From d4ded5c7fb5fdf69c03f9cbc81e7a542d31519b0 Mon Sep 17 00:00:00 2001 From: Deepak Unni Date: Mon, 2 Aug 2021 17:30:03 +0000 Subject: [PATCH] Regenerate artifacts from biolink-model.yaml --- biolink-model.owl.ttl | 802 +++++++++++++++++++++--------------------- biolink-model.ttl | 422 +++++++++++----------- biolink/model.py | 2 +- context.jsonld | 2 +- contextn.jsonld | 2 +- 5 files changed, 615 insertions(+), 615 deletions(-) diff --git a/biolink-model.owl.ttl b/biolink-model.owl.ttl index e9619635f7..5c0d33cfd5 100644 --- a/biolink-model.owl.ttl +++ b/biolink-model.owl.ttl @@ -11,10 +11,10 @@ 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 "2021-08-02 17:09" ; + linkml:generation_date "2021-08-02 17:28" ; linkml:metamodel_version "1.7.0" ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Mon Aug 2 17:08:22 2021" ; + linkml:source_file_date "Mon Aug 2 17:26:25 2021" ; linkml:source_file_size 315210 . a owl:Class, @@ -74,14 +74,6 @@ 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 ], @@ -89,6 +81,14 @@ 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 ], , , ; @@ -169,13 +169,13 @@ 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 ; @@ -256,13 +256,13 @@ 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 ], , , ; @@ -304,12 +304,12 @@ linkml:ClassDefinition ; rdfs:label "genome" ; 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 ], , , , @@ -324,18 +324,18 @@ rdfs:label "genomic background exposure" ; rdfs:subClassOf [ 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:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , , @@ -610,12 +610,12 @@ linkml:ClassDefinition ; rdfs:label "reagent targeted gene" ; 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 ], , , , @@ -2539,14 +2539,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, 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:qualifiedCardinality 1 ], , , . @@ -2729,22 +2729,22 @@ 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 ; - 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 ], , ; skos:definition "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." . @@ -2756,14 +2756,14 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Double ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; @@ -2786,34 +2786,34 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene has variant that contributes to 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 ], . a owl:Class, 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: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 ; @@ -2836,25 +2836,25 @@ 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 ], + 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 ], + [ 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 ], , , ; @@ -2877,11 +2877,11 @@ 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 , @@ -2937,6 +2937,10 @@ 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:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -2948,10 +2952,6 @@ 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 ], , , . @@ -3004,16 +3004,16 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, a owl:Class, linkml:ClassDefinition ; rdfs:label "socioeconomic exposure" ; - rdfs:subClassOf [ a owl:Class ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], + [ a owl:Class ; owl:intersectionOf ( [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ] [ a owl:Restriction ; owl:onProperty ; owl:someValuesFrom ] ) ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." . @@ -3051,14 +3051,6 @@ linkml:variant_to_population_association_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "variant to gene expression 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 ], @@ -3070,6 +3062,14 @@ 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 ], , ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" . @@ -3078,25 +3078,25 @@ 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: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 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , . @@ -5259,11 +5259,7 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:onProperty ], [ a owl:Restriction ; owl:onClass linkml:Uriorcurie ; owl:onProperty ; @@ -5271,7 +5267,11 @@ 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 ], . a owl:Class, @@ -5295,28 +5295,28 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:label "behavior to behavioral feature 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: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:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + 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." . @@ -5333,11 +5333,11 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass linkml:String ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." . @@ -5346,13 +5346,13 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "book chapter" ; rdfs:subClassOf [ 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:Restriction ; + owl:onClass linkml:Uriorcurie ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -5494,13 +5494,13 @@ 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" . @@ -5533,13 +5533,13 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to go term 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:altLabel "functional association" ; skos:exactMatch . @@ -5551,14 +5551,18 @@ linkml:variant_to_gene_association_predicate 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 ], [ 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 ; @@ -5567,10 +5571,6 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], , , ; @@ -5652,33 +5652,33 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; + owl:onClass linkml:Integer ; + 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 linkml:Integer ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], . a owl:Class, 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" . @@ -5687,25 +5687,25 @@ 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 ], - [ 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 ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + 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 +5733,18 @@ linkml:variant_to_gene_association_predicate a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; 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 ], , , ; @@ -6053,7 +6053,7 @@ 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 +6061,7 @@ 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." . @@ -6134,11 +6134,11 @@ 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 +6155,10 @@ 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 +6170,6 @@ 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." . @@ -6189,14 +6189,14 @@ 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 "A regulatory relationship between two genes" . @@ -6204,14 +6204,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene 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:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -6219,6 +6211,14 @@ linkml:publication_type 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 ], , , ; @@ -6238,10 +6238,6 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6249,6 +6245,10 @@ 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 gene is transcribed and potentially translated to a gene product" . @@ -6265,13 +6265,13 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "genotype 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 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -6286,14 +6286,14 @@ 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 one genotype and a genotypic entity that is a sub-component of it" . @@ -6301,13 +6301,13 @@ 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 ; @@ -6365,6 +6365,10 @@ 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:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6372,10 +6376,6 @@ linkml:publication_type a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], , . @@ -6401,30 +6401,30 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organism to organism association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + 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 ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], . 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 +6446,10 @@ 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 +6457,6 @@ 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" . @@ -6496,6 +6496,10 @@ linkml:publication_type a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -6503,10 +6507,6 @@ linkml:publication_type a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], . a owl:Class, @@ -6520,13 +6520,13 @@ 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)" . @@ -6784,6 +6784,10 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], @@ -6791,10 +6795,6 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - 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: IF @@ -6809,19 +6809,19 @@ 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:allValuesFrom ; - owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; + 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" . @@ -6833,14 +6833,14 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; 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 ], ; skos:definition "an item that holds version level information about a dataset." . @@ -6848,38 +6848,38 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + 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 linkml:String ; - owl:onProperty ], + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:allValuesFrom ; + owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ] ; + owl:onClass ; + owl:onProperty ] ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." . a owl:Class, @@ -6903,7 +6903,7 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, rdfs:label "genotype to disease association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; @@ -6911,16 +6911,16 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, 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 ; @@ -6964,11 +6964,11 @@ 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 ], , ; @@ -6978,9 +6978,9 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -6990,9 +6990,9 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], ; 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" . @@ -7011,13 +7011,13 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Double ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty ], ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" . @@ -7025,28 +7025,28 @@ linkml:sequence_feature_relationship_subject a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "variant to disease 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: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 ], - [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], , , @@ -7203,6 +7203,10 @@ linkml:functional_association_object a owl:ObjectProperty, rdfs:label "gene to expression site association" ; rdfs:seeAlso "https://github.com/monarch-initiative/ingest-artifacts/tree/master/sources/BGee" ; rdfs:subClassOf [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], @@ -7210,18 +7214,14 @@ linkml:functional_association_object a owl:ObjectProperty, 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 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + 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 +7231,11 @@ 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" ; @@ -7268,13 +7268,9 @@ linkml:functional_association_object a owl:ObjectProperty, linkml:ClassDefinition ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -7288,9 +7284,13 @@ linkml:functional_association_object a owl:ObjectProperty, owl:onProperty ; owl:qualifiedCardinality 1 ], [ 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 linkml:String ; + owl:onProperty ], ; skos:definition "An interaction at the molecular level between two physical entities" . @@ -7299,11 +7299,11 @@ 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" ; @@ -7326,13 +7326,9 @@ linkml:functional_association_object a owl:ObjectProperty, owl:onClass linkml:Double ; owl:onProperty ], [ 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:onClass ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:onClass ; owl:onProperty ; @@ -7341,14 +7337,18 @@ linkml:functional_association_object a owl:ObjectProperty, owl:maxQualifiedCardinality 1 ; owl:onClass linkml:Integer ; 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:Integer ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Double ; + owl:onProperty ], , , , @@ -7617,13 +7617,13 @@ linkml:Boolean 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." . @@ -7727,13 +7727,13 @@ 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" . @@ -7755,12 +7755,12 @@ linkml:Float 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 ], , , ; @@ -7821,10 +7821,6 @@ linkml:Float a owl:Class, linkml:ClassDefinition ; rdfs:label "entity to phenotypic feature association mixin" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], @@ -7832,6 +7828,10 @@ linkml:Float a owl:Class, owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , linkml:mixin . @@ -7940,14 +7940,14 @@ linkml:Double a owl:Class, 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:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], + [ a owl:Restriction ; + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty ], @@ -7972,11 +7972,11 @@ linkml:Double a owl:Class, linkml:ClassDefinition ; rdfs:label "biological process or 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 ], @@ -8006,25 +8006,17 @@ linkml:Double a owl:Class, linkml:ClassDefinition ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Integer ; - 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 linkml:Integer ; - owl:onProperty ], + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; @@ -8034,9 +8026,17 @@ linkml:Double a owl:Class, owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + owl:onProperty ], + [ a owl:Restriction ; + owl:onClass ; + owl:onProperty ; owl:qualifiedCardinality 1 ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Integer ; + 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." . @@ -8083,24 +8083,24 @@ linkml:Uriorcurie a owl:Class, linkml:ClassDefinition ; rdfs:label "attribute" ; rdfs:subClassOf [ 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:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + 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:maxQualifiedCardinality 1 ; owl:onClass ; @@ -8220,14 +8220,14 @@ linkml:topValue a owl:DatatypeProperty ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Date ; - owl:onProperty ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Date ; + owl:onProperty ], ; skos:altLabel "information", "information artefact", @@ -8302,12 +8302,12 @@ linkml:Integer a owl:Class, linkml:ClassDefinition ; rdfs:label "publication" ; rdfs:subClassOf [ 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 ], [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8317,21 +8317,21 @@ linkml:Integer a owl:Class, owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:allValuesFrom linkml:String ; - owl:onProperty ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:String ; owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom linkml:Uriorcurie ; owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass ; - owl:onProperty ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom linkml:String ; + 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 ; @@ -8394,19 +8394,19 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onClass linkml:String ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:onClass linkml:String ; + owl:onProperty ; + owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], , , , @@ -8461,12 +8461,11 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "gene" ; rdfs:subClassOf [ a owl:Restriction ; - 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:maxQualifiedCardinality 1 ; owl:onClass linkml:String ; @@ -8475,8 +8474,9 @@ linkml:TypeDefinition a owl:Class ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], + owl:maxQualifiedCardinality 1 ; + owl:onClass ; + owl:onProperty ], , , , @@ -8493,12 +8493,12 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "organism taxon" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; owl:maxQualifiedCardinality 1 ; owl:onClass ; owl:onProperty linkml:has_taxonomic_rank ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty ], ; skos:altLabel "taxon", "taxonomic classification" ; @@ -8603,38 +8603,38 @@ linkml:TypeDefinition a owl:Class ; linkml:ClassDefinition ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:String ; - owl:onProperty ], - [ a owl:Restriction ; owl:onClass ; - owl:onProperty ; + owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; owl:allValuesFrom ; owl:onProperty ], [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty ], - [ a owl:Restriction ; - owl:maxQualifiedCardinality 1 ; - owl:onClass linkml:Boolean ; - 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:onClass ; owl:onProperty ; owl:qualifiedCardinality 1 ], [ a owl:Restriction ; - owl:onClass ; - owl:onProperty ; - owl:qualifiedCardinality 1 ], + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:String ; + owl:onProperty ], + [ a owl:Restriction ; + owl:maxQualifiedCardinality 1 ; + owl:onClass linkml:Boolean ; + owl:onProperty ], ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch , @@ -8663,12 +8663,12 @@ 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 ], , , , diff --git a/biolink-model.ttl b/biolink-model.ttl index 56d348c3b2..bc06b2a065 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 "2.2.0" ; + pav:version "2.2.1" ; skos:definition "Entity and association taxonomy and datamodel for life-sciences data" ; linkml:classes , , @@ -293,218 +293,218 @@ , , ; - linkml:generation_date "2021-08-02 17:10"^^xsd:dateTime ; + linkml:generation_date "2021-08-02 17:28"^^xsd:dateTime ; linkml:id ; linkml:imports linkml:types ; linkml:metamodel_version "1.7.0" ; - linkml:prefixes [ linkml:prefix_prefix "os" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.RCLASS" ; + linkml:prefixes [ linkml:prefix_prefix "KEGG.RCLASS" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SNPEFF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EFO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "issn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "prov" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "isbn" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "wgs" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "INO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "REPODB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UBERGRAPH" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Xenbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NDDF" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "HsapDv" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "LOINC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dcat" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "dct" ; - linkml:prefix_reference dcterms: ], - [ linkml:prefix_prefix "gtpo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.DGROUP" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gpi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "RTXKG1" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PathWhiz" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PANTHER.FAMILY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "mirbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.BRITE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NLMID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "SEMMEDDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MAXO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "alliancegenome" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "oboformat" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GOP" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "PATO-PROPERTY" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.ENZYME" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "dcat" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "medgen" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "Aeolus" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VANDF" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PHAROS" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "XPO" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "HANCESTRO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GTOPDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "chembio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "interpro" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "apollo" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.ENZYME" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "isbn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DGIdb" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ECTO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-DATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "doi" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ChemBank" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-FORMAT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD9" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "COAR_RESOURCE" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UBERGRAPH" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "gff3" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "pav" ; - linkml:prefix_reference pav: ], - [ linkml:prefix_prefix "isni" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-TOPIC" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "PDQ" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ICD10" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GSID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "MI" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "OBOREL" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "GOP" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "CHADO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "UMLSSG" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UBERON_CORE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "qud" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NCBIGene" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "VMC" ; - linkml:prefix_reference ], [ linkml:prefix_prefix "GTEx" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "OBAN" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VMC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-OPERATION" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "GOREL" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "WBVocab" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "issn" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CAID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ScopusID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORCID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CTD" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD10" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MAXO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "linkml" ; + linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "UMLSSC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "qud" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SNPEFF" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GTOPDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "RXCUI" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "alliancegenome" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "CPT" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "REPODB" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "PDQ" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CTD" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "ICD0" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ExO" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "WBVocab" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "RXNORM" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "OBAN" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "UMLSSG" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "SEMMEDDB" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NCBIGene" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "NLMID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "mirbase" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "VANDF" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "MetaCyc" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "MSigDB" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "HCPCS" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "EDAM-OPERATION" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "INO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ResearchID" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "Xenbase" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "WIKIDATA_PROPERTY" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "schema" ; - linkml:prefix_reference schema: ], - [ linkml:prefix_prefix "linkml" ; - linkml:prefix_reference linkml: ], + [ linkml:prefix_prefix "gtpo" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "foodb.compound" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "fabio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CPT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PHAROS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GAMMA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORPHA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DrugCentral" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-TOPIC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "apollo" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "hetio" ; linkml:prefix_reference ], + [ linkml:prefix_prefix "OBOREL" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "interpro" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "UMLSST" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "CHADO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "fabio" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "NDDF" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "isni" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gff3" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "COG" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "KEGG.GENE" ; + [ linkml:prefix_prefix "os" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "Aeolus" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PANTHER.FAMILY" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.BRITE" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "SIO" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "prov" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "ORPHA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "foodb.compound" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "ResearchID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ChemBank" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "GSID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "gpi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ICD9" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CAID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MSigDB" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "biolink" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "GAMMA" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "DrugCentral" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "wgs" ; - linkml:prefix_reference ], - [ linkml:prefix_prefix "oboformat" ; - linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-FORMAT" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HCPCS" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EDAM-DATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "DGIdb" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ECTO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "MI" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "chembio" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "HANCESTRO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "LOINC" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "COAR_RESOURCE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "RTXKG1" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "CHEMBL.MECHANISM" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "EFO" ; + linkml:prefix_reference ], [ linkml:prefix_prefix "foaf" ; linkml:prefix_reference ], - [ linkml:prefix_prefix "RO" ; - linkml:prefix_reference ] ; + [ linkml:prefix_prefix "dct" ; + linkml:prefix_reference dcterms: ], + [ linkml:prefix_prefix "KEGG.GENE" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "PathWhiz" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ORCID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ScopusID" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "schema" ; + linkml:prefix_reference schema: ], + [ linkml:prefix_prefix "doi" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "KEGG.DGROUP" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "WIKIDATA" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "SIO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "ExO" ; + linkml:prefix_reference ], + [ linkml:prefix_prefix "pav" ; + linkml:prefix_reference pav: ] ; linkml:slots , , , @@ -1109,7 +1109,7 @@ , ; linkml:source_file "biolink-model.yaml" ; - linkml:source_file_date "Mon Aug 2 17:08:22 2021"^^xsd:dateTime ; + linkml:source_file_date "Mon Aug 2 17:26:25 2021"^^xsd:dateTime ; linkml:source_file_size 315210 ; linkml:subsets , , @@ -1769,11 +1769,11 @@ 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 ; @@ -1880,11 +1880,11 @@ 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 ; @@ -1943,12 +1943,12 @@ linkml:examples [ a linkml:Example ; skos:definition "axon morphology variant" ; skos:example "WBPhenotype:0000180" ], - [ a linkml:Example ; - skos:definition "abnormal circulating bilirubin level" ; - skos:example "MP:0001569" ], [ a linkml:Example ; skos:definition "Hyperkinesis" ; - skos:example "HP:0002487" ] ; + skos:example "HP:0002487" ], + [ a linkml:Example ; + skos:definition "abnormal circulating bilirubin level" ; + skos:example "MP:0001569" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -3351,11 +3351,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" ; - skos:example "ClinVar:38077" ], - [ a linkml:Example ; skos:definition "chr13:g.32921033G>C (hg19) in ClinGen" ; - skos:example "ClinGen:CA024716" ] ; + skos:example "ClinGen:CA024716" ], + [ a linkml:Example ; + skos:definition "ClinVar representation of NM_000059.3(BRCA2):c.7007G>A (p.Arg2336His)" ; + skos:example "ClinVar:38077" ] ; linkml:is_a ; linkml:is_usage_slot true ; linkml:owner ; @@ -4859,11 +4859,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "ti282a allele from ZFIN" ; - skos:example "ZFIN:ZDB-ALT-980203-1091" ], - [ a linkml:Example ; skos:definition "NM_007294.3(BRCA1):c.2521C>T (p.Arg841Trp)" ; - skos:example "ClinVarVariant:17681" ] ; + skos:example "ClinVarVariant:17681" ], + [ a linkml:Example ; + skos:definition "ti282a allele from ZFIN" ; + skos:example "ZFIN:ZDB-ALT-980203-1091" ] ; linkml:identifier true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -11467,11 +11467,11 @@ linkml:domain ; linkml:domain_of ; linkml:examples [ a linkml:Example ; - skos:definition "postsynaptic membrane" ; - skos:example "GO:0045211" ], - [ a linkml:Example ; skos:definition "kinase activity" ; - skos:example "GO:0016301" ] ; + skos:example "GO:0016301" ], + [ a linkml:Example ; + skos:definition "postsynaptic membrane" ; + skos:example "GO:0045211" ] ; linkml:inlined true ; linkml:is_a ; linkml:is_usage_slot true ; @@ -12798,10 +12798,10 @@ linkml:is_a ; linkml:local_names [ a linkml:LocalName ; skos:altLabel "population" ; - linkml:local_name_source "ga4gh" ], + linkml:local_name_source "agr" ], [ a linkml:LocalName ; skos:altLabel "population" ; - linkml:local_name_source "agr" ] ; + linkml:local_name_source "ga4gh" ] ; linkml:mixins ; linkml:slot_usage [ ] ; linkml:slots , @@ -16977,11 +16977,11 @@ 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 "predicate" ; - linkml:local_name_source "translator" ], - [ a linkml:LocalName ; skos:altLabel "annotation predicate" ; - linkml:local_name_source "ga4gh" ] ; + linkml:local_name_source "ga4gh" ], + [ a linkml:LocalName ; + skos:altLabel "predicate" ; + linkml:local_name_source "translator" ] ; linkml:owner ; linkml:range ; linkml:required true ; @@ -17198,11 +17198,11 @@ 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 ; diff --git a/biolink/model.py b/biolink/model.py index ff6e530229..0c6302d015 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: 2021-08-02 17:10 +# Generation date: 2021-08-02 17:28 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model diff --git a/context.jsonld b/context.jsonld index 4f0e0541aa..4cad2f1f1b 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: 2021-08-02 17:09\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: 2021-08-02 17:28\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_", diff --git a/contextn.jsonld b/contextn.jsonld index 7d278e017b..a7b6ef793e 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: 2021-08-02 17:09\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: 2021-08-02 17:28\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_",