native Wikipathways schema (E86)
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| language code | label | description | aliases | edit |
|---|---|---|---|---|
| en | native Wikipathways schema | basic schema of a Pathway in Wikipathways as expressed on http://www.wikipathways.org | edit |
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms: <http://purl.org/dc/terms/>
prefix dc: <http://purl.org/dc/elements/1.1/>
prefix foaf: <http://xmlns.com/foaf/0.1/>
prefix pav: <http://purl.org/pav/>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
# original IRI
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
prefix wpInstance: <http://www.wikipathways.org/instance/>
PREFIX gpml: <http://vocabularies.wikipathways.org/gpml#>
PREFIX pubmed: <http://www.ncbi.nlm.nih.gov/pubmed/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX curationTag: <http://vocabularies.wikipathways.org/wp#Curation:>
# identifier.org based iris
PREFIX hmdbio: <http://identifiers.org/hmdb/>
PREFIX chebiio: <http://identifiers.org/chebi>
PREFIX wdio: <http://identifiers.org/wikidata/>
PREFIX uniprotio: <http://identifiers.org/uniprot/>
PREFIX pubmedio: <http://identifiers.org/pubmed/>
PREFIX wpio: <http://identifiers.org/wikipathways/>
PREFIX ncbigeneio: <http://identifiers.org/ncbigene/>
PREFIX ensemblio: <http://identifiers.org/ensembl/>
PREFIX uniprotio: <http://identifiers.org/uniprot/>
PREFIX chemspiderio: <http://identifiers.org/chemspider/>
PREFIX pubchemio: <http://identifiers.org/pubchem/>
# Wikidata
PREFIX wd: <http://www.wikidata.org/entity/>
start = @<#Pathway>
<#Pathway> {
pav:hasVersion @<#PathwayVersion> ;
}
<#PathwayVersion> {
rdf:type wp:Pathway AND skos:Collection ;
dcterms:description LITERAL ;
dc:identifier [wpio:~] ;
dcterms:identifier xsd:string ;
dc:source xsd:string ;
dc:title LITERAL ;
dcterms:reference [pubmedio:~]* ;
wp:isAbout wp:Pathway ;
wp:ontologyTag [obo:~]* ;
wp:ontologyTag [curationTag:~]+ ;
wp:organism [obo:~] ;
wp:organismName xsd:string ;
wp:pathwayOntologyTag [obo:~]* ;
foaf:page [wpInstance:~] ;
}
<#PathwayPart> {
dcterms:isPartOf @<#PathwayVersion> ;
}
<#Interaction> {
rdf:type wp:Interaction ;
dcterms:isPartOf @<#PathwayVersion> ;
wp:isAbout wp:Interaction ;
wp:participants @<#PathwayPart>+ ;
}
<#datanode> [
<#geneproduct>
<#metabolite>
]
<#geneproduct> {
rdf:type wp:DataNode ;
rdf:type wp:GeneProduct ;
rdfs:label xsd:string ;
dc:identifier [ncbigeneio:~] ;
dcterms:identifier xsd:string ;
wp:bdbEnsembl [ensemblio:~] ;
wp:bdbEntrezGene [ncbigeneio:~] ;
wp:bdbUniprot [uniprotio:~]* ;
wp:isAbout IRI ; # Needs to be more specific.
}
<#metabolite> {
rdf:type wp:DataNode ;
rdf:type wp:Metabolite ;
rdfs:label xsd:string ;
dc:identifier [hmdbio:~ chebiio:~ wdio:~] ;
dc:source xsd:string ;
dcterms:identifier xsd:string ;
dcterms:isPartOf @<#PathwayVersion> ;
dcterms:isPartOf @<#interaction> ;
wp:bdbChEBI [chebiio:~]* ;
wp:bdbChemspider [chemspiderio:~]* ;
wp:bdbHmdb [hmdbio:~]* ;
wp:bdbPubChem [pubchemio:~]* ;
wp:bdbWikidata [wdio:~]*;
wp:isAbout IRI ; # needs to be more specific (i.e. pointing to the GPML view)
}
<#interaction> {
rdf:type [wp:Interaction];
rdf:type @<#interactiontypes>* ;
dcterms:isPartOf @<#PathwayVersion> ;
wp:participants @<#datanode> ;
wp:participants @<#datanode>* ;
wp:source [wp:DataNode]* ;
wp:target [wp:DataNode]* ;
}
<#interactiontypes> [
wp:DirectedInteraction
wp:Catalysis
wp:Binding
wp:ComplexBinding
wp:Inhibition
wp:Stimulation
wp:TranscriptionTranslation
wp:Conversion
wp:Translocation
]
<#reference> {
rdf:type wp:PublicationReference ;
dcterms:isPartOf @<#PathwayVersion> ;
foaf:page [pubmed:~] ;
}