From WikiPathways

Revision as of 22:48, 23 November 2013

On http://sparql.wikipathways.org/ wikipathways content is replicated. Currently this SPARQL endpoint is being developed, with very irregular updates.

Resources

• WikiPathways internal vocabularies: http://vocabularies.wikipathways.org
• WikiPathways data as RDF: http://rdf.wikipathways.org
• WikiPathways SPARQL endpoint http://sparql.wikipathways.org

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

Other sparql endpoints

• Gene Wiki: http://genewiki.semwebinsi.de
• ChEMBL: http://rdf.farmbio.uu.se/chembl/sparql/
• [1]
• ubo text mining

Submit ideas

• submit your query
• submit ideas and suggestions

Prefixes

Below are example queries. For readability we have omitted the prefixes. We use the following prefixes: (Not complete yet)

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

Example queries

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

Data curation oriented queries

Get the pathway with the erroneous data source "null"

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

sparqlbin 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

select ?entity count(?identifier) as ?count where {
  ?entity <http://purl.org/dc/terms/identifier> ?identifier .
} order by desc(?count) LIMIT 12

Pathway oriented queries

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

SELECT DISTINCT ?organism ?label
WHERE {
    ?concept wp:organism ?organism .
    ?organism rdfs:label ?label .
 } 

Sparqlbin

List pathways and their species

SELECT DISTINCT ?title ?label 
WHERE {
    ?pathway dc:title ?title .
    ?pathway wp:organism ?organism .
    ?organism rdfs:label ?label .
 } 

Execute

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

SELECT DISTINCT ?organism ?label count(?pathway) as ?noPathways
WHERE {
    ?pathway dc:title ?title .
    ?pathway wp:organism ?organism .
    ?organism rdfs:label ?label .
 }
ORDER BY DESC(?noPathways)

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.

SELECT DISTINCT ?wpIdentifier ?pathway ?page
WHERE {
    ?pathway dc:title ?title .
    ?pathway wp:organism ?organism .
    ?pathway foaf:page ?page .
    ?pathway dc:identifier ?wpIdentifier .
    ?organism rdfs:label "Mus musculus"^^<http://www.w3.org/2001/XMLSchema#string> .
 }
ORDER BY ?wpIdentifier 

Execute Perl

List all mouse pathways that require curation attention

The following query lists all pathways for the mouse that contains elements that requires attention.. It lists the canonical identifier (ie the page that always point to the latest revision), the wiki page with the latest revision loaded in the Sparql endpoint and the last URI of that page.

SELECT DISTINCT ?wpIdentifier ?elementneedsattention ?elementLabel
WHERE {
    ?pathway dc:title ?title .
    ?elementneedsattention a gpml:requiresCurationAttention .
    ?elementneedsattention dcterms:isPartOf ?pathway .
    ?elementneedsattention rdfs:label ?elementLabel . 
    ?pathway wp:organism ?organism .
    ?pathway foaf:page ?page .
    ?pathway dc:identifier ?wpIdentifier .
    ?organism rdfs:label "Mus musculus"^^<http://www.w3.org/2001/XMLSchema#string> .
 }
ORDER BY ?wpIdentifier 

Execute Perl

Count the pathways per pathway category

SELECT DISTINCT  ?category count(?category) as ?noCategories
WHERE {
        ?pathway wp:category ?category .
        ?pathway dc:title ?title .
} 
ORDER BY ?category

execute

List all pathways of category Metabolic Process

SELECT DISTINCT  *
WHERE {
        ?pathway wp:category wp:MetabolicProcess .
        ?pathway dc:title ?title .
} 

Sparqlbin execute

Get all pathways with CYP protein

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

Count the number of Pathways per Pathway Ontology term

In WikiPathways pathways can be labeled according to terms from Pathway ontology, Cell Line ontology and the disease ontology. The following query get a pathway count for each ontological term being used in WikiPathways

 SELECT DISTINCT ?label as ?pwOntologyTerm count(?pathway) as ?pathwayCount
 WHERE {
	?pathwayRDF wp:pathwayOntology ?o .
        ?pathwayRDF foaf:page ?pathway .
        ?pathwayRDF dc:title ?title .
        ?o <http://www.w3.org/2000/01/rdf-schema#label> ?label .
        ?o rdfs:subClassOf ?superClass .
        ?superClass rdfs:label ?superClassLabel .
 }
 ORDER BY DESC(?pathwayCount)

Sparqlbin

Execute

Get all pathways with Pubmed references

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

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 from the analytical set and they 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 ?title ?speciesLabel ?identifier ?ontology ?label 
WHERE {
	?pathway foaf:page ?depicts .
        ?pathway dc:title ?title .
        ?pathway wp:organism ?species .
        ?species rdfs:label ?speciesLabel .
        ?pathway dc:identifier ?identifier .
        OPTIONAL {?pathway wp:pathwayOntology ?ontology .
        ?ontology rdfs:label ?label .}
} 

Execute

Interaction oriented queries

Get all connected Datanodes through a line

Find all datanodes (GeneProducts, Metabolites, Pathways) that are connected in the curated pathways set of WikiPathways of a HMDB entry with the identifier "HMDB01586".

SELECT DISTINCT ?wpIdentifier ?dn2Identifier  WHERE {
?pathway dc:identifier ?wpIdentifier .
{SELECT DISTINCT * WHERE {
?datanode2 dc:identifier ?dn2Identifier .
?datanode2 a gpml:DataNode .
?datanode2 dcterms:isPartOf ?pathway .
?datanode2 gpml:graphid ?dn2GraphId .
?line gpml:graphref ?dn2GraphId .
FILTER (?datanode2 != ?datanode1) 
FILTER (?datanode2 != <http://commonchemistry.org/ChemicalDetail.aspx?ref=noIdentifier>)

{SELECT DISTINCT * WHERE {   
   ?datanode1 dc:identifier <http://identifiers.org/hmdb/HMDB01586> .
   ?datanode1 gpml:graphid ?dn1GraphId .
   ?datanode1 a gpml:DataNode .
   ?datanode1 dcterms:isPartOf ?pathway .

   ?line gpml:graphref ?dn1GraphId .
   ?line a gpml:Line .
   ?line gpml:graphid ?lineGraphId .
   ?line dcterms:isPartOf ?pathway .}}

}}
}

Execute

Get all interactions per pathway

SELECT DISTINCT ?wpIdentifier ?dn1Identifier ?dn2Identifier  WHERE {
?pathway dc:identifier ?wpIdentifier .
{SELECT DISTINCT * WHERE {
?datanode2 dc:identifier ?dn2Identifier .
?datanode2 a gpml:DataNode .
?datanode2 dcterms:isPartOf ?pathway .
?datanode2 gpml:graphid ?dn2GraphId .
?line gpml:graphref ?dn2GraphId .
FILTER (?datanode2 != ?datanode1) 
FILTER (!regex(str(?datanode2), "noIdentifier")) .
{SELECT DISTINCT * WHERE {   
   ?datanode1 dc:identifier ?dn1Identifier .
   ?datanode1 gpml:graphid ?dn1GraphId .
   ?datanode1 a gpml:DataNode .
   ?datanode1 dcterms:isPartOf ?pathway .
   ?line gpml:graphref ?dn1GraphId .
   ?line a gpml:Line .
   ?line gpml:graphid ?lineGraphId .
   ?line dcterms:isPartOf ?pathway .}}
   FILTER (!regex(str(?datanode1), "noIdentifier")) .

}}
}

Execute

Get all Interactions

SELECT DISTINCT ?dn1Identifier ?dn2Identifier  WHERE {
?pathway dc:identifier ?wpIdentifier .
{SELECT DISTINCT * WHERE {
?datanode2 dc:identifier ?dn2Identifier .
?datanode2 a gpml:DataNode .
?datanode2 dcterms:isPartOf ?pathway .
?datanode2 gpml:graphid ?dn2GraphId .
?line gpml:graphref ?dn2GraphId .
FILTER (?datanode2 != ?datanode1) 
FILTER (!regex(str(?datanode2), "noIdentifier")) .
{SELECT DISTINCT * WHERE {   
   ?datanode1 dc:identifier ?dn1Identifier .
   ?datanode1 gpml:graphid ?dn1GraphId .
   ?datanode1 a gpml:DataNode .
   ?datanode1 dcterms:isPartOf ?pathway .
   ?line gpml:graphref ?dn1GraphId .
   ?line a gpml:Line .
   ?line gpml:graphid ?lineGraphId .
   ?line dcterms:isPartOf ?pathway .}}
   FILTER (!regex(str(?datanode1), "noIdentifier")) .

}}
}

Execute

Datasource oriented queries

Get all datasources currently captured in WikiPathways

SELECT DISTINCT ?datasource 
WHERE {
         ?concept dc:source ?datasource
} 

Execute

Get the number of entries per datasource in WikiPathways

SELECT DISTINCT ?datasource count(?datasource) as ?numberEntries 
WHERE {
        ?concept dc:source ?datasource
} 
ORDER BY DESC(?numberEntries)

Sparqlbin

Count the identifiers per data source

SELECT DISTINCT ?datasource ?identifier count(?identifier) AS ?numberEntries 
WHERE {
        ?concept dc:source ?datasource .
        ?concept dc:identifier ?identifier
} 

Sparqlbin

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

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

Sparqlbin

Return all Chembl compounds in WikiPathways and the pathways they are in

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

Sparqlbin

Curators oriented queries

Extract contributors

SELECT DISTINCT ?contributor  
WHERE {
       ?pathway dc:contributor ?contributor
}

Sparqlbin

Extract the amount of pathways edited per contributor

SELECT DISTINCT ?contributor, count(?pathway) as ?pathwaysEdited  
WHERE {
       ?pathway dc:contributor ?contributor
}
ORDER BY DESC(?pathwaysEdited)

Sparqlbin

find the pathways a user have edited so far.

SELECT DISTINCT ?pathway, ?pathwayLabel
WHERE {
       ?pathway dc:contributor wpuser:Andra .
       ?pathway dc:contributor ?contributor .
       ?pathway rdfs:label ?pathwayLabel .
}

Sparqlbin

Federated queries

WikiPathways with GeneWiki

SELECT DISTINCT ?wplabel ?identifier ?snp where {

                        ?s dc:identifier <http://identifiers.org/ncbigene/53975> .
                        ?s dc:identifier ?identifier .
                        ?s rdfs:label ?wplabel .
                        ?s dc:source ?source .
                    SERVICE <http://genewiki.semwebinsi.de/> {
                       ?gws dc:identifier ?identifier .
                       ?gws rdf:type ?gwtype .
                       ?gws <http://genewikiplus.org/wiki/Special:URIResolver/Property-3AHasSNP> ?snp . 
                    }

             }

prefix dc: <http://purl.org/dc/elements/1.1/>
prefix dcterms:  <http://purl.org/dc/terms/>

select distinct * where { 
            ?pwEntity dc:identifier ?identifier . 
            ?pwEntity dcterms:isPartOf ?pathway .
        SERVICE <http://genewiki.semwebinsi.de/> {
            ?concept dc:identifier <http://identifiers.org/ncbigene/12189> .
            ?concept dc:identifier ?identifier .
            ?concept <http://genewikiplus.org/wiki/Special:URIResolver/Property-3AIs_associated_with_disease> ?disease .
        }
}

WikiPathways with ChEMBL: ChEMBL compounds in WikiPathways (without BridgeDB)

SELECT *
  WHERE {{
        SELECT DISTINCT ?pathway ?concept iri(bif:concat("http://linkedchemistry.info/chembl/chemblid/", bif:regexp_substr('http://identifiers.org/chembl.compound/(.*)',?identifier, 1))) as ?ChEMBLId where {
                        ?concept dcterms:isPartOf ?pathway .
                        ?concept dc:source "ChEMBL compound"^^xsd:string .
                        ?concept dc:identifier ?identifier .     
                        FILTER regex(str(?identifier), "^http").      
        }
} SERVICE <http://rdf.farmbio.uu.se/chembl/sparql/>{
        ?ChEMBLId ?p ?o .
} }

Execute

WikiPathways with ChEMBL: all ChEMBL assays for pathways

SELECT ?pathway ?target ?assay WHERE {
{
  SELECT DISTINCT
    ?pathway ?uniprot
    iri(
      bif:concat("http://bio2rdf.org/uniprot:",
      bif:regexp_substr('http://identifiers.org/uniprot/(.*)',?uniprot, 1))
    ) as ?chembluniprot
  WHERE {
    ?s ?p ?uniprot .
    ?s dcterms:isPartOf ?pathway .
    FILTER regex(?uniprot, "uniprot")
  }
}
  SERVICE <http://rdf.farmbio.uu.se/chembl/sparql/> {
    ?target owl:sameAs ?chembluniprot .
    ?score chembl:forTarget ?target .
    ?assay chembl:hasTargetScore ?score .
}
}

Execute

WikiPathways with ChEMBL: all molecules targeting pathways

SELECT ?pathway ?target ?assay ?smiles WHERE {
{
  SELECT DISTINCT
    ?pathway ?uniprot
    iri(
      bif:concat("http://bio2rdf.org/uniprot:",
      bif:regexp_substr('http://identifiers.org/uniprot/(.*)',?uniprot, 1))
    ) as ?chembluniprot
  WHERE {
    ?s ?p ?uniprot .
    ?s dcterms:isPartOf ?pathway .
    FILTER regex(?uniprot, "uniprot")
  }
}
  SERVICE <http://rdf.farmbio.uu.se/chembl/sparql/> {
    ?target owl:sameAs ?chembluniprot .
    ?score chembl:forTarget ?target .
    ?assay chembl:hasTargetScore ?score .
    ?activity chembl:onAssay ?assay ;
      chembl:forMolecule ?molecule .
    ?molecule bo:smiles ?smiles .
    
}
}

Execute

WikiPathways with EBI Atlas RDF

Genes differentially expressed in asthma and Pathways

For the genes differentially expressed in asthma, get the gene products associated to a WikiPathways pathway. (Built upon example query 5 in: http://www.ebi.ac.uk/rdf/services/atlas/sparql ). You can substitute the EFO number for other disease codes.

PREFIX identifiers:<http://identifiers.org/ensembl/>
PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>

SELECT DISTINCT ?wpURL ?pwTitle ?expressionValue ?pvalue where {

SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
     ?factor rdf:type efo:EFO_0000270 . 
     ?value atlasterms:hasFactorValue ?factor . 
     ?value atlasterms:isMeasurementOf ?probe . 
     ?value atlasterms:pValue ?pvalue . 
     ?value rdfs:label ?expressionValue . 
     ?probe atlasterms:dbXref ?dbXref .
}
     ?pwElement dcterms:isPartOf ?pathway .
     ?pathway dc:title ?pwTitle .
     ?pathway dc:identifier ?wpURL .
     ?pwElement wp:bdbEnsembl ?dbXref .
}
ORDER BY ASC(?pvalue)

Execute

Genes differentially expressed in type II diabetes mellitus and Pathways

PREFIX identifiers:<http://identifiers.org/ensembl/>
PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>

SELECT DISTINCT ?wpURL ?pwTitle ?expressionValue ?pvalue where {

SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
     ?factor rdf:type efo:EFO_0001360 . 
     ?value atlasterms:hasFactorValue ?factor . 
     ?value atlasterms:isMeasurementOf ?probe . 
     ?value atlasterms:pValue ?pvalue . 
     ?value rdfs:label ?expressionValue . 
     ?probe atlasterms:dbXref ?dbXref .
}
     ?pwElement dcterms:isPartOf ?pathway .
     ?pathway dc:title ?pwTitle .
     ?pathway dc:identifier ?wpURL .
     ?pwElement wp:bdbEnsembl ?dbXref .
}
ORDER BY ASC(?pvalue)

Execute

Genes differentially expressed in obesity and Pathways

PREFIX identifiers:<http://identifiers.org/ensembl/>
PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>

SELECT DISTINCT ?wpURL ?pwTitle ?expressionValue ?pvalue where {
SERVICE <http://www.ebi.ac.uk/rdf/services/atlas/sparql> {
     ?factor rdf:type efo:EFO_0001073 . 
     ?value atlasterms:hasFactorValue ?factor . 
     ?value atlasterms:isMeasurementOf ?probe . 
     ?value atlasterms:pValue ?pvalue . 
     ?value rdfs:label ?expressionValue . 
     ?probe atlasterms:dbXref ?dbXref .
}
     ?pwElement dcterms:isPartOf ?pathway .
     ?pathway dc:title ?pwTitle .
     ?pathway dc:identifier ?wpURL .
     ?pwElement wp:bdbEnsembl ?dbXref .
}
ORDER BY ASC(?pvalue)

Execute

Code examples

Perl

There is an RDF api available. Below is an example that extracts the data by converting the query into a url and extracts the data as CSV.

#!/usr/bin/perl
 
use LWP::Simple;
use URI::Escape;
my $sparql = "SELECT DISTINCT ?wpIdentifier ?elementneedsattention ?elementLabel
WHERE {
    ?pathway dc:title ?title .
    ?elementneedsattention a gpml:requiresCurationAttention .
    ?elementneedsattention dcterms:isPartOf ?pathway .
    ?elementneedsattention rdfs:label ?elementLabel . 
    ?pathway wp:organism ?organism .
    ?pathway foaf:page ?page .
    ?pathway dc:identifier ?wpIdentifier .
    ?organism rdfs:label \"Mus musculus\"^^<http://www.w3.org/2001/XMLSchema#string> .
 }
ORDER BY ?wpIdentifier";
 
my $url = 'http://sparql.wikipathways.org/?default-graph-uri=&query='.uri_escape($sparql).'&format=text%2Fcsv&timeout=0&debug=on';
 
my $content = get $url;
die "Couldn't get $url" unless defined $content;
 
print $content;

Java

For java we recommend the Jena Framework.

import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.ResultSet;

public class javaCodeExample {

	public static void main(String[] args) {
		String sparqlQueryString = "SELECT * WHERE {?s ?p ?o} LIMIT 10";
		Query query = QueryFactory.create(sparqlQueryString);
		QueryExecution queryExecution = QueryExecutionFactory.sparqlService("http://sparql.wikipathways.org", query);
		ResultSet resultSet = queryExecution.execSelect();
		while (resultSet.hasNext()) {
			QuerySolution solution = resultSet.next();
			System.out.print(solution.get("s"));
			System.out.print("\t"+solution.get("p"));
			System.out.println("\t"+solution.get("o"));
		}
	}
}

php

For php we recommend the arc2: Easy RDF and SPARQL for LAMP systems

R

   library(rrdf)
   sparql.remote(
     "http://sparql.wikipathways.org/",
     "SELECT DISTINCT ?p WHERE { ?s ?p ?o }"
   )

Bioclipse

The below code works in both the JavaScript and the Groovy console:

   rdf.sparqlRemote(
     "http://sparql.wikipathways.org/",
     "SELECT DISTINCT ?p WHERE { ?s ?p ?o }"
   )

SPARQL from the command line

For quick and easy querying, we recommend to use curl (Linux and OS X)

curl -F "query=SELECT * WHERE {?s ?p ?o} LIMIT 10" http://sparql.wikipathways.org

Return to Help Contents