From e37280594b84718e778b2db2b1b5979a5aab076e Mon Sep 17 00:00:00 2001 From: Deepak Unni Date: Mon, 16 Aug 2021 16:51:39 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.owl.ttl | 1109 +++++++++++++++++++---------------------- biolink-model.ttl | 847 ++++++++++++++----------------- biolink/model.py | 11 +- context.jsonld | 11 +- contextn.jsonld | 11 +- 5 files changed, 924 insertions(+), 1065 deletions(-) diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index 58c378dd57..eec9df820c 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -11,11 +11,11 @@ rdfs:label "Biolink-Model" ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; - linkml:generation_date "2021-08-04 17:31" ; + linkml:generation_date "2021-08-16 16:48" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Wed Aug 4 17:29:39 2021" ; - linkml:source_file_size 315217 . + linkml:source_file_date "Mon Aug 16 16:47:14 2021" ; + linkml:source_file_size 313678 . a owl:Class, linkml:ClassDefinition ; @@ -25,22 +25,14 @@ skos:definition "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; skos:exactMatch , , - , - ; + ; skos:narrowMatch , , , , , , - , - , - , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -74,13 +66,13 @@ linkml:ClassDefinition ; rdfs:label "case to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -102,7 +94,6 @@ , , , - , . a owl:Class, @@ -123,11 +114,7 @@ skos:narrowMatch , , , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -169,21 +156,21 @@ linkml:ClassDefinition ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , ; @@ -249,20 +236,19 @@ rdfs:subClassOf ; skos:definition "Something that happens at a given place and time." ; skos:exactMatch , - , - . + . a owl:Class, linkml:ClassDefinition ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , ; @@ -273,8 +259,7 @@ rdfs:label "food" ; rdfs:subClassOf ; skos:definition "A substance consumed by a living organism as a source of nutrition" ; - skos:exactMatch , - . + skos:exactMatch . a owl:Class, linkml:ClassDefinition ; @@ -323,19 +308,19 @@ linkml:ClassDefinition ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , , , @@ -373,18 +358,11 @@ rdfs:subClassOf ; skos:altLabel "organ", "tissue" ; - skos:exactMatch , - , - , - , - , + skos:exactMatch , ; skos:narrowMatch , , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -533,18 +511,12 @@ ; skos:broadMatch , , - , - , - , - ; + ; skos:definition "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; skos:exactMatch ; skos:narrowMatch , , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -568,16 +540,11 @@ ; skos:altLabel "physiology" ; skos:exactMatch , - , ; skos:narrowMatch , , , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -674,8 +641,7 @@ rdfs:label "vitamin" ; rdfs:subClassOf ; skos:relatedMatch , - , - . + . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -2532,21 +2498,21 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], , , . @@ -2726,25 +2692,25 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -2753,13 +2719,9 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "frequency quantifier" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; @@ -2767,7 +2729,11 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty ], , linkml:mixin . @@ -2799,17 +2765,9 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -2818,6 +2776,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." . @@ -2836,21 +2802,21 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -2877,16 +2843,15 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Float ; - owl:onProperty ], + owl:onProperty ], ; skos:definition "a location that can be described in lat/long coordinates" ; skos:exactMatch , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -2937,14 +2902,6 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -2952,6 +2909,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , , . @@ -2970,9 +2935,7 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; skos:narrowMatch , , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -3052,24 +3015,24 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . @@ -3078,6 +3041,10 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -3085,10 +3052,6 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -3410,7 +3373,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases abundance of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the amount of the other within a system of interest" . @@ -3419,7 +3383,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases activity of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the activity of the other within a system of interest" . @@ -3428,7 +3393,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases degradation of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the rate of degradation of the other within a system of interest" . @@ -3437,7 +3403,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases expression of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the level of expression of the other within a system of interest" . @@ -3446,7 +3413,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases folding of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between a chemical entity and a nucleic acid entity where the action or effect of one decreases the rate or quality of folding of the other" . @@ -3455,7 +3423,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases localization of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the proper localization of the other within a system of interest" . @@ -3464,7 +3433,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases metabolic processing of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the rate of metabolic processing of the other within a system of interest" . @@ -3473,7 +3443,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases molecular interaction" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "indicates that the source decreases the molecular interaction between the target and some other chemical entity" . @@ -3482,7 +3453,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases molecular modification of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one leads to decreased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)" . @@ -3491,7 +3463,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases mutation rate of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity decreases the rate of mutation of the nucleic acid entity within a system of interest" . @@ -3500,7 +3473,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases response to" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other" . @@ -3509,7 +3483,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases secretion of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the rate of secretion of the other out of a cell, gland, or organ" . @@ -3518,7 +3493,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases splicing of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between a chemical entity and an mRNA where the action or effect of the chemical entity decreases the proper splicing of the mRNA" . @@ -3527,7 +3503,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases stability of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the stability of the other within a system of interest" . @@ -3536,7 +3513,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases synthesis of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the rate of chemical synthesis of the other" . @@ -3545,7 +3523,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases transport of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the rate of transport of the other across some boundary in a system of interest" . @@ -3554,7 +3533,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "decreases uptake of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one decreases the rate of uptake of the other into of a cell, gland, or organ" . @@ -4137,7 +4117,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases abundance of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the amount of the other within a system of interest" . @@ -4146,7 +4127,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases activity of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the activity of the other within a system of interest" . @@ -4155,7 +4137,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases degradation of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate of degradation of the other within a system of interest" . @@ -4164,7 +4147,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases expression of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the level of expression of the other within a system of interest" . @@ -4173,7 +4157,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases folding of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate or quality of folding of the other" . @@ -4182,7 +4167,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases localization of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the proper localization of the other within a system of interest" . @@ -4191,7 +4177,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases metabolic processing of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate of metabolic processing of the other within a system of interest" . @@ -4200,7 +4187,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases molecular interaction" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "indicates that the source increases the molecular interaction between the target and some other chemical entity" . @@ -4209,7 +4197,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases molecular modification of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one leads to increased molecular modification(s) of the other (e.g. via post-translational modifications of proteins such as the addition of phosphoryl group, or via redox reaction that adds or subtracts electrons)" . @@ -4218,7 +4207,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases mutation rate of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between a chemical entity and a nucleic acid entity where the action or effect of the chemical entity increases the rate of mutation of the nucleic acid entity within a system of interest" . @@ -4227,7 +4217,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases response to" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the susceptibility of a biological entity or system (e.g. an organism, cell, cellular component, macromolecular machine mixin, biological or pathological process) to the other" . @@ -4236,7 +4227,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases secretion of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate of secretion of the other out of a cell, gland, or organ" . @@ -4245,7 +4237,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases splicing of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between a chemical entity and an mRNA where the action or effect of the chemical entity increases the proper splicing of the mRNA" . @@ -4254,7 +4247,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases stability of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the stability of the other within a system of interest" . @@ -4263,7 +4257,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases synthesis of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate of chemical synthesis of the other" . @@ -4272,7 +4267,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases transport of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate of transport of the other across some boundary in a system of interest" . @@ -4281,7 +4277,8 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, rdfs:label "increases uptake of" ; rdfs:domain ; rdfs:range ; - rdfs:subPropertyOf ; + rdfs:subPropertyOf , + ; owl:inverseOf ; skos:definition "holds between two chemical entities where the action or effect of one increases the rate of uptake of the other into of a cell, gland, or organ" . @@ -5281,30 +5278,22 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, , ; skos:exactMatch , - , - ; + ; skos:narrowMatch , , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -5315,8 +5304,12 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." . @@ -5349,14 +5342,14 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass linkml:Uriorcurie ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], . a owl:Class, @@ -5420,11 +5413,7 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, , , , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -5460,13 +5449,13 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "entity to feature or disease qualifiers mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , linkml:mixin ; skos:definition "Qualifiers for entity to disease or phenotype associations." . @@ -5494,13 +5483,13 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "A transcript is formed from multiple exons" . @@ -5548,9 +5537,9 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -5568,9 +5557,9 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , , ; @@ -5604,8 +5593,7 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:label "organism attribute" ; rdfs:subClassOf ; skos:definition "describes a characteristic of an organismal entity." ; - skos:exactMatch , - . + skos:exactMatch . a owl:Class, linkml:ClassDefinition ; @@ -5627,21 +5615,17 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, skos:narrowMatch , , , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; rdfs:label "RNA product" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , ; skos:exactMatch , @@ -5672,13 +5656,13 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:note "An alternate way to model the same information could be via a qualifier" . @@ -5687,9 +5671,9 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty ; @@ -5697,15 +5681,15 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onProperty ], ; skos:altLabel "journal" ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -5733,18 +5717,18 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], , , ; @@ -6053,7 +6037,7 @@ linkml:publication_type a owl:ObjectProperty, rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; @@ -6061,7 +6045,7 @@ linkml:publication_type a owl:ObjectProperty, owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." . @@ -6075,11 +6059,11 @@ linkml:publication_type a owl:ObjectProperty, owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" . @@ -6088,12 +6072,13 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "cellular component" ; rdfs:subClassOf ; + skos:altLabel "cell component", + "cell part" ; skos:broadMatch ; skos:definition "A location in or around a cell" ; skos:exactMatch , , , - , . a owl:Class, @@ -6134,11 +6119,11 @@ linkml:publication_type a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], ; skos:definition "an item that holds summary level information about a dataset." . @@ -6155,6 +6140,10 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene expression mixin" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -6166,10 +6155,6 @@ linkml:publication_type a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], linkml:mixin ; skos:definition "Observed gene expression intensity, context (site, stage) and associated phenotypic status within which the expression occurs." . @@ -6186,6 +6171,10 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene regulatory relationship" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6193,10 +6182,6 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], ; skos:definition "A regulatory relationship between two genes" . @@ -6205,16 +6190,16 @@ linkml:publication_type a owl:ObjectProperty, rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -6268,14 +6253,14 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" . @@ -6284,11 +6269,11 @@ linkml:publication_type a owl:ObjectProperty, rdfs:label "genotype to genotype part association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; @@ -6301,13 +6286,13 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -6322,14 +6307,14 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An association between a material sample and the material entity from which it is derived." . @@ -6337,16 +6322,16 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "named thing to information content entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." . @@ -6365,16 +6350,16 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], , . @@ -6383,16 +6368,16 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" . @@ -6404,27 +6389,27 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], . a owl:Class, linkml:ClassDefinition ; rdfs:label "pairwise gene to gene interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" . @@ -6446,6 +6431,10 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6453,10 +6442,6 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], ; skos:definition "An association between a two populations" . @@ -6464,11 +6449,11 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "protein" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , , ; @@ -6477,9 +6462,7 @@ linkml:publication_type a owl:ObjectProperty, , ; skos:narrowMatch , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -6520,13 +6503,13 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , ; skos:definition "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" . @@ -6757,11 +6740,11 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:label "anatomical entity to anatomical entity association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], . @@ -6781,19 +6764,19 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "chemical to chemical derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition """A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: @@ -6809,8 +6792,8 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; @@ -6820,8 +6803,8 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" . @@ -6830,6 +6813,10 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -6837,10 +6824,6 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], ; skos:definition "an item that holds version level information about a dataset." . @@ -6848,38 +6831,38 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; - owl:onProperty ] ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . a owl:Class, @@ -6902,28 +6885,28 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], , , @@ -6964,11 +6947,11 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:label "organism taxon to organism taxon association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], , ; @@ -6978,21 +6961,21 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" . @@ -7002,10 +6985,8 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:subClassOf , ; skos:definition "An entity that has material reality (a.k.a. physical essence)." ; - skos:exactMatch , - ; - skos:narrowMatch , - . + skos:exactMatch ; + skos:narrowMatch . a owl:Class, linkml:ClassDefinition ; @@ -7025,16 +7006,16 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -7045,8 +7026,8 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], , , @@ -7195,8 +7176,7 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:label "clinical attribute" ; rdfs:subClassOf ; skos:definition "Attributes relating to a clinical manifestation" ; - skos:exactMatch , - . + skos:exactMatch . a owl:Class, linkml:ClassDefinition ; @@ -7211,17 +7191,17 @@ linkml:functional_association_object a owl:ObjectProperty, owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], ; skos:definition "An association between a gene and an expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" . @@ -7231,11 +7211,11 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:label "gene to gene association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:altLabel "molecular or genetic interaction" ; @@ -7252,8 +7232,7 @@ linkml:functional_association_object a owl:ObjectProperty, skos:altLabel "organism" ; skos:definition "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; skos:exactMatch , - , - ; + ; skos:narrowMatch , . @@ -7269,12 +7248,16 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -7285,11 +7268,7 @@ linkml:functional_association_object a owl:ObjectProperty, owl:onProperty ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -7299,11 +7278,11 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; @@ -7324,23 +7303,23 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -7348,7 +7327,7 @@ linkml:functional_association_object a owl:ObjectProperty, [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onProperty ], , , , @@ -7562,13 +7541,13 @@ linkml:Boolean a owl:Class, linkml:ClassDefinition ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." . @@ -7594,7 +7573,6 @@ linkml:Boolean a owl:Class, , , , - , ; skos:narrowMatch , , @@ -7603,27 +7581,19 @@ linkml:Boolean a owl:Class, , , , - , - , - , - , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; rdfs:label "functional association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." . @@ -7652,7 +7622,6 @@ linkml:Boolean a owl:Class, , ; skos:narrowMatch , - , , . @@ -7711,11 +7680,11 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "gene product mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , linkml:mixin ; skos:definition "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; @@ -7727,13 +7696,13 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "model to disease association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], linkml:mixin ; skos:definition "This mixin is used for any association class for which the subject (source node) plays the role of a 'model', in that it recapitulates some features of the disease in a way that is useful for studying the disease outside a patient carrying the disease" . @@ -7753,14 +7722,14 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , , ; @@ -7769,8 +7738,7 @@ linkml:Float a owl:Class, "reaction" ; skos:definition "An execution of a molecular function carried out by a gene product or macromolecular complex." ; skos:exactMatch , - , - . + . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -7821,10 +7789,6 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -7832,6 +7796,10 @@ linkml:Float a owl:Class, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], , linkml:mixin . @@ -7864,8 +7832,7 @@ linkml:Float a owl:Class, skos:exactMatch , , , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -7941,16 +7908,16 @@ linkml:Double a owl:Class, owl:onClass linkml:String ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -7961,12 +7928,7 @@ linkml:Double a owl:Class, , , , - , - , - , - , - , - . + . a owl:Class, linkml:ClassDefinition ; @@ -7974,12 +7936,12 @@ linkml:Double a owl:Class, rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , , ; @@ -7991,15 +7953,12 @@ linkml:Double a owl:Class, rdfs:subClassOf , , ; - skos:broadMatch , - ; + skos:broadMatch ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; skos:exactMatch , , - , ; - skos:narrowMatch , - ; + skos:narrowMatch ; skos:note "The CHEBI ID represents a role rather than a substance" . a owl:Class, @@ -8007,36 +7966,36 @@ linkml:Double a owl:Class, rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass linkml:Integer ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], ; skos:definition "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." . @@ -8084,27 +8043,27 @@ linkml:Uriorcurie a owl:Class, rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; @@ -8117,13 +8076,13 @@ linkml:Uriorcurie a owl:Class, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], , , , @@ -8167,7 +8126,6 @@ linkml:Uriorcurie a owl:Class, skos:altLabel "bioentity" ; skos:narrowMatch , , - , . a owl:Class, @@ -8245,18 +8203,23 @@ linkml:topValue a owl:DatatypeProperty ; , , , - , - , - , - , - , - , - , - , - , - , - , - . + . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "decreases amount or activity of" ; + rdfs:domain ; + rdfs:range ; + rdfs:subPropertyOf ; + skos:definition "A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object." . + + a owl:ObjectProperty, + linkml:SlotDefinition ; + rdfs:label "increases amount or activity of" ; + rdfs:domain ; + rdfs:range ; + rdfs:subPropertyOf ; + skos:definition "A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object." . a owl:Class, linkml:ClassDefinition ; @@ -8302,42 +8265,41 @@ linkml:Integer a owl:Class, linkml:ClassDefinition ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:allValuesFrom linkml:Uriorcurie ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom linkml:Uriorcurie ; - owl:onProperty ], + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], ; skos:definition "Any published piece of information. Can refer to a whole publication, its encompassing publication (i.e. journal or book) or to a part of a publication, if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP). The scope is intended to be general and include information published on the web, as well as printed materials, either directly or in one of the Publication Biolink category subclasses." ; skos:exactMatch IAO:0000311 ; skos:narrowMatch , - IAO:0000013, - . + IAO:0000013 . a owl:Class, linkml:ClassDefinition ; @@ -8349,17 +8311,10 @@ linkml:Integer a owl:Class, , ; skos:definition "A subcellular location, cell type or gross anatomical part" ; - skos:exactMatch , + skos:exactMatch , + , , - ; - skos:narrowMatch , - , - , - , - , - , - , - . + . linkml:TypeDefinition a owl:Class ; rdfs:label "type_definition" ; @@ -8375,8 +8330,7 @@ linkml:TypeDefinition a owl:Class ; ; skos:altLabel "phenome" ; skos:definition "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate." ; - skos:narrowMatch , - . + skos:narrowMatch . a owl:Class, linkml:ClassDefinition ; @@ -8394,19 +8348,19 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass linkml:String ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , , @@ -8462,18 +8416,18 @@ linkml:TypeDefinition a owl:Class ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], @@ -8503,35 +8457,8 @@ linkml:TypeDefinition a owl:Class ; skos:altLabel "taxon", "taxonomic classification" ; skos:definition "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; - skos:exactMatch ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - . + skos:exactMatch , + . a owl:ObjectProperty, linkml:SlotDefinition ; @@ -8603,38 +8530,38 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch , @@ -8663,32 +8590,23 @@ linkml:String a owl:Class, linkml:ClassDefinition ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , , , , ; - skos:broadMatch ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; - skos:exactMatch , + skos:exactMatch , + , , ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - . + skos:narrowMatch . a owl:Class, linkml:ClassDefinition ; @@ -8704,7 +8622,6 @@ linkml:String a owl:Class, skos:exactMatch , , , - , . linkml:ClassDefinition a owl:Class ; diff --git a/biolink-model.ttl b/biolink-model.ttl index 2891803278..f3501a6845 100644 --- a/biolink-model.ttl +++ b/biolink-model.ttl @@ -13,7 +13,7 @@ a linkml:SchemaDefinition ; dcterms:license "https://creativecommons.org/publicdomain/zero/1.0/" ; - pav:version "2.2.1" ; + pav:version "2.2.2" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -294,218 +294,216 @@ , , ; - linkml:generation_date "2021-08-04 17:31"^^xsd:dateTime ; + linkml:generation_date "2021-08-16 16:49"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], + linkml:prefixes [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD0" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "XPO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "oboformat" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "Aeolus" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.RCLASS" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "KEGG.BRITE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PDQ" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "CHADO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "medgen" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORPHA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "DrugCentral" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXCUI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HsapDv" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTEx" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "biolink" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], [ linkml:prefix_prefix "GOP" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MetaCyc" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORPHA" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "ICD10" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "hetio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RXNORM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foaf" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSST" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "VANDF" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTEx" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PATO-PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RTXKG1" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBOREL" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "STY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOREL" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "EFO" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COG" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ORCID" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "Aeolus" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERON_CORE" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "MAXO" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "foaf" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "OBOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "schema" ; linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "UBERON_CORE" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "chembio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "Xenbase" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "RXCUI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "RTXKG1" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "hetio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PATO-PROPERTY" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "doi" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "medgen" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SNPEFF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PDQ" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "XPO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "MetaCyc" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RXNORM" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "alliancegenome" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "biolink" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD0" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COG" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], [ linkml:prefix_prefix "EDAM-DATA" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "GOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HsapDv" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "chembio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNPEFF" ; + linkml:prefix_reference ] ; linkml:slots , , , @@ -634,6 +632,7 @@ , , , + , , , , @@ -830,6 +829,7 @@ , , , + , , , , @@ -1110,8 +1110,8 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Wed Aug 4 17:29:39 2021"^^xsd:dateTime ; - linkml:source_file_size 315217 ; + linkml:source_file_date "Mon Aug 16 16:47:14 2021"^^xsd:dateTime ; + linkml:source_file_size 313678 ; linkml:subsets , , , @@ -1770,11 +1770,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ], - [ a linkml:Example ; skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ] ; + skos:example "MP:0013229" ], + [ a linkml:Example ; + skos:definition "Ehlers-Danlos syndrome, vascular type" ; + skos:example "MONDO:0017314" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -1881,11 +1881,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "abnormal brain ventricle size" ; - skos:example "MP:0013229" ], - [ a linkml:Example ; skos:definition "Ehlers-Danlos syndrome, vascular type" ; - skos:example "MONDO:0017314" ] ; + skos:example "MONDO:0017314" ], + [ a linkml:Example ; + skos:definition "abnormal brain ventricle size" ; + skos:example "MP:0013229" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -1944,12 +1944,12 @@ linkml:examples [ a linkml:Example ; skos:definition "abnormal circulating bilirubin level" ; skos:example "MP:0001569" ], - [ a linkml:Example ; - skos:definition "axon morphology variant" ; - skos:example "WBPhenotype:0000180" ], [ a linkml:Example ; skos:definition "Hyperkinesis" ; - skos:example "HP:0002487" ] ; + skos:example "HP:0002487" ], + [ a linkml:Example ; + skos:definition "axon morphology variant" ; + skos:example "WBPhenotype:0000180" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -3478,23 +3478,15 @@ skos:definition "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; skos:exactMatch , , - , - ; - skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - , - , - ; + ; + skos:inScheme ; + skos:narrowMatch , + , + , + , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -3574,8 +3566,7 @@ skos:exactMatch , , , - , - , + , ; skos:inScheme ; linkml:class_uri ; @@ -3627,14 +3618,10 @@ skos:definition "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -3855,8 +3842,7 @@ a linkml:ClassDefinition ; skos:definition "Something that happens at a given place and time." ; skos:exactMatch , - , - ; + ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -3874,8 +3860,7 @@ a linkml:ClassDefinition ; skos:definition "A substance consumed by a living organism as a source of nutrition" ; - skos:exactMatch , - ; + skos:exactMatch ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -4034,18 +4019,11 @@ skos:altLabel "organ", "tissue" ; skos:exactMatch , - , - , - , - , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - ; + skos:narrowMatch , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "FAO", @@ -4325,21 +4303,15 @@ linkml:slot_usage [ ] . a linkml:ClassDefinition ; - skos:broadMatch , - , - , - , - , - ; + skos:broadMatch , + , + ; skos:definition "a fact or situation that is observed to exist or happen, especially one whose cause or explanation is in question" ; skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - ; + skos:narrowMatch , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -4388,18 +4360,13 @@ a linkml:ClassDefinition ; skos:altLabel "physiology" ; - skos:exactMatch , - , + skos:exactMatch , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "GO", @@ -4612,8 +4579,7 @@ a linkml:ClassDefinition ; skos:inScheme ; skos:relatedMatch , - , - ; + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -5013,15 +4979,11 @@ a linkml:ClassDefinition ; skos:exactMatch , - , - ; - skos:inScheme ; - skos:narrowMatch , - , - , - , - , - ; + ; + skos:inScheme ; + skos:narrowMatch , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -5188,15 +5150,11 @@ a linkml:ClassDefinition ; skos:definition "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -5453,10 +5411,8 @@ skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; skos:inScheme ; skos:narrowMatch , - , - , - , - ; + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "ENSEMBL", @@ -5484,14 +5440,10 @@ skos:definition "A series of actions conducted in a certain order or manner" ; skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -6824,12 +6776,13 @@ . a linkml:ClassDefinition ; + skos:altLabel "cell component", + "cell part" ; skos:broadMatch ; skos:definition "A location in or around a cell" ; skos:exactMatch , , - , - , + , ; skos:inScheme ; linkml:class_uri ; @@ -7036,8 +6989,7 @@ a linkml:ClassDefinition ; skos:definition "describes a characteristic of an organismal entity." ; - skos:exactMatch , - ; + skos:exactMatch ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -7632,6 +7584,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7678,6 +7631,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7698,6 +7652,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7717,6 +7672,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7735,6 +7691,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7753,6 +7710,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7771,6 +7729,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7788,6 +7747,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7838,6 +7798,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7857,6 +7818,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7877,6 +7839,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7896,6 +7859,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7915,6 +7879,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7933,6 +7898,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7952,6 +7918,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7970,6 +7937,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -7989,6 +7957,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8129,11 +8098,11 @@ linkml:inherited true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "negatively regulates" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "activity directly negatively regulates activity of" ; - linkml:local_name_source "ro" ] ; + linkml:local_name_source "ro" ], + [ a linkml:LocalName ; + skos:altLabel "negatively regulates" ; + linkml:local_name_source "translator" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -8171,11 +8140,11 @@ linkml:inherited true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "activity directly positively regulates activity of" ; - linkml:local_name_source "ro" ], - [ a linkml:LocalName ; skos:altLabel "positively regulates" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "activity directly positively regulates activity of" ; + linkml:local_name_source "ro" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -8769,6 +8738,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8805,6 +8775,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8831,6 +8802,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8848,6 +8820,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8866,6 +8839,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8884,6 +8858,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8903,6 +8878,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8920,6 +8896,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8971,6 +8948,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -8990,6 +8968,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9008,6 +8987,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9027,6 +9007,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9046,6 +9027,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9065,6 +9047,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9083,6 +9066,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9103,6 +9087,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -9122,6 +9107,7 @@ linkml:domain ; linkml:inherited true ; linkml:is_a ; + linkml:mixins ; linkml:multivalued true ; linkml:owner ; linkml:range ; @@ -10931,8 +10917,7 @@ skos:altLabel "organism" ; skos:definition "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; skos:exactMatch , - , - ; + ; skos:inScheme ; skos:narrowMatch , ; @@ -11071,11 +11056,9 @@ a linkml:ClassDefinition ; skos:definition "An entity that has material reality (a.k.a. physical essence)." ; - skos:exactMatch , - ; + skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - ; + skos:narrowMatch ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -11114,10 +11097,8 @@ , ; skos:inScheme ; - skos:narrowMatch , - , - , - ; + skos:narrowMatch , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "ENSEMBL", @@ -11181,7 +11162,7 @@ skos:altLabel "chemical substance" ; skos:definition "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; skos:inScheme ; - skos:narrowMatch ; + skos:narrowMatch ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "Aeolus", @@ -12048,8 +12029,7 @@ a linkml:ClassDefinition ; skos:definition "Attributes relating to a clinical manifestation" ; - skos:exactMatch , - ; + skos:exactMatch ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -12318,11 +12298,11 @@ linkml:inherited true ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "regulates" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "activity directly regulates activity of" ; - linkml:local_name_source "ro" ] ; + linkml:local_name_source "ro" ], + [ a linkml:LocalName ; + skos:altLabel "regulates" ; + linkml:local_name_source "translator" ] ; linkml:mixins ; linkml:multivalued true ; linkml:owner ; @@ -12578,27 +12558,18 @@ , , , - , + , , - , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + , + , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "DOID", @@ -12731,9 +12702,8 @@ a linkml:ClassDefinition ; skos:definition "a location that can be described in lat/long coordinates" ; - skos:exactMatch , - , - ; + skos:exactMatch , + ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -12790,8 +12760,7 @@ skos:exactMatch , , , - , - ; + ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -13441,8 +13410,7 @@ , ; skos:inScheme ; - skos:narrowMatch , - , + skos:narrowMatch , , ; linkml:class_uri ; @@ -15080,16 +15048,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t . a linkml:ClassDefinition ; - skos:broadMatch , - ; + skos:broadMatch ; skos:definition "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; skos:exactMatch , - , - , + , ; skos:inScheme ; - skos:narrowMatch , - ; + skos:narrowMatch ; skos:note "The CHEBI ID represents a role rather than a substance" ; linkml:class_uri ; linkml:definition_uri ; @@ -15147,7 +15112,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t OIO:inSubset ; skos:inScheme ; skos:narrowMatch , - ; + ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -15482,8 +15447,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t "reaction" ; skos:definition "An execution of a molecular function carried out by a gene product or macromolecular complex." ; skos:exactMatch , - , - ; + ; skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; @@ -15702,17 +15666,10 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t OIO:inSubset ; skos:definition "A subcellular location, cell type or gross anatomical part" ; skos:exactMatch , + , , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "CL", @@ -15740,8 +15697,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:altLabel "bioentity" ; skos:inScheme ; skos:narrowMatch , - , - , + , ; linkml:abstract true ; linkml:class_uri ; @@ -15966,17 +15922,12 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:exactMatch , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + , + , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "GSID", @@ -16004,36 +15955,9 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:altLabel "taxon", "taxonomic classification" ; skos:definition "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; - skos:exactMatch ; - skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - ; + skos:exactMatch , + ; + skos:inScheme ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "MESH", @@ -16053,6 +15977,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t ; linkml:values_from . + a linkml:SlotDefinition ; + skos:definition "A grouping mixin to help with searching for all the predicates that decrease the amount or activity of the object." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:inherited true ; + linkml:is_a ; + linkml:mixin true ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:SlotDefinition ; skos:definition "connects a genomic feature to its sequence" ; skos:inScheme ; @@ -16064,6 +16001,19 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:range ; linkml:slot_uri . + a linkml:SlotDefinition ; + skos:definition "A grouping mixin to help with searching for all the predicates that increase the amount or activity of the object." ; + skos:inScheme ; + linkml:definition_uri ; + linkml:domain ; + linkml:inherited true ; + linkml:is_a ; + linkml:mixin true ; + linkml:multivalued true ; + linkml:owner ; + linkml:range ; + linkml:slot_uri . + a linkml:ClassDefinition ; OIO:inSubset ; skos:altLabel "experimental condition", @@ -16164,8 +16114,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:altLabel "phenome" ; skos:definition "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate." ; skos:inScheme ; - skos:narrowMatch , - ; + skos:narrowMatch ; linkml:class_uri ; linkml:definition_uri ; linkml:is_a ; @@ -16212,29 +16161,18 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:definition "a piece of information that typically describes some topic of discourse or is used as support." ; skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - , - ; + skos:narrowMatch , + , + , + , + , + , + , + , + , + , + , + ; linkml:abstract true ; linkml:class_uri ; linkml:definition_uri ; @@ -16325,8 +16263,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t OIO:inSubset ; skos:definition "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; skos:inScheme ; - skos:narrowMatch , - ; + skos:narrowMatch , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "Aeolus", @@ -16373,8 +16311,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:definition "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; skos:exactMatch ; skos:inScheme ; - skos:narrowMatch , - ; + skos:narrowMatch , + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "Aeolus", @@ -16498,11 +16436,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:inScheme ; skos:note "This class is for modeling the specific state at a locus. A single DBSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)" ; linkml:alt_descriptions [ a linkml:AltDescription ; - skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; - linkml:source "AGR" ], - [ a linkml:AltDescription ; skos:definition "A contiguous change at a Location" ; - linkml:source "VMC" ] ; + linkml:source "VMC" ], + [ a linkml:AltDescription ; + skos:definition "An entity that describes a single affected, endogenous allele. These can be of any type that matches that definition" ; + linkml:source "AGR" ] ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "CAID", @@ -16601,8 +16539,7 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t skos:exactMatch ; skos:inScheme ; skos:narrowMatch , - , - ; + ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "NLMID" ; @@ -16978,11 +16915,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "predicate" ; - linkml:local_name_source "translator" ] ; + linkml:local_name_source "translator" ], + [ a linkml:LocalName ; + skos:altLabel "annotation predicate" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -17089,11 +17026,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "descriptor" ; - linkml:local_name_source "ga4gh" ], - [ a linkml:LocalName ; skos:altLabel "node with incoming relationship" ; - linkml:local_name_source "neo4j" ] ; + linkml:local_name_source "neo4j" ], + [ a linkml:LocalName ; + skos:altLabel "descriptor" ; + linkml:local_name_source "ga4gh" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -17199,11 +17136,11 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t linkml:domain_of ; linkml:is_a ; linkml:local_names [ a linkml:LocalName ; - skos:altLabel "node with outgoing relationship" ; - linkml:local_name_source "neo4j" ], - [ a linkml:LocalName ; skos:altLabel "annotation subject" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "node with outgoing relationship" ; + linkml:local_name_source "neo4j" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -17217,9 +17154,8 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t a linkml:ClassDefinition ; skos:definition "a databased entity or concept/class" ; skos:exactMatch , - , + , , - , ; skos:inScheme ; linkml:class_uri ; @@ -17238,22 +17174,13 @@ In an RDF database, nodes will typically have an rdf:type triples. This can be t a linkml:ClassDefinition ; OIO:inSubset ; - skos:broadMatch ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; skos:exactMatch , , + , ; skos:inScheme ; - skos:narrowMatch , - , - , - , - , - , - , - , - , - ; + skos:narrowMatch ; linkml:class_uri ; linkml:definition_uri ; linkml:id_prefixes "CAS", diff --git a/biolink/model.py b/biolink/model.py index a21fd5a69f..441bf18855 100644 --- a/biolink/model.py +++ b/biolink/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0 -# Generation date: 2021-08-04 17:31 +# Generation date: 2021-08-16 16:49 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -178,6 +178,7 @@ SNOMEDCT = CurieNamespace('SNOMEDCT', 'http://identifiers.org/snomedct/') SNPEFF = CurieNamespace('SNPEFF', 'http://translator.ncats.nih.gov/SNPEFF_') SO = CurieNamespace('SO', 'http://purl.obolibrary.org/obo/SO_') +STY = CurieNamespace('STY', 'http://purl.bioontology.org/ontology/STY/') SUPFAM = CurieNamespace('SUPFAM', 'http://identifiers.org/supfam/') SCOPUSID = CurieNamespace('ScopusID', 'https://www.scopus.com/authid/detail.uri?authorId=') TAXRANK = CurieNamespace('TAXRANK', 'http://purl.obolibrary.org/obo/TAXRANK_') @@ -187,9 +188,7 @@ UBERON = CurieNamespace('UBERON', 'http://purl.obolibrary.org/obo/UBERON_') UBERON_CORE = CurieNamespace('UBERON_CORE', 'http://purl.obolibrary.org/obo/uberon/core#') UMLS = CurieNamespace('UMLS', 'http://identifiers.org/umls/') -UMLSSC = CurieNamespace('UMLSSC', 'http://purl.bioontology.org/ontology/STY/') UMLSSG = CurieNamespace('UMLSSG', 'https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#') -UMLSST = CurieNamespace('UMLSST', 'https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/type#') UNII = CurieNamespace('UNII', 'http://identifiers.org/unii/') UNIPROT_ISOFORM = CurieNamespace('UNIPROT_ISOFORM', 'http://identifiers.org/uniprot.isoform/') UO = CurieNamespace('UO', 'http://purl.obolibrary.org/obo/UO_') @@ -8384,6 +8383,12 @@ class slots: slots.affected_by = Slot(uri=BIOLINK.affected_by, name="affected by", curie=BIOLINK.curie('affected_by'), model_uri=BIOLINK.affected_by, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) +slots.increases_amount_or_activity_of = Slot(uri=BIOLINK.increases_amount_or_activity_of, name="increases amount or activity of", curie=BIOLINK.curie('increases_amount_or_activity_of'), + model_uri=BIOLINK.increases_amount_or_activity_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) + +slots.decreases_amount_or_activity_of = Slot(uri=BIOLINK.decreases_amount_or_activity_of, name="decreases amount or activity of", curie=BIOLINK.curie('decreases_amount_or_activity_of'), + model_uri=BIOLINK.decreases_amount_or_activity_of, domain=NamedThing, range=Optional[Union[Union[str, NamedThingId], List[Union[str, NamedThingId]]]]) + slots.chemical_role_mixin = Slot(uri=BIOLINK.chemical_role_mixin, name="chemical role mixin", curie=BIOLINK.curie('chemical_role_mixin'), model_uri=BIOLINK.chemical_role_mixin, domain=None, range=Optional[str]) diff --git a/context.jsonld b/context.jsonld index 083aebaabe..2006704629 100644 --- a/context.jsonld +++ b/context.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-08-04 17:31\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-08-16 16:48\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -401,6 +401,7 @@ "@id": "http://purl.obolibrary.org/obo/STATO_", "@prefix": true }, + "STY": "http://purl.bioontology.org/ontology/STY/", "SUPFAM": "http://identifiers.org/supfam/", "ScopusID": { "@id": "https://www.scopus.com/authid/detail.uri?authorId=", @@ -419,9 +420,7 @@ }, "UBERON_CORE": "http://purl.obolibrary.org/obo/uberon/core#", "UMLS": "http://identifiers.org/umls/", - "UMLSSC": "http://purl.bioontology.org/ontology/STY/", "UMLSSG": "https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#", - "UMLSST": "https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/type#", "UNII": "http://identifiers.org/unii/", "UNIPROT.ISOFORM": "http://identifiers.org/uniprot.isoform/", "UPHENO": { @@ -763,6 +762,9 @@ "decreases_activity_of": { "@type": "@id" }, + "decreases_amount_or_activity_of": { + "@type": "@id" + }, "decreases_degradation_of": { "@type": "@id" }, @@ -1165,6 +1167,9 @@ "increases_activity_of": { "@type": "@id" }, + "increases_amount_or_activity_of": { + "@type": "@id" + }, "increases_degradation_of": { "@type": "@id" }, diff --git a/contextn.jsonld b/contextn.jsonld index daee9a9544..933a5d34a2 100644 --- a/contextn.jsonld +++ b/contextn.jsonld @@ -1,5 +1,5 @@ { - "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-08-04 17:31\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-08-16 16:48\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "APO": { "@id": "http://purl.obolibrary.org/obo/APO_", @@ -401,6 +401,7 @@ "@id": "http://purl.obolibrary.org/obo/STATO_", "@prefix": true }, + "STY": "http://purl.bioontology.org/ontology/STY/", "SUPFAM": "http://identifiers.org/supfam/", "ScopusID": { "@id": "https://www.scopus.com/authid/detail.uri?authorId=", @@ -419,9 +420,7 @@ }, "UBERON_CORE": "http://purl.obolibrary.org/obo/uberon/core#", "UMLS": "http://identifiers.org/umls/", - "UMLSSC": "http://purl.bioontology.org/ontology/STY/", "UMLSSG": "https://metamap.nlm.nih.gov/Docs/SemGroups_2018.txt/group#", - "UMLSST": "https://metamap.nlm.nih.gov/Docs/SemanticTypes_2018AB.txt/type#", "UNII": "http://identifiers.org/unii/", "UNIPROT.ISOFORM": "http://identifiers.org/uniprot.isoform/", "UPHENO": { @@ -760,6 +759,9 @@ "decreases_activity_of": { "@type": "@id" }, + "decreases_amount_or_activity_of": { + "@type": "@id" + }, "decreases_degradation_of": { "@type": "@id" }, @@ -1154,6 +1156,9 @@ "increases_activity_of": { "@type": "@id" }, + "increases_amount_or_activity_of": { + "@type": "@id" + }, "increases_degradation_of": { "@type": "@id" },