:label "has biomarker" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ;
@@ -544,49 +562,43 @@ biolink:has_biomarker a owl:ObjectProperty,
skos:narrowMatch ,
.
-biolink:has_catalyst a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_catalyst a owl:DatatypeProperty ;
rdfs:label "has catalyst" ;
rdfs:subPropertyOf biolink:has_participant ;
owl:inverseOf biolink:catalyzes ;
skos:inScheme .
-biolink:has_chemical_formula a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_chemical_formula a owl:DatatypeProperty ;
rdfs:label "has chemical formula" ;
- rdfs:range biolink:chemical_formula_value ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:node_property ;
skos:definition "description of chemical compound based on element symbols" ;
skos:exactMatch WIKIDATA_PROPERTY:P274 ;
skos:inScheme .
-biolink:has_confidence_level a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_confidence_level a owl:ObjectProperty ;
rdfs:label "has confidence level" ;
rdfs:range biolink:ConfidenceLevel ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "connects an association to a qualitative term denoting the level of confidence" ;
skos:inScheme .
-biolink:has_constituent a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_constituent a owl:ObjectProperty ;
rdfs:label "has constituent" ;
rdfs:range biolink:MolecularEntity ;
rdfs:subPropertyOf biolink:node_property ;
skos:definition "one or more molecular entities within a chemical mixture" ;
skos:inScheme .
-biolink:has_contraindication a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_contraindication a owl:ObjectProperty ;
rdfs:label "has contraindication" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
- rdfs:range biolink:Drug ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
- owl:inverseOf biolink:contraindicated_for ;
+ owl:inverseOf biolink:contraindicated_in ;
skos:inScheme .
-biolink:has_editor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_editor a owl:ObjectProperty ;
rdfs:label "has editor" ;
rdfs:domain biolink:Publication ;
rdfs:range biolink:Agent ;
@@ -594,8 +606,7 @@ biolink:has_editor a owl:ObjectProperty,
owl:inverseOf biolink:editor ;
skos:inScheme .
-biolink:has_frameshift_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_frameshift_variant a owl:ObjectProperty ;
rdfs:label "has frameshift variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -606,8 +617,7 @@ biolink:has_frameshift_variant a owl:ObjectProperty,
"splice region variant" ;
skos:inScheme .
-biolink:has_missense_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_missense_variant a owl:ObjectProperty ;
rdfs:label "has missense variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -615,8 +625,7 @@ biolink:has_missense_variant a owl:ObjectProperty,
owl:inverseOf biolink:is_missense_variant_of ;
skos:inScheme .
-biolink:has_nearby_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_nearby_variant a owl:ObjectProperty ;
rdfs:label "has nearby variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -629,8 +638,7 @@ biolink:has_nearby_variant a owl:ObjectProperty,
"non coding transcript exon variant" ;
skos:inScheme .
-biolink:has_negative_upstream_actor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_negative_upstream_actor a owl:ObjectProperty ;
rdfs:label "has negative upstream actor" ;
rdfs:domain biolink:BiologicalProcess ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -638,8 +646,7 @@ biolink:has_negative_upstream_actor a owl:ObjectProperty,
owl:inverseOf biolink:acts_upstream_of_negative_effect ;
skos:inScheme .
-biolink:has_negative_upstream_or_within_actor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_negative_upstream_or_within_actor a owl:ObjectProperty ;
rdfs:label "has negative upstream or within actor" ;
rdfs:domain biolink:BiologicalProcess ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -647,8 +654,7 @@ biolink:has_negative_upstream_or_within_actor a owl:ObjectProperty,
owl:inverseOf biolink:acts_upstream_of_or_within_negative_effect ;
skos:inScheme .
-biolink:has_non_coding_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_non_coding_variant a owl:ObjectProperty ;
rdfs:label "has non coding variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -656,8 +662,7 @@ biolink:has_non_coding_variant a owl:ObjectProperty,
owl:inverseOf biolink:is_non_coding_variant_of ;
skos:inScheme .
-biolink:has_nonsense_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_nonsense_variant a owl:ObjectProperty ;
rdfs:label "has nonsense variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -665,8 +670,7 @@ biolink:has_nonsense_variant a owl:ObjectProperty,
owl:inverseOf biolink:is_nonsense_variant_of ;
skos:inScheme .
-biolink:has_positive_upstream_actor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_positive_upstream_actor a owl:ObjectProperty ;
rdfs:label "has positive upstream actor" ;
rdfs:domain biolink:BiologicalProcess ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -674,8 +678,7 @@ biolink:has_positive_upstream_actor a owl:ObjectProperty,
owl:inverseOf biolink:acts_upstream_of_positive_effect ;
skos:inScheme .
-biolink:has_positive_upstream_or_within_actor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_positive_upstream_or_within_actor a owl:ObjectProperty ;
rdfs:label "has positive upstream or within actor" ;
rdfs:domain biolink:BiologicalProcess ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -683,15 +686,7 @@ biolink:has_positive_upstream_or_within_actor a owl:ObjectProperty,
owl:inverseOf biolink:acts_upstream_of_or_within_positive_effect ;
skos:inScheme .
-biolink:has_predisposing_factor a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "has predisposing factor" ;
- rdfs:subPropertyOf biolink:risk_affected_by ;
- owl:inverseOf biolink:predisposes ;
- skos:inScheme .
-
-biolink:has_provider a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_provider a owl:ObjectProperty ;
rdfs:label "has provider" ;
rdfs:domain biolink:InformationContentEntity ;
rdfs:range biolink:Agent ;
@@ -699,8 +694,7 @@ biolink:has_provider a owl:ObjectProperty,
owl:inverseOf biolink:provider ;
skos:inScheme .
-biolink:has_publisher a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_publisher a owl:ObjectProperty ;
rdfs:label "has publisher" ;
rdfs:domain biolink:Publication ;
rdfs:range biolink:Agent ;
@@ -708,8 +702,7 @@ biolink:has_publisher a owl:ObjectProperty,
owl:inverseOf biolink:publisher ;
skos:inScheme .
-biolink:has_receptor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_receptor a owl:ObjectProperty ;
rdfs:label "has receptor" ;
rdfs:domain biolink:ExposureEvent ;
rdfs:range biolink:OrganismalEntity ;
@@ -718,8 +711,7 @@ biolink:has_receptor a owl:ObjectProperty,
skos:exactMatch ExO:0000001 ;
skos:inScheme .
-biolink:has_route a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_route a owl:DatatypeProperty ;
rdfs:label "has route" ;
rdfs:domain biolink:ExposureEvent ;
rdfs:subPropertyOf biolink:node_property ;
@@ -730,8 +722,7 @@ biolink:has_route a owl:ObjectProperty,
,
.
-biolink:has_splice_site_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_splice_site_variant a owl:ObjectProperty ;
rdfs:label "has splice site variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -741,8 +732,7 @@ biolink:has_splice_site_variant a owl:ObjectProperty,
"upstream gene variant" ;
skos:inScheme .
-biolink:has_stressor a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_stressor a owl:DatatypeProperty ;
rdfs:label "has stressor" ;
rdfs:domain biolink:ExposureEvent ;
rdfs:subPropertyOf biolink:node_property ;
@@ -751,15 +741,13 @@ biolink:has_stressor a owl:ObjectProperty,
skos:exactMatch ExO:0000000 ;
skos:inScheme .
-biolink:has_supporting_study_result a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_supporting_study_result a owl:DatatypeProperty ;
rdfs:label "has supporting study result" ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "connects an association to an instance of supporting study result" ;
skos:inScheme .
-biolink:has_synonymous_variant a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_synonymous_variant a owl:ObjectProperty ;
rdfs:label "has synonymous variant" ;
rdfs:domain biolink:GenomicEntity ;
rdfs:range biolink:SequenceVariant ;
@@ -768,8 +756,7 @@ biolink:has_synonymous_variant a owl:ObjectProperty,
skos:altLabel "stop gained" ;
skos:inScheme .
-biolink:has_target a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_target a owl:ObjectProperty ;
rdfs:label "has target" ;
rdfs:domain biolink:Disease ;
rdfs:range biolink:Gene ;
@@ -777,8 +764,7 @@ biolink:has_target a owl:ObjectProperty,
owl:inverseOf biolink:target_for ;
skos:inScheme .
-biolink:has_topic a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:has_topic a owl:ObjectProperty ;
rdfs:label "has topic" ;
rdfs:range biolink:OntologyClass ;
rdfs:subPropertyOf biolink:node_property ;
@@ -789,8 +775,7 @@ biolink:has_topic a owl:ObjectProperty,
skos:inScheme .
biolink:in_cell_population_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "in cell population with" ;
rdfs:domain biolink:GeneOrGeneProduct ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -799,9 +784,19 @@ biolink:in_cell_population_with a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
+biolink:in_clinical_trials_for a owl:ObjectProperty ;
+ rdfs:label "in clinical trials for" ;
+ rdfs:domain biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:range biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:subPropertyOf biolink:studied_to_treat,
+ biolink:treats_or_taken_to_treat_or_studied_to_treat ;
+ skos:definition "Holds between an intervention and a medical condition, and reports that a clinical trial is being or has been performed in human patients to test the potential of the intervention to treat the medical condition (e.g. to ameliorate, stabilize, or cure the condition, or to delay, prevent, or reduce the risk of it manifesting in the first place)." ;
+ skos:editorialNote "This predicate should be used when a source reports a clinical trial where the intervention is being or was interrogated, regardless of the phase of the trial, or its ultimate outcome. Information about phase and outcome can be capture using other modeling elements. A knowledge level of \"\"Observation\"\" MUST be used with this predicate (because it is merely reporting that a study was observed to have been performed). Note that if the source reports an intervention to be in a phase 4 trial, or a completed phase 3 trial where clinical benefit was demonstrated, a separate 'treats' edge SHOULD also be created (with knowledge_level = Assertion)." ;
+ skos:inScheme ;
+ biolink:canonical_predicate true .
+
biolink:in_complex_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "in complex with" ;
rdfs:domain biolink:GeneOrGeneProduct ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -812,9 +807,8 @@ biolink:in_complex_with a owl:ObjectProperty,
skos:relatedMatch SIO:010497 ;
biolink:canonical_predicate true .
-biolink:in_linkage_disequilibrium_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:in_linkage_disequilibrium_with a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "in linkage disequilibrium with" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
skos:definition "holds between two sequence variants, the presence of which are correlated in a population" ;
@@ -823,8 +817,7 @@ biolink:in_linkage_disequilibrium_with a owl:ObjectProperty,
biolink:canonical_predicate true .
biolink:in_pathway_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "in pathway with" ;
rdfs:domain biolink:GeneOrGeneProduct ;
rdfs:range biolink:GeneOrGeneProduct ;
@@ -834,30 +827,26 @@ biolink:in_pathway_with a owl:ObjectProperty,
skos:relatedMatch SIO:010532 ;
biolink:canonical_predicate true .
-biolink:increased_amount_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:increased_amount_of a owl:DatatypeProperty ;
rdfs:label "increased amount of" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:has_increased_amount ;
skos:inScheme .
-biolink:increased_likelihood_associated_with a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:increased_likelihood_associated_with a owl:DatatypeProperty ;
rdfs:label "increased likelihood associated with" ;
rdfs:subPropertyOf biolink:likelihood_associated_with ;
owl:inverseOf biolink:associated_with_increased_likelihood_of ;
skos:inScheme .
-biolink:indirectly_physically_interacts_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:indirectly_physically_interacts_with a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "indirectly physically interacts with" ;
rdfs:subPropertyOf biolink:physically_interacts_with ;
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:is_assessed_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_assessed_by a owl:ObjectProperty ;
rdfs:label "is assessed by" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:NamedThing ;
@@ -865,8 +854,7 @@ biolink:is_assessed_by a owl:ObjectProperty,
owl:inverseOf biolink:assesses ;
skos:inScheme .
-biolink:is_diagnosed_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_diagnosed_by a owl:ObjectProperty ;
rdfs:label "is diagnosed by" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
rdfs:range biolink:DiagnosticAid ;
@@ -874,17 +862,7 @@ biolink:is_diagnosed_by a owl:ObjectProperty,
owl:inverseOf biolink:diagnoses ;
skos:inScheme .
-biolink:is_exacerbated_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "is exacerbated by" ;
- rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
- rdfs:range biolink:BiologicalEntity ;
- rdfs:subPropertyOf biolink:affected_by ;
- owl:inverseOf biolink:exacerbates ;
- skos:inScheme .
-
-biolink:is_excipient_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_excipient_of a owl:ObjectProperty ;
rdfs:label "is excipient of" ;
rdfs:domain biolink:MolecularEntity ;
rdfs:range biolink:Drug ;
@@ -894,8 +872,7 @@ biolink:is_excipient_of a owl:ObjectProperty,
skos:inScheme ;
skos:mappingRelation WIKIDATA:Q902638 .
-biolink:is_metabolite_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_metabolite_of a owl:ObjectProperty ;
rdfs:label "is metabolite of" ;
rdfs:domain biolink:MolecularEntity ;
rdfs:range biolink:MolecularEntity ;
@@ -906,16 +883,14 @@ biolink:is_metabolite_of a owl:ObjectProperty,
skos:inScheme ;
skos:note "The CHEBI ID represents a role rather than a predicate" .
-biolink:is_molecular_consequence_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_molecular_consequence_of a owl:DatatypeProperty ;
rdfs:label "is molecular consequence of" ;
rdfs:domain biolink:OntologyClass ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:has_molecular_consequence ;
skos:inScheme .
-biolink:is_output_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_output_of a owl:ObjectProperty ;
rdfs:label "is output of" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:BiologicalProcessOrActivity ;
@@ -925,8 +900,7 @@ biolink:is_output_of a owl:ObjectProperty,
skos:inScheme ;
skos:narrowMatch RO:0002354 .
-biolink:is_side_effect_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_side_effect_of a owl:ObjectProperty ;
rdfs:label "is side effect of" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
rdfs:range biolink:ChemicalOrDrugOrTreatment ;
@@ -934,8 +908,7 @@ biolink:is_side_effect_of a owl:ObjectProperty,
owl:inverseOf biolink:has_side_effect ;
skos:inScheme .
-biolink:is_substrate_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:is_substrate_of a owl:ObjectProperty ;
rdfs:label "is substrate of" ;
rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ;
rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ;
@@ -943,47 +916,47 @@ biolink:is_substrate_of a owl:ObjectProperty,
owl:inverseOf biolink:has_substrate ;
skos:inScheme .
-biolink:ln_ratio a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:likelihood_affected_by a owl:DatatypeProperty ;
+ rdfs:label "likelihood affected by" ;
+ rdfs:subPropertyOf biolink:related_to_at_instance_level ;
+ owl:inverseOf biolink:affects_likelihood_of ;
+ skos:inScheme .
+
+biolink:ln_ratio a owl:DatatypeProperty ;
rdfs:label "ln ratio" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "the natural log of the ratio of co-occurrence to expected" ;
skos:inScheme .
-biolink:ln_ratio_confidence_interval a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:ln_ratio_confidence_interval a owl:DatatypeProperty ;
rdfs:label "ln ratio confidence interval" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The 99% confidence interval for the ln_ratio calculation (i.e. the range of values within which the true value has a 99% chance of falling)" ;
skos:inScheme .
-biolink:location_of_disease a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:location_of_disease a owl:DatatypeProperty ;
rdfs:label "location of disease" ;
rdfs:subPropertyOf biolink:related_to ;
owl:inverseOf biolink:disease_has_location ;
skos:inScheme .
-biolink:log_odds_ratio a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:log_odds_ratio a owl:DatatypeProperty ;
rdfs:label "log odds ratio" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The logarithm of the odds ratio, or the ratio of the odds of event Y occurring in an exposed group versus the odds of event Y occurring in a non-exposed group." ;
skos:inScheme .
-biolink:log_odds_ratio_95_ci a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:log_odds_ratio_95_ci a owl:DatatypeProperty ;
rdfs:label "log odds ratio 95 ci" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The ninety-five percent confidence range in which the true log odds ratio for the sample population falls." ;
skos:inScheme .
-biolink:logical_interpretation a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:logical_interpretation a owl:ObjectProperty ;
rdfs:label "logical interpretation" ;
rdfs:domain biolink:Association ;
rdfs:range biolink:LogicalInterpretationEnum ;
@@ -991,10 +964,9 @@ biolink:logical_interpretation a owl:ObjectProperty,
skos:exactMatch os:LogicalInterpretation ;
skos:inScheme .
-biolink:mechanism_of_action a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:mechanism_of_action a owl:DatatypeProperty ;
rdfs:label "mechanism of action" ;
- rdfs:range linkml:Boolean ;
+ rdfs:range xsd:boolean ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "a boolean flag to indicate if the edge is part of a path or subgraph of a knowledge graph that constitutes the mechanism of action for a result." ;
skos:exactMatch LOINC:MTHU019741,
@@ -1002,8 +974,7 @@ biolink:mechanism_of_action a owl:ObjectProperty,
;
skos:inScheme .
-biolink:member_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:member_of a owl:DatatypeProperty ;
rdfs:label "member of" ;
rdfs:subPropertyOf biolink:related_to_at_concept_level ;
owl:inverseOf biolink:has_member ;
@@ -1012,23 +983,20 @@ biolink:member_of a owl:ObjectProperty,
skos:exactMatch RO:0002350 ;
skos:inScheme .
-biolink:mentioned_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:mentioned_by a owl:DatatypeProperty ;
rdfs:label "mentioned by" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:mentions ;
skos:definition "refers to is a relation between one named thing and the information content entity that it makes reference to." ;
skos:inScheme .
-biolink:missing_from a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:missing_from a owl:DatatypeProperty ;
rdfs:label "missing from" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:lacks_part ;
skos:inScheme .
-biolink:mode_of_inheritance_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:mode_of_inheritance_of a owl:ObjectProperty ;
rdfs:label "mode of inheritance of" ;
rdfs:domain biolink:GeneticInheritance ;
rdfs:range biolink:DiseaseOrPhenotypicFeature ;
@@ -1036,29 +1004,25 @@ biolink:mode_of_inheritance_of a owl:ObjectProperty,
owl:inverseOf biolink:has_mode_of_inheritance ;
skos:inScheme .
-biolink:models a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:models a owl:DatatypeProperty ;
rdfs:label "models" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:model_of ;
skos:inScheme .
-biolink:narrow_matches a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:narrow_matches a owl:DatatypeProperty ;
rdfs:label "narrow matches" ;
skos:definition "A list of terms from different schemas or terminology systems that have a narrower meaning. Such terms often describe a more specific concept from different ontological perspectives." ;
skos:inScheme .
-biolink:narrow_synonym a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:narrow_synonym a owl:DatatypeProperty ;
rdfs:label "narrow synonym" ;
rdfs:subPropertyOf biolink:synonym ;
skos:exactMatch OIO:hasNarrowSynonym ;
skos:inScheme .
biolink:negatively_correlated_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "negatively correlated with" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:NamedThing ;
@@ -1069,15 +1033,13 @@ biolink:negatively_correlated_with a owl:ObjectProperty,
biolink:canonical_predicate true ;
biolink:opposite_of "positively correlated with" .
-biolink:not_completed_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:not_completed_by a owl:DatatypeProperty ;
rdfs:label "not completed by" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:has_not_completed ;
skos:inScheme .
-biolink:nutrient_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:nutrient_of a owl:ObjectProperty ;
rdfs:label "nutrient of" ;
rdfs:domain biolink:ChemicalEntity ;
rdfs:range biolink:ChemicalEntity ;
@@ -1086,24 +1048,21 @@ biolink:nutrient_of a owl:ObjectProperty,
skos:definition "holds between a one or more chemical entities present in food, irrespective of nutritional value (i.e. could also be a contaminant or additive)" ;
skos:inScheme .
-biolink:object_location_in_text a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:object_location_in_text a owl:DatatypeProperty ;
rdfs:label "object location in text" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "Character offsets for the text span(s) in the supporting text corresponding to the object concept of the extracted assertion" ;
skos:inScheme .
-biolink:occurs_in_disease a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:occurs_in_disease a owl:DatatypeProperty ;
rdfs:label "occurs in disease" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:disease_has_basis_in ;
skos:inScheme .
biolink:occurs_together_in_literature_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "occurs together in literature with" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:NamedThing ;
@@ -1112,9 +1071,8 @@ biolink:occurs_together_in_literature_with a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:opposite_of a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:opposite_of a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "opposite of" ;
rdfs:seeAlso ,
;
@@ -1124,9 +1082,8 @@ biolink:opposite_of a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:orthologous_to a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:orthologous_to a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "orthologous to" ;
rdfs:subPropertyOf biolink:homologous_to ;
skos:definition "a homology relationship between entities (typically genes) that diverged after a speciation event." ;
@@ -1135,9 +1092,8 @@ biolink:orthologous_to a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:paralogous_to a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:paralogous_to a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "paralogous to" ;
rdfs:subPropertyOf biolink:homologous_to ;
skos:definition "a homology relationship that holds between entities (typically genes) that diverged after a duplication event." ;
@@ -1145,12 +1101,7 @@ biolink:paralogous_to a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:percentage_frequency_value a owl:Class,
- linkml:TypeDefinition ;
- rdfs:subClassOf linkml:Double .
-
-biolink:phenotype_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:phenotype_of a owl:ObjectProperty ;
rdfs:label "phenotype of" ;
rdfs:domain biolink:PhenotypicFeature ;
rdfs:range biolink:BiologicalEntity ;
@@ -1158,16 +1109,14 @@ biolink:phenotype_of a owl:ObjectProperty,
owl:inverseOf biolink:has_phenotype ;
skos:inScheme .
-biolink:plasma_membrane_part_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:plasma_membrane_part_of a owl:DatatypeProperty ;
rdfs:label "plasma membrane part of" ;
rdfs:subPropertyOf biolink:part_of ;
owl:inverseOf biolink:has_plasma_membrane_part ;
skos:inScheme .
biolink:positively_correlated_with a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+ owl:SymmetricProperty ;
rdfs:label "positively correlated with" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:NamedThing ;
@@ -1178,43 +1127,26 @@ biolink:positively_correlated_with a owl:ObjectProperty,
biolink:canonical_predicate true ;
biolink:opposite_of "negatively correlated with" .
-biolink:prevented_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "prevented by" ;
- rdfs:subPropertyOf biolink:risk_affected_by ;
- owl:inverseOf biolink:prevents ;
- skos:definition "holds between a potential outcome of which the likelihood was reduced by the application or use of an entity." ;
- skos:inScheme ;
- biolink:opposite_of "enabled by" .
-
-biolink:primarily_composed_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:primarily_composed_of a owl:DatatypeProperty ;
rdfs:label "primarily composed of" ;
rdfs:subPropertyOf biolink:related_to ;
owl:inverseOf biolink:composed_primarily_of ;
skos:inScheme .
-biolink:produced_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:produced_by a owl:DatatypeProperty ;
rdfs:label "produced by" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
owl:inverseOf biolink:produces ;
skos:exactMatch RO:0003001 ;
skos:inScheme .
-biolink:quotient a owl:Class,
- linkml:TypeDefinition ;
- rdfs:subClassOf linkml:Double .
-
-biolink:reaction_balanced a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:reaction_balanced a owl:DatatypeProperty ;
rdfs:label "reaction balanced" ;
- rdfs:range linkml:Boolean ;
+ rdfs:range xsd:boolean ;
rdfs:subPropertyOf biolink:association_slot ;
skos:inScheme .
-biolink:regulated_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:regulated_by a owl:ObjectProperty ;
rdfs:label "regulated by" ;
rdfs:domain biolink:PhysicalEssenceOrOccurrent ;
rdfs:range biolink:PhysicalEssenceOrOccurrent ;
@@ -1222,61 +1154,53 @@ biolink:regulated_by a owl:ObjectProperty,
owl:inverseOf biolink:regulates ;
skos:inScheme .
-biolink:related_condition a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:related_condition a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "related condition" ;
rdfs:subPropertyOf biolink:related_to_at_instance_level ;
skos:exactMatch ;
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:related_synonym a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:related_synonym a owl:DatatypeProperty ;
rdfs:label "related synonym" ;
rdfs:subPropertyOf biolink:synonym ;
skos:exactMatch OIO:hasRelatedSynonym ;
skos:inScheme .
-biolink:relation a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:relation a owl:DatatypeProperty ;
rdfs:label "relation" ;
skos:inScheme .
-biolink:relative_frequency_object a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:relative_frequency_object a owl:DatatypeProperty ;
rdfs:label "relative frequency object" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the object concept appears in these same records." ;
skos:inScheme .
-biolink:relative_frequency_object_confidence_interval a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:relative_frequency_object_confidence_interval a owl:DatatypeProperty ;
rdfs:label "relative frequency object confidence interval" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The 99% confidence interval for the relative_frequency_object calculation (i.e. the range of values within which the true value has a 99% chance of falling)" ;
skos:inScheme .
-biolink:relative_frequency_subject a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:relative_frequency_subject a owl:DatatypeProperty ;
rdfs:label "relative frequency subject" ;
- rdfs:range linkml:Float ;
+ rdfs:range xsd:float ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The frequency at which subject and object concepts co-occur in records within a dataset/cohort, relative to the frequency at which the subject concept appears in these same records." ;
skos:inScheme .
-biolink:relative_frequency_subject_confidence_interval a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:relative_frequency_subject_confidence_interval a owl:DatatypeProperty ;
rdfs:label "relative frequency subject confidence interval" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The 99% confidence interval for the relative_frequency_subject calculation (i.e. the range of values within which the true value has a 99% chance of falling)" ;
skos:inScheme .
-biolink:resistance_associated_with a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:resistance_associated_with a owl:ObjectProperty ;
rdfs:label "resistance associated with" ;
rdfs:domain biolink:ChemicalEntity ;
rdfs:range biolink:NamedThing ;
@@ -1284,8 +1208,7 @@ biolink:resistance_associated_with a owl:ObjectProperty,
owl:inverseOf biolink:associated_with_resistance_to ;
skos:inScheme .
-biolink:response_decreased_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:response_decreased_by a owl:ObjectProperty ;
rdfs:label "response decreased by" ;
rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ;
rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ;
@@ -1293,8 +1216,7 @@ biolink:response_decreased_by a owl:ObjectProperty,
owl:inverseOf biolink:decreases_response_to ;
skos:inScheme .
-biolink:response_increased_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:response_increased_by a owl:ObjectProperty ;
rdfs:label "response increased by" ;
rdfs:domain biolink:ChemicalEntityOrGeneOrGeneProduct ;
rdfs:range biolink:ChemicalEntityOrGeneOrGeneProduct ;
@@ -1302,18 +1224,16 @@ biolink:response_increased_by a owl:ObjectProperty,
owl:inverseOf biolink:increases_response_to ;
skos:inScheme .
-biolink:retrieved_on a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:retrieved_on a owl:DatatypeProperty ;
rdfs:label "retrieved on" ;
rdfs:domain biolink:Dataset ;
- rdfs:range linkml:Date ;
+ rdfs:range xsd:date ;
rdfs:subPropertyOf biolink:node_property ;
skos:exactMatch pav:retrievedOn ;
skos:inScheme .
-biolink:same_as a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:same_as a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "same as" ;
rdfs:subPropertyOf biolink:exact_match ;
skos:closeMatch owl:equivalentClass ;
@@ -1327,16 +1247,14 @@ biolink:same_as a owl:ObjectProperty,
skos:narrowMatch ;
biolink:canonical_predicate true .
-biolink:semmed_agreement_count a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:semmed_agreement_count a owl:DatatypeProperty ;
rdfs:label "semmed agreement count" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The number of times this concept has been asserted in the SemMedDB literature database." ;
skos:inScheme .
-biolink:sensitivity_associated_with a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:sensitivity_associated_with a owl:ObjectProperty ;
rdfs:label "sensitivity associated with" ;
rdfs:domain biolink:ChemicalEntity ;
rdfs:range biolink:NamedThing ;
@@ -1344,8 +1262,7 @@ biolink:sensitivity_associated_with a owl:ObjectProperty,
owl:inverseOf biolink:associated_with_sensitivity_to ;
skos:inScheme .
-biolink:sequence_location_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:sequence_location_of a owl:ObjectProperty ;
rdfs:label "sequence location of" ;
rdfs:domain biolink:NucleicAcidEntity ;
rdfs:range biolink:NucleicAcidEntity ;
@@ -1353,16 +1270,14 @@ biolink:sequence_location_of a owl:ObjectProperty,
owl:inverseOf biolink:has_sequence_location ;
skos:inScheme .
-biolink:sequence_variant_qualifier a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:sequence_variant_qualifier a owl:ObjectProperty ;
rdfs:label "sequence variant qualifier" ;
rdfs:range biolink:SequenceVariant ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "a qualifier used in an association with the variant" ;
skos:inScheme .
-biolink:start_coordinate a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:start_coordinate a owl:DatatypeProperty ;
rdfs:label "start coordinate" ;
rdfs:subPropertyOf biolink:base_coordinate ;
skos:altLabel "start" ;
@@ -1371,57 +1286,26 @@ biolink:start_coordinate a owl:ObjectProperty,
skos:exactMatch gff3:start ;
skos:inScheme .
-biolink:subclass_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
- rdfs:label "subclass of" ;
- rdfs:domain biolink:OntologyClass ;
- rdfs:range biolink:OntologyClass ;
- rdfs:subPropertyOf biolink:related_to_at_concept_level ;
- skos:closeMatch LOINC:class_of,
- LOINC:has_class ;
- skos:definition "holds between two classes where the domain class is a specialization of the range class" ;
- skos:exactMatch MESH:isa,
- RXNORM:isa,
- ,
- rdfs:subClassOf,
- SEMMEDDB:ISA,
- CHEMBL.MECHANISM:subset_of,
- VANDF:isa,
- WIKIDATA_PROPERTY:P279 ;
- skos:inScheme ;
- skos:narrowMatch LOINC:has_archetype,
- LOINC:has_parent_group,
- LOINC:is_presence_guidance_for,
- NDDF:has_dose_form,
- RXNORM:has_dose_form,
- RXNORM:has_doseformgroup,
- ,
- ,
- ,
- ,
- ,
- ,
- ,
- ,
- ,
- ,
- rdfs:subPropertyOf ;
- biolink:canonical_predicate true .
+biolink:studied_for_treatment_with a owl:ObjectProperty ;
+ rdfs:label "studied for treatment with" ;
+ rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:range biolink:ChemicalOrDrugOrTreatment ;
+ owl:inverseOf biolink:studied_to_treat ;
+ skos:inScheme .
-biolink:subject_location_in_text a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:subject_location_in_text a owl:DatatypeProperty ;
rdfs:label "subject location in text" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "Character offsets for the text span(s) in the supporting text corresponding to the subject concept of the extracted assertion." ;
skos:inScheme .
-biolink:superclass_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:superclass_of a owl:ObjectProperty ;
rdfs:label "superclass of" ;
rdfs:domain biolink:OntologyClass ;
rdfs:range biolink:OntologyClass ;
rdfs:subPropertyOf biolink:related_to_at_concept_level ;
+ owl:inverseOf biolink:subclass_of ;
skos:definition "holds between two classes where the domain class is a super class of the range class" ;
skos:exactMatch MESH:inverse_isa,
RXNORM:inverse_isa,
@@ -1437,118 +1321,103 @@ biolink:superclass_of a owl:ObjectProperty,
,
.
-biolink:support_graphs a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:support_graphs a owl:DatatypeProperty ;
rdfs:label "support graphs" ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "A list of knowledge graphs that support the existence of this node." ;
skos:inScheme .
-biolink:supporting_data_set a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_data_set a owl:DatatypeProperty ;
rdfs:label "supporting data set" ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "A set of data used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data)." ;
skos:inScheme .
-biolink:supporting_data_source a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_data_source a owl:DatatypeProperty ;
rdfs:label "supporting data source" ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "An Information Resource from which data was retrieved and subsequently used as evidence to generate the knowledge expressed in an Association (e.g. through computation on, reasoning or inference over the retrieved data)." ;
skos:editorialNote "For example, in this Feature Variable Association Edge generated by the Exposure Agent’s ICEES KP, through statistical analysis of clinical and environmental data supplied by the UNC Clinical Data Warehouse, the Edge is passed to the Ranking Agent’s ARAGORN ARA, and then on to the ARS. The retrieval path for this Edge is as follows: ARS--retrieved_from--> ARAGORN --retrieved_from--> ICEES --supporting_data_from--> UNC Data Warehouse This example illustrates how to represent the source provenance of KP-generated knowledge, including the source of data from which the knowledge was derived. The \"primary knowledge source\" for this edge is \"infores:icees-asthma\". A \"supporting data source\" for this KP- generated knowledge is \"infores:unc-cdw-health.\" The \"aggregator knowledge source\" for this data is \"infores:aragorn-ara\"" ;
skos:inScheme .
-biolink:supporting_document_type a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_document_type a owl:DatatypeProperty ;
rdfs:label "supporting document type" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The document type (e.g., Journal Article, Case Study, Preprint) for the supporting document used in a Text Mining Result." ;
skos:inScheme .
-biolink:supporting_document_year a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_document_year a owl:DatatypeProperty ;
rdfs:label "supporting document year" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The document year (typically the publication year) for the supporting document used in a Text Mining Result." ;
skos:inScheme .
-biolink:supporting_documents a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_documents a owl:DatatypeProperty ;
rdfs:label "supporting documents" ;
- rdfs:range linkml:Uriorcurie ;
+ rdfs:range xsd:anyURI ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "One or more referenceable documents that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ;
skos:inScheme .
-biolink:supporting_study_cohort a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_study_cohort a owl:DatatypeProperty ;
rdfs:label "supporting study cohort" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:supporting_study_metadata ;
skos:definition "A description of a study population/cohort that was interrogated to provide evidence for the association (e.g. the inclusion and exclusion criteria)." ;
skos:inScheme .
-biolink:supporting_study_context a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_study_context a owl:DatatypeProperty ;
rdfs:label "supporting study context" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:supporting_study_metadata ;
skos:definition "A term or terms describing the experimental setting/context in which evidence supporting the Association was generated ('context' may be defined by many factors, including taxon, model system (e.g. cell line type), tissue type, disease, etc.)." ;
skos:inScheme .
-biolink:supporting_study_date_range a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_study_date_range a owl:DatatypeProperty ;
rdfs:label "supporting study date range" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:supporting_study_metadata ;
skos:definition "The date range over which data was collected in a study that provided evidence for an Association." ;
skos:inScheme .
-biolink:supporting_study_method_description a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_study_method_description a owl:DatatypeProperty ;
rdfs:label "supporting study method description" ;
- rdfs:range linkml:Uriorcurie ;
+ rdfs:range xsd:anyURI ;
rdfs:subPropertyOf biolink:supporting_study_metadata ;
skos:definition "A uri or curie pointing to information about the methodology used to generate data supporting an Association." ;
skos:inScheme .
-biolink:supporting_study_method_type a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_study_method_type a owl:DatatypeProperty ;
rdfs:label "supporting study method type" ;
- rdfs:range linkml:Uriorcurie ;
+ rdfs:range xsd:anyURI ;
rdfs:subPropertyOf biolink:supporting_study_metadata ;
skos:definition "A type of method that was applied in a study used to generate the information used as evidence (e.g. a type of experimental assay, or statistical calculation, or computational analysis)." ;
skos:inScheme .
-biolink:supporting_study_size a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_study_size a owl:DatatypeProperty ;
rdfs:label "supporting study size" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:supporting_study_metadata ;
skos:definition "The sample size used in a study that provided evidence for the association (e.g. 'n' of a cohort for a clinical study)." ;
skos:inScheme .
-biolink:supporting_text a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_text a owl:DatatypeProperty ;
rdfs:label "supporting text" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The segment of text from a document that supports the mined assertion." ;
skos:inScheme .
-biolink:supporting_text_section_type a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:supporting_text_section_type a owl:DatatypeProperty ;
rdfs:label "supporting text section type" ;
- rdfs:range linkml:String ;
+ rdfs:range xsd:string ;
rdfs:subPropertyOf biolink:association_slot ;
skos:definition "The section of the supporting text of a Text Mining Result within the supporting document. This is in the form of the name of the document section (e.g., Abstract, Introduction) that contains the supporting text." ;
skos:inScheme .
-biolink:systematic_synonym a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:systematic_synonym a owl:DatatypeProperty ;
rdfs:label "systematic synonym" ;
rdfs:domain biolink:NamedThing ;
rdfs:range biolink:label_type ;
@@ -1556,8 +1425,7 @@ biolink:systematic_synonym a owl:ObjectProperty,
skos:definition "more commonly used for gene symbols in yeast" ;
skos:inScheme .
-biolink:taxon_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:taxon_of a owl:ObjectProperty ;
rdfs:label "taxon of" ;
rdfs:domain biolink:OrganismTaxon ;
rdfs:range biolink:ThingWithTaxon ;
@@ -1565,51 +1433,43 @@ biolink:taxon_of a owl:ObjectProperty,
owl:inverseOf biolink:in_taxon ;
skos:inScheme .
-biolink:temporal_interval_qualifier a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:temporal_interval_qualifier a owl:DatatypeProperty ;
rdfs:label "temporal interval qualifier" ;
rdfs:subPropertyOf biolink:temporal_context_qualifier ;
skos:definition "a constraint of a time interval placed upon the truth value of an association." ;
skos:inScheme .
-biolink:total_sample_size a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:total_sample_size a owl:DatatypeProperty ;
rdfs:label "total sample size" ;
- rdfs:range linkml:Integer ;
+ rdfs:range xsd:integer ;
rdfs:subPropertyOf biolink:dataset_count ;
skos:definition "The total number of patients or participants within a sample population." ;
skos:inScheme .
-biolink:treated_by a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:treated_by a owl:ObjectProperty ;
rdfs:label "treated by" ;
rdfs:domain biolink:DiseaseOrPhenotypicFeature ;
rdfs:range biolink:ChemicalOrDrugOrTreatment ;
- rdfs:subPropertyOf biolink:is_ameliorated_by ;
owl:inverseOf biolink:treats ;
- skos:definition "holds between a disease or phenotypic feature and a therapeutic process or chemical entity that is used to treat the condition" ;
skos:exactMatch ,
WIKIDATA_PROPERTY:P2176 ;
skos:inScheme ;
skos:narrowMatch RO:0002302 .
-biolink:update_date a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:update_date a owl:DatatypeProperty ;
rdfs:label "update date" ;
- rdfs:range linkml:Date ;
+ rdfs:range xsd:date ;
rdfs:subPropertyOf biolink:node_property ;
skos:definition "date on which an entity was updated. This can be applied to nodes or edges" ;
skos:inScheme .
-biolink:variant_part_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:variant_part_of a owl:DatatypeProperty ;
rdfs:label "variant part of" ;
rdfs:subPropertyOf biolink:part_of ;
owl:inverseOf biolink:has_variant_part ;
skos:inScheme .
-biolink:version a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:version a owl:DatatypeProperty ;
rdfs:label "version" ;
rdfs:domain biolink:Dataset ;
rdfs:subPropertyOf biolink:node_property ;
@@ -1617,8 +1477,7 @@ biolink:version a owl:ObjectProperty,
owl:versionInfo ;
skos:inScheme .
-biolink:version_of a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:version_of a owl:ObjectProperty ;
rdfs:label "version of" ;
rdfs:domain biolink:DatasetVersion ;
rdfs:range biolink:DatasetSummary ;
@@ -1626,9 +1485,22 @@ biolink:version_of a owl:ObjectProperty,
skos:exactMatch dct:isVersionOf ;
skos:inScheme .
-biolink:xenologous_to a owl:ObjectProperty,
- owl:SymmetricProperty,
- linkml:SlotDefinition ;
+biolink:was_applied_to_treat a owl:ObjectProperty ;
+ rdfs:label "was applied to treat" ;
+ rdfs:domain biolink:ChemicalOrDrugOrTreatment ;
+ rdfs:range biolink:DiseaseOrPhenotypicFeature ;
+ rdfs:subPropertyOf biolink:related_to_at_instance_level,
+ biolink:treats_or_taken_to_treat_or_studied_to_treat ;
+ skos:altLabel "administered to treat",
+ "given to treat",
+ "used to treat" ;
+ skos:definition "Holds between an substance, procedure, or activity and a medical condition, and reports that the substance, procedure, or activity was actually taken by one or more patients with the intent of treating the condition." ;
+ skos:editorialNote "This predicate is used simply to report observations of use in the real world, and is agnostic to whether the treatment is approved for or might be effective in treating the condition. The treatment could be taken by a patient on their own accord or prescribed by a clinician, as an off-label or an approved intervention. In practice, it would be used to represent records/statements from patient self-reporting sources like FAERS / AEOLUS where patients directly report the condition for which they took a drug, or statements from a database cataloging instances of off-label prescription of drugs for specific conditions (e.g. here, here, here). A knowledge level of Observation MUST be used with this predicate (because it is merely reporting that an intervention was used / prescribed for use at some point in time)." ;
+ skos:inScheme ;
+ biolink:canonical_predicate true .
+
+biolink:xenologous_to a owl:DatatypeProperty,
+ owl:SymmetricProperty ;
rdfs:label "xenologous to" ;
rdfs:subPropertyOf biolink:homologous_to ;
skos:definition "a homology relationship characterized by an interspecies (horizontal) transfer since the common ancestor." ;
@@ -1636,130 +1508,29 @@ biolink:xenologous_to a owl:ObjectProperty,
skos:inScheme ;
biolink:canonical_predicate true .
-biolink:Annotation a owl:Class,
- linkml:ClassDefinition ;
+biolink:Annotation a owl:Class ;
rdfs:label "annotation" ;
+ rdfs:subClassOf linkml:ClassDefinition ;
skos:definition "Biolink Model root class for entity annotations." ;
skos:inScheme .
-biolink:CaseToEntityAssociationMixin a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "case to entity association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Case ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ] ;
- skos:definition "An abstract association for use where the case is the subject" ;
- skos:inScheme .
-
-biolink:CellLineToEntityAssociationMixin a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "cell line to entity association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:CellLine ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ] ;
- skos:definition "An relationship between a cell line and another entity" ;
- skos:inScheme .
-
- a owl:Class,
- biolink:ChemicalEntityDerivativeEnum ;
+ a owl:Class ;
rdfs:label "metabolite" ;
- rdfs:subClassOf biolink:ChemicalEntityDerivativeEnum .
-
-biolink:DrugToEntityAssociationMixin a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "drug to entity association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Drug ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ],
- biolink:ChemicalEntityToEntityAssociationMixin ;
- skos:definition "An interaction between a drug and another entity" ;
- skos:inScheme .
-
-biolink:EntityToExposureEventAssociationMixin a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "entity to exposure event association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:ExposureEvent ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ] ;
- skos:definition "An association between some entity and an exposure event." ;
- skos:inScheme .
-
-biolink:EntityToOutcomeAssociationMixin a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "entity to outcome association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:allValuesFrom biolink:Outcome ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:object ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:object ] ;
- skos:definition "An association between some entity and an outcome" ;
- skos:inScheme .
-
-biolink:EpigenomicEntity a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "epigenomic entity" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 0 ;
- owl:onProperty biolink:has_biological_sequence ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:biological_sequence ;
- owl:onProperty biolink:has_biological_sequence ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:has_biological_sequence ] ;
- skos:inScheme .
+ rdfs:subClassOf biolink:ChemicalEntityDerivativeEnum,
+ linkml:PermissibleValue .
-biolink:MaterialSampleToEntityAssociationMixin a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "material sample to entity association mixin" ;
- rdfs:subClassOf [ a owl:Restriction ;
- owl:minCardinality 1 ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:allValuesFrom biolink:MaterialSample ;
- owl:onProperty biolink:subject ],
- [ a owl:Restriction ;
- owl:maxCardinality 1 ;
- owl:onProperty biolink:subject ] ;
- skos:definition "An association between a material sample and something." ;
+biolink:PathognomonicityQuantifier a owl:Class ;
+ rdfs:label "pathognomonicity quantifier" ;
+ rdfs:subClassOf biolink:SpecificityQuantifier ;
+ skos:definition "A relationship quantifier between a variant or symptom and a disease, which is high when the presence of the feature implies the existence of the disease" ;
skos:inScheme .
-biolink:SpecificityQuantifier a owl:Class,
- linkml:ClassDefinition ;
- rdfs:label "specificity quantifier" ;
+biolink:SensitivityQuantifier a owl:Class ;
+ rdfs:label "sensitivity quantifier" ;
rdfs:subClassOf biolink:RelationshipQuantifier ;
skos:inScheme .
-biolink:active_in a owl:ObjectProperty,
- linkml:SlotDefinition ;
+biolink:active_in a owl:ObjectProperty ;
rdfs:label "active in" ;
rdfs:domain biolink:GeneOrGeneProduct ;
rdfs:range biolink:CellularComponent ;
@@ -1768,8 +1539,7 @@ biolink:active_in a owl:ObjectProperty,
skos:inScheme