Help:WikiPathways SPARQL queries
From WikiPathways
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= Code examples = | = Code examples = | ||
==Java== | ==Java== | ||
| + | For java we recommend the [http://jena.apache.org/documentation/query/index.html Jena Framework]. | ||
== php == | == php == | ||
== bash == | == bash == | ||
Revision as of 15:10, 23 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.
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 .
}
| Execute |
| 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 |
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)
| Execute | |
| 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 .
}
| Execute |
Curators oriented queries
| Extract contributors | SELECT DISTINCT ?contributor
WHERE {
?pathway dc:contributor ?contributor
}
| Execute |
| Extract the amount of pathways edited per contributor | SELECT DISTINCT ?contributor, count(?pathway) as ?pathwaysEdited
WHERE {
?pathway dc:contributor ?contributor
}
ORDER BY DESC(?pathwaysEdited)
| Execute |
| find the pathways a user have edited so far. Change the name in the query | SELECT DISTINCT ?pathway, ?pathwayLabel
WHERE {
?pathway dc:contributor wpuser:Andra .
?pathway dc:contributor ?contributor .
?pathway rdfs:label ?pathwayLabel .
}
| Execute |
Federated queries
Code examples
Java
For java we recommend the Jena Framework.
