From WikiPathways

Current revision

On http://sparql.wikipathways.org/ WikiPathways content is replicated in a SPARQL endpoint. Queries can be performed in three ways:

1. Either go to the endpoint directly and create your own SPARQL query.

2. Copy and paste an example query listed below in the endpoint.

3. Adapt a code examples to programmatically make a SPARQL query

This project is written up in the "Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources" paper.

NOTIFICATION: Due to an Apache update, we are now creating RDF data according to SPARQL 1.1. 

However, our SPARQL-endpoint running on Virtuoso is still using SPARQL 1.0. 

This influences the way to query strings, and might affect federated queries.

Please remove the ^^xsd:string suffix, as shown in the example below.

Resources

• WikiPathways internal vocabularies: http://vocabularies.wikipathways.org
• WikiPathways SPARQL endpoint https://sparql.wikipathways.org/sparql

• Identifiers.org: https://identifiers.org
• Searches prefixes: http://prefix.cc

Submit ideas

• submit your query
• submit ideas and suggestions

Prefixes

Within the example queries, we have omitted the prefixes. These prefixes are automatically used in the SPARQL endpoint. The following prefixes are used in the WikiPathways RDF:

PREFIX gpml:    <http://vocabularies.wikipathways.org/gpml#>
PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX cur:     <http://vocabularies.wikipathways.org/wp#Curation:>
PREFIX wprdf:   <http://rdf.wikipathways.org/>
PREFIX biopax:  <http://www.biopax.org/release/biopax-level3.owl#> 
PREFIX cas:     <https://identifiers.org/cas/>
PREFIX dc:      <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX foaf:    <http://xmlns.com/foaf/0.1/> 
PREFIX ncbigene:<https://identifiers.org/ncbigene/>
PREFIX pubmed:  <http://www.ncbi.nlm.nih.gov/pubmed/> 
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos:    <http://www.w3.org/2004/02/skos/core#>
PREFIX xsd:     <http://www.w3.org/2001/XMLSchema#> 

Example queries

Queries with a * require a bit more time for results.

Metadata queries

List the information about the data sets in the SPARQL endpoint:

select distinct ?dataset (str(?titleLit) as ?title) ?date ?license where {
  ?dataset a void:Dataset ;
    dcterms:title ?titleLit ;
    dcterms:license ?license ;
    pav:createdOn ?date .
}

Execute

Pathway oriented queries

Get the species currently in WikiPathways with their respective URI's

PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?organism (str(?label) as ?name)
WHERE {
    ?concept wp:organism ?organism ;
      wp:organismName ?label .
}

Execute

List pathways and their species

PREFIX dc:      <http://purl.org/dc/elements/1.1/> 
PREFIX wp:     <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT (str(?title) as ?pathway) (str(?label) as ?organism)
WHERE {
    ?pw dc:title ?title ;
      wp:organism ?organism ;
      wp:organismName ?label .
} 

Execute

List the species captured in WikiPathways and the number of pathways per species

PREFIX dc:      <http://purl.org/dc/elements/1.1/> 
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?organism (str(?label) as ?name) (count(?pw) as ?pathwayCount)
WHERE {
    ?pw dc:title ?title ;
      wp:organism ?organism ;
      wp:organismName ?label .
}
ORDER BY DESC(?pathwayCount)

Execute

List all pathways for species "Mus musculus"

The following query list all mouse pathways. ?wpIdentifier is the link through identifiers.org, ?pathway points to the RDF version of WikiPathways and ?page is the revision which is loaded in the SPARQL endpoint.

PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dc:      <http://purl.org/dc/elements/1.1/> 
PREFIX foaf:    <http://xmlns.com/foaf/0.1/> 
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>

SELECT DISTINCT ?wpIdentifier ?pathway ?page
WHERE {
    ?pathway dc:title ?title .
    ?pathway foaf:page ?page .
    ?pathway dc:identifier ?wpIdentifier .
    ?pathway wp:organismName "Mus musculus" .
 }
ORDER BY ?wpIdentifier

Execute Perl

Get all pathways with a particular gene

List all pathways per instance of a particular gene or protein (wp:GeneProduct)

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>

SELECT DISTINCT ?pathway (str(?label) as ?geneProduct)
WHERE {
    ?geneProduct a wp:GeneProduct . 
    ?geneProduct rdfs:label ?label .
    ?geneProduct dcterms:isPartOf ?pathway .
    ?pathway a wp:Pathway .
    
    FILTER regex(str(?label), "CYP"). 
}

Execute

Get all groups and complexes containing a particular gene

List all groups and complexes per instance of a particular gene or protein (wp:GeneProduct)

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>

SELECT DISTINCT ?pathway (str(?label) as ?geneProduct)
WHERE {
    ?geneProduct a wp:GeneProduct . 
    ?geneProduct rdfs:label ?label .
    ?geneProduct dcterms:isPartOf ?pathway .

    FILTER NOT EXISTS { ?pathway a wp:Interaction } .
    FILTER NOT EXISTS { ?pathway a wp:Pathway } .
    FILTER regex(str(?label), "CYP"). 
}

Execute

Get all the genes on a particular pathway

List all the genes and proteins (wp:GeneProduct) associated with a particular pathway WPID.

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>

select distinct ?pathway (str(?label) as ?geneProduct) where {
    ?geneProduct a wp:GeneProduct . 
    ?geneProduct rdfs:label ?label .
    ?geneProduct dcterms:isPartOf ?pathway .
    ?pathway a wp:Pathway .
    ?pathway dcterms:identifier "WP1560" . 
}

Execute

Count the number of pathways per ontology term

In WikiPathways, pathways can be tagged with ontology terms from Pathway, Cell Line and Disease ontology. The following query returns a pathway count for each term from any of the available ontologies. These terms are collectively modeled as wp:pathwayOntology; but this includes all ontologies, not just the "Pathway" ontology.

SELECT DISTINCT ?pwOntologyTerm count(?pwOntologyTerm) as ?pathwayCount
 WHERE {
	?pathwayRDF wp:ontologyTag ?pwOntologyTerm .
 }
 ORDER BY DESC(?pathwayCount)

Execute

Get all pathways with a particular ontology term

In WikiPathways, pathways can be tagged with ontology terms from Pathway, Cell Line and Disease ontology. The following query returns a list of pathways tagged with PW_0000296.

PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT ?pathway (str(?titleLit) AS ?title)
WHERE {
  ?pathwayRDF wp:ontologyTag obo:PW_0000296 ;
              foaf:page ?pathway ;
              dc:title ?titleLit .
}

Execute

Get all ontology terms for a particular pathway

List all the ontology terms tagged on a particular pathway.

SELECT (?o as ?pwOntologyTerm) (str(?titleLit) as ?title) ?pathway 
WHERE {
  ?pathwayRDF wp:ontologyTag ?o ;
    foaf:page ?pathway ;
    dc:title ?titleLit ;
    dcterms:identifier "WP1560" . 

  FILTER (! regex(str(?pathway), "group"))
}

Execute

Get all Reactome pathways

List all the ontology terms tagged on a particular pathway.

PREFIX cur: <http://vocabularies.wikipathways.org/wp#Curation:>

SELECT DISTINCT ?pathway (str(?titleLit) as ?title)
WHERE {
  ?pathway wp:ontologyTag cur:Reactome_Approved ;
           dc:title ?titleLit .
}

Execute

Get all Proteins from Community pathways

Obtain all Protein DataNodes (so not GeneProducts) from specific communities. Note: All community tags are available in the WikiPathways SPARQL endpoint now (the "Blau" community was updated to "IEM").

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX cur: <http://vocabularies.wikipathways.org/wp#Curation:>

SELECT DISTINCT ?pathway (str(?label) as ?Protein)
WHERE {
  ?pathway wp:ontologyTag    cur:Lipids   ; # Other communities: AOP; CIRM_Related ; COVID19 ; IEM ; RareDiseases ; SGD_Approved ; WormBase_Approved
           a                 wp:Pathway . 

  ?protein a                 wp:Protein ; 
           rdfs:label        ?label     ;
           dcterms:isPartOf  ?pathway   .

}

Execute

Get all pathways with PubMed references

SELECT DISTINCT ?pathway ?pubmed 
WHERE 
     {?pubmed a       wp:PublicationReference . 
      ?pubmed dcterms:isPartOf ?pathway }
ORDER BY ?pathway LIMIT 100

Execute

Get all pathways with a particular PubMed reference

SELECT DISTINCT ?pathway ?pubmed 
WHERE {
      ?pubmed a       wp:PublicationReference . 
      ?pubmed dcterms:isPartOf ?pathway .

      FILTER regex(str(?pubmed), "14769483$") 
}
ORDER BY ?pathway

The $ at the end of the PubMed identifier ensures that, for example, 147694831 does not match too; the regex instruction '$' means "end of the string".

Execute

Get all pathways and the number of refences per pathway

SELECT DISTINCT ?pathway COUNT(?pubmed) AS ?numberOfReferences
WHERE 
     {?pubmed a       wp:PublicationReference . 
      ?pubmed dcterms:isPartOf ?pathway }
ORDER BY DESC(?numberOfReferences) 

Execute

Get a full dump of all pathways and their pathway ontological terms

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dc:  <http://purl.org/dc/elements/1.1/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX schema: <http://schema.org/>
PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX dcterms:  <http://purl.org/dc/terms/>

SELECT DISTINCT ?depicts (str(?titleLit) as ?title) (str(?speciesLabelLit) as ?speciesLabel) ?identifier ?ontology
WHERE {
	?pathway foaf:page ?depicts .
        ?pathway dc:title ?titleLit .
        ?pathway wp:organism ?species .
        ?pathway wp:organismName ?speciesLabelLit .
        ?pathway dc:identifier ?identifier .

        OPTIONAL {?pathway wp:ontologyTag ?ontology .}
} LIMIT 100

Execute

Count how many genes from a list occur in one or more pathways

The gene list is given in the line starting with VALUES. For this example, we use the HGNC gene nomenclature.

Other gene IDs can be used to fill the list. However, keep in mind they use different URLs and therefore the prefix (first line of query) should be adapted. A list of these URLs can be found on identifiers.org (or by looking at the "raw" RDF files).

prefix hgnc:      <https://identifiers.org/hgnc.symbol/>
select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (count(distinct ?hgncId) AS ?GenesInPWs)
where {
VALUES ?hgncId {hgnc:GPD1L hgnc:SCN3B hgnc:BAD}
  ?gene a wp:GeneProduct ;
    dcterms:identifier ?id ;
    dcterms:isPartOf ?pathwayRes ;
    wp:bdbHgncSymbol ?hgncId .
  ?pathwayRes a wp:Pathway ;
              wp:organismName "Homo sapiens" ; 
    dcterms:identifier ?wpid ;
    dc:title ?title .
}

ORDER BY DESC(?GenesInPWs)

Execute

LIPID MAPS related queries:

Count amount of lipids per pathways in WikiPathways with LIPID MAPS identifier

Converts all Metabolite identifiers to LipidMaps (provided by BridgeDb), and create an ordered list of pathways including lipid compounds.

prefix lipidmaps:      <https://identifiers.org/lipidmaps/>
select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (count(distinct ?lipidID) AS ?LipidsInPWs)
where {
  ?metabolite a wp:Metabolite ;
    dcterms:identifier ?id ;
    dcterms:isPartOf ?pathwayRes ;
    wp:bdbLipidMaps ?lipidID .
  ?pathwayRes a wp:Pathway ;
              wp:organismName "Homo sapiens" ; 
    dcterms:identifier ?wpid ;
    dc:title ?title .
}

ORDER BY DESC(?LipidsInPWs)

Execute

Count amount of lipids per LIPID MAPS ontology class

Counts unique LIPID MAPS identifier (provided by BridgeDb) for the fatty acid (FA) class, other examples are provided as a comment.

select count(distinct ?lipidID) as ?IndividualLipidsPerClass_FA
where {     ?metabolite a wp:Metabolite ;
    dcterms:identifier ?id ;
    dcterms:isPartOf ?pathwayRes ;
    wp:bdbLipidMaps ?lipidID .
  ?pathwayRes a wp:Pathway ;
              wp:organismName "Homo sapiens" ; 
    dcterms:identifier ?wpid ;
    dc:title ?title .
  FILTER regex(str(?lipidID), "FA" ). # Other classes: GL, GP, SP, ST, PR, SL, PK
}

Execute

Find pathways per LIPID MAPS ontology class, sorted on amount of unique lipids

Filter all unique LIPID MAPS identifier (provided by BridgeDb) for the fatty acid (FA) class, and find all pathways with individual lipids in there.

select distinct ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) (count(distinct ?lipidID) AS ?FA_LipidsInPWs)
where {     ?metabolite a wp:Metabolite ;
    dcterms:identifier ?id ;
    dcterms:isPartOf ?pathwayRes ;
    wp:bdbLipidMaps ?lipidID .
  ?pathwayRes a wp:Pathway ;
              wp:organismName "Homo sapiens" ; 
    dcterms:identifier ?wpid ;
    dc:title ?title .
  FILTER regex(str(?lipidID), "FA" ). # Fatty acids, Other classes: GL, GP, SP, ST, PR, SL, PK
}

ORDER BY DESC(?FA_LipidsInPWs)

Execute

Data statistics oriented queries

Count the number of metabolites per species

Though strictly speaking, it guesstimates it, because it counts the number of unique metabolite identifiers. Normalization in the RDF generation code ensures we do not double count metabolites with identifiers from different databases, but it still differentially counts metabolites with different charge states.

PREFIX gpml:    <http://vocabularies.wikipathways.org/gpml#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

select (count(distinct ?metabolite) as ?count) (str(?label) as ?species) where {
  ?metabolite a wp:Metabolite ;
    dcterms:isPartOf ?pw .
  ?pw dc:title ?title ;
    wp:organism ?organism ;
    wp:organismName ?label .
} GROUP BY ?label ORDER BY DESC(?count)

Execute

Interaction oriented queries

Get all interactions for a particular datanode

Find all interactions that are connected to a particular datanode. (wp:Interaction).

PREFIX gpml:    <http://vocabularies.wikipathways.org/gpml#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>
PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 

#Find all interactions that are connected to a particular datanode.

SELECT DISTINCT ?interaction ?pathway  WHERE {

   ?pathway a wp:Pathway .
   ?interaction dcterms:isPartOf ?pathway . 
   ?interaction a wp:Interaction . 
   ?interaction wp:participants <https://identifiers.org/ensembl/ENSG00000125845> .   
}

Execute

Find all datanodes (GeneProducts, Metabolites, Pathways) that are connected to a particular datanode via any type of interaction (wp:Interaction)

SELECT DISTINCT ?participants ?DataNodeLabel ?interaction WHERE {
   ?interaction a wp:Interaction .
   
   ?interaction wp:participants <https://identifiers.org/ensembl/ENSG00000125845> .   
   ?interaction wp:participants ?participants .
   ?participants a wp:DataNode .
   ?participants rdfs:label ?DataNodeLabel .   
}

Execute

Get all interactions for a particular pathway

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?pathway ?interaction   
WHERE {

   ?pathway a wp:Pathway .
   ?pathway dc:identifier <https://identifiers.org/wikipathways/WP1425> .
   ?interaction dcterms:isPartOf ?pathway . 
   ?interaction a wp:Interaction .  
}

Execute

Get all interactions for a particular pathway and their participants

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?pathway ?interaction ?participants ?DataNodeLabel
WHERE {

   ?pathway a wp:Pathway .
   ?pathway dc:identifier <https://identifiers.org/wikipathways/WP1425> .
   ?interaction dcterms:isPartOf ?pathway . 
   ?interaction a wp:Interaction .
   ?interaction wp:participants ?participants .
   ?participants a wp:DataNode .
   ?participants rdfs:label ?DataNodeLabel .  
}

Execute

Get all Interactions

Limited to 100 interactions.

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?pathway ?interaction ?participant
WHERE {

   ?pathway a wp:Pathway . 
   ?interaction dcterms:isPartOf ?pathway .
   ?interaction a wp:Interaction .
   ?interaction wp:participants ?participant . 
}

LIMIT 100

Execute

Get all Interactions for a species (Homo sapiens)

We've added a LIMIT to this query (since it takes some time to run). Remove the 'LIMIT 100' to obtain all interactions

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?pathway ?interaction   
WHERE {

   ?pathway a wp:Pathway .
   ?pathway wp:organismName "Homo sapiens" . 
   ?interaction dcterms:isPartOf ?pathway . 
   ?interaction a wp:Interaction .  
} LIMIT 100

Execute

Get downstream adjacent nodes from a source

A directed interaction always runs from source to target. (eg. s --> t)

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?source ?label ?target ?label1 ?pathway ?interaction
WHERE {
    ?source dc:identifier <https://identifiers.org/ensembl/ENSG00000125845> .
    ?source dcterms:isPartOf ?pathway .
    ?pathway a wp:Pathway .

    ?interaction dcterms:isPartOf ?pathway .
    ?interaction a wp:Interaction .
    ?interaction wp:source ?source .
    ?interaction wp:target ?target .

    ?source rdfs:label ?label .
    ?target rdfs:label ?label1 .
 }

Execute

Get upstream adjacent nodes from a target

A directed interaction always runs from source to target. (eg. t <-- s)

PREFIX wp:    <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?target ?label1 ?source ?label ?pathway ?interaction
WHERE {
    ?target dc:identifier <https://identifiers.org/ncbigene/659> .
    ?target dcterms:isPartOf ?pathway .
    ?pathway a wp:Pathway .

    ?interaction dcterms:isPartOf ?pathway .
    ?interaction a wp:Interaction .
    ?interaction wp:target ?target .
    ?interaction wp:source ?source .

    ?target rdfs:label ?label1 .
    ?source rdfs:label ?label .  
 }

Execute

Get the number of interactions with some data source

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>

SELECT DISTINCT (STR(?sourceLit) AS ?source) (COUNT(DISTINCT ?identifier) AS ?count)
WHERE {
    ?interaction a                  wp:Interaction ;
                 dcterms:identifier ?identifier ;
                 dc:source          ?sourceLit .
} GROUP BY ?sourceLit
  ORDER BY DESC(?count)

Execute

Get the number of normalized identifiers by data source

This query gives some idea of how the interaction identifier mapping database works in practice:

PREFIX wp:      <http://vocabularies.wikipathways.org/wp#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc:      <http://purl.org/dc/elements/1.1/>

SELECT DISTINCT (STR(?sourceLit) AS ?source) ?normalizedIdentifier (COUNT(DISTINCT ?identifier) AS ?count)
WHERE {
  VALUES ?normalizedIdentifier { wp:bdbRhea wp:bdbReactome }
  ?interaction ?normalizedIdentifier ?identifier ;
               dc:source ?sourceLit .
} GROUP BY ?sourceLit ?normalizedIdentifier
  ORDER BY DESC(?count) ?source

Execute

Datasource oriented queries

Get all datasources currently captured in WikiPathways

SELECT DISTINCT (str(?datasourceLit) as ?datasource)
WHERE {
         ?concept dc:source ?datasourceLit
} 

Execute

Get the number of entries per datasource in WikiPathways

SELECT DISTINCT (str(?datasourceLit) as ?datasource) (count(?dataNode) as ?numberEntries)
WHERE {
  ?concept dc:source ?datasourceLit ;
    wp:isAbout ?dataNode .
} 
ORDER BY DESC(?numberEntries)

Execute

Count the identifiers per data source

SELECT (str(?datasourceLit) as ?datasource) (count(distinct ?identifier) AS ?numberEntries)
WHERE {
  ?concept dc:source ?datasourceLit .
  ?concept dc:identifier ?identifier
} 

Execute

Count the identifiers per data source and order them from high to low

SELECT (str(?datasourceLit) as ?datasource) (count(distinct ?identifier) AS ?numberEntries)
WHERE {
  ?concept dc:source ?datasourceLit .
  ?concept dc:identifier ?identifier
} ORDER BY DESC(?numberEntries)

Execute

Return all compounds annotated with the "ChEMBL compound" as data source and the pathways they are in

SELECT DISTINCT ?identifier ?pathway
WHERE {
        ?concept dcterms:isPartOf ?pathway .
        ?concept dc:source "ChEMBL compound" .
        ?concept dc:identifier ?identifier .
        
} 

Execute

Curators oriented queries

Get the pathway with the erroneous data source "null"

SELECT DISTINCT  ?identifier ?pathway ?label
WHERE {
        ?concept dc:source "null" .
        ?concept dc:identifier ?identifier .
        ?concept dcterms:isPartOf ?pathway .
        ?concept rdfs:label ?label
} 

Execute

Get all geneproducts that lack either a DataSource or an Identifier

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms:  <http://purl.org/dc/terms/>

select distinct ?pathway ?label where {?geneProduct a wp:GeneProduct . 
      ?geneProduct rdfs:label ?label .
      ?geneProduct dcterms:isPartOf ?pathway .
      
      FILTER regex(str(?geneProduct), "^node"). 
      FILTER regex(str(?pathway), "^http").
      }

Execute

Get entities with more than one identifier

This query contains a limit, since it might take some time to run.

select ?entity count(?identifier) as ?count where {
  ?entity <http://purl.org/dc/terms/identifier> ?identifier .
}  order by desc(?count) LIMIT 100

Execute

PubChem-compound 1004

Warning: may time out, which indicates there is no current use of this identifier value.

Wrongly used for phosphate. It is the uncharged compound. Phosphate is, instead, and particularly thinkgs like "Pi", CID 1061 for ortho-phosphate, aka [PO4]2-.

prefix wp:      <http://vocabularies.wikipathways.org/wp#>
prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
prefix dcterms:  <http://purl.org/dc/terms/>
prefix xsd:     <http://www.w3.org/2001/XMLSchema#>

select ?pathway ?source
where {
  ?mb dc:source ?source ;
    dcterms:isPartOf ?pathway ;
    dc:source "Pubchem Compound" ;
    dcterms:identifier "1004".
}

Execute

Entrez Gene 1004

This query will return results, since the ID '1004' is in use by Entrez Gene, and we are not filtering for a specific database name.