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Welcome to WikiProject Gene Wiki This page documents the Pathway bot, that it is maintained within the Wikiproject Gene Wiki. It is a WikiProject dedicated to make and maintiain Wikidata as a central hub of linked knowledge on Genes, Proteins, Diseases, Drugs, and related concepts.

WikiPathways

Wikipathways is an online open repository on biological pathways. Pathways from Wikipathways are regularly converted to a semantic web format (RDF) and made available through a SPARQL endpoint. Q26261238. Our bot synchronizes Wikidata with WIkipathways using the RDF output from WIkipathways.

Data model

Source in CMAP

Shape Expression

  # Shape Expression for Human genes in Wikidata 
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX prv: <http://www.wikidata.org/prop/reference/value/>
PREFIX pr:  <http://www.wikidata.org/prop/reference/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX schema: <http://schema.org/> 
PREFIX po: <http://purl.obolibrary.org/obo/PW>

start = @<wikidata-wp_pathway>

<wikidata-wp_pathway> {
   # Descriptors
   rdfs:label LITERAL+ ;
   schema:description LITERAL+ ;

    # Statements 
    p:P31 @<pathway_ontology_term> ; 	# instance of 
    p:P527 @<has_part>* ;		# has part  
    p:P2860 @<wikicite>* ;		# cites

    # Identifiers
    p:P2410 @<wikipathway-identifier> ;	# Wikipathways ID
}

<pathway_ontology_term>  {
       ps:P2888	[po:~] ;
       prov:wasDerivedFrom @<wikipathways-reference> ;  
}

<wikipathway-identifier>   {
       ps:P2410	 LITERAL /WP[0-9]+/	 ;
       prov:wasDerivedFrom @<wikipathways-reference> ;
}

<has_part> {
	ps:P527  @<gene_product> or @<protein> or @<metabolite> or @<wikidata-wp_pathway> ;
	prov:wasDerivedFrom @<wikipathways-reference> ;
}

<wikicite> {
    ps:P2860	@<pubmed_entry> ;
    prov:wasDerivedFrom	@<wikipathways-reference> ;
}

<wikipathways-reference> { # Wikipathways item in Wikidata
	pr:P248	wd:Q7999828 ;
	pr:P813 xsd:dateTime ;
	pr:P2410 LITERAL /WP[0-9]+/ ;
}

<gene_product> .
<protein> .
<metabolite> .

<pubmed_entry> {
	p:P698	{
		ps:P698 LITERAL /[0-9]+/ ;
	}
}

Reactome

Data model

Shape expression

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX pr: <http://www.wikidata.org/prop/reference/>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX wdref: <http://www.wikidata.org/reference/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX schema: <http://schema.org/> 
PREFIX po: <http://purl.obolibrary.org/obo/PW>
PREFIX go: <http://purl.obolibrary.org/obo/GO>
PREFIX prov: <http://www.w3.org/ns/prov#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

start = @<wikidata-reactome_pathway>

<wikidata-reactome_pathway> {
	# Descriptors
	rdfs:label LITERAL+ ;
	schema:description LITERAL+ ;

	# Statements
	p:P31 @<gene_ontology_term> ;
	p:P361 @<part_of>*	;			# part of
	p:P527 @<has_part>* ;				# has part 
	p:P2860 @<wikicite>* ;				# cites
	p:P703 @<found_in_taxon>	;		# species 

	# Identifiers
	p:P3937  @<reactome-identifier> ;

}

<gene_ontology_term>  {					#
       ps:P2888	[go:~] ;
       prov:wasDerivedFrom @<reactome-reference> ;  
	}

<part_of> {
	ps:P361  @<wikidata-reactome_pathway> ;
	prov:wasDerivedFrom @<reactome-reference> ;
}

<has_part> {
	ps:P527  @<wikidata-reactome_pathway> or @<protein> ;
	prov:wasDerivedFrom @<reactome-reference> ;
}

<protein> {
	p:P31	{
		ps:P31	[wd:Q8054] ;
	}
}

<wikicite> {
    ps:P2860	@<pubmed_entry> ;
    prov:wasDerivedFrom	@<reactome-reference> ;
}

<pubmed_entry> {
	p:P698	{
		ps:P698 LITERAL /[0-9]+/ ;
	}
}


<found_in_taxon> {
	ps:P703		<reactome_taxons> ;
	prov:wasDerivedFrom	@<reactome-reference> ;
}

<reactome_taxons> [
	wd:Q15978631 		# Homo sapiens
]

<reactome-identifier> {
	ps:P3937	LITERAL /R-[A-Z]{3}-[0-9]+/  ;
	prov:wasDerivedFrom	@<reactome-reference>
}

<reactome-reference> {		# Wikipathways item in Wikidata
	pr:P248	wd:Q2134522 ;
	pr:P813 xsd:dateTime ;
	pr:P3937 LITERAL /R-[A-Z]{3}-[0-9]+/ ;
}