Help:WikiPathways SPARQL queries
From WikiPathways
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[http://sparqlbin.com/#6d0615f7c5da47a7a8ce076cc60ca7a7 Execute] | [http://sparqlbin.com/#6d0615f7c5da47a7a8ce076cc60ca7a7 Execute] | ||
| - | + | == Curators oriented queries == | |
| - | + | ||
| - | + | Extract contributors | |
| - | + | <pre>SELECT DISTINCT ?contributor | |
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WHERE { | WHERE { | ||
?pathway dc:contributor ?contributor | ?pathway dc:contributor ?contributor | ||
}</pre> | }</pre> | ||
| - | + | [http://sparqlbin.com/#ff17d4240f1c0848c21652d87576862b Execute] | |
| - | + | ===Extract the amount of pathways edited per contributor=== | |
| - | + | <pre>SELECT DISTINCT ?contributor, count(?pathway) as ?pathwaysEdited | |
| - | + | ||
WHERE { | WHERE { | ||
?pathway dc:contributor ?contributor | ?pathway dc:contributor ?contributor | ||
} | } | ||
ORDER BY DESC(?pathwaysEdited)</pre> | ORDER BY DESC(?pathwaysEdited)</pre> | ||
| - | + | [http://sparqlbin.com/#1d70dbc532f8d785b57a42b5d2d92ad4 Execute] | |
| - | + | ||
| - | + | ===find the pathways a user have edited so far.=== | |
| - | + | <pre>SELECT DISTINCT ?pathway, ?pathwayLabel | |
WHERE { | WHERE { | ||
?pathway dc:contributor wpuser:Andra . | ?pathway dc:contributor wpuser:Andra . | ||
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} | } | ||
</pre> | </pre> | ||
| - | + | [http://sparqlbin.com/#11e121d4593914dfadb96916bf95feb5 Execute] | |
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=== Federated queries === | === Federated queries === | ||
Revision as of 15:38, 24 October 2012
On sparql.wikipathways.org wikipathways content is replicated. Currently this SPARQL endpoint is being developed, with very irregular updates.
Contents |
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 foaf: <http://xmlns.com/foaf/0.1/> PREFIX schema: <http://schema.org/>
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
}
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 .
}
List pathways and their species
SELECT DISTINCT ?title ?label
WHERE {
?pathway dc:title ?title .
?pathway wp:organism ?organism .
?organism rdfs:label ?label .
}
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)
Datasource oriented queries
Get all datasource 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)
Count the identifiers per data source
SELECT DISTINCT ?datasource ?identifier count(?identifier) AS ?numberEntries
WHERE {
?concept dc:source ?datasource .
?concept dc:identifier ?identifier
}
Execute
===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)
Execute
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 .
}
Curators oriented queries
Extract contributors
SELECT DISTINCT ?contributor
WHERE {
?pathway dc:contributor ?contributor
}
Extract the amount of pathways edited per contributor
SELECT DISTINCT ?contributor, count(?pathway) as ?pathwaysEdited
WHERE {
?pathway dc:contributor ?contributor
}
ORDER BY DESC(?pathwaysEdited)
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 .
}
Federated queries
Code examples
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
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
