From WikiPathways
On sparql.wikipathways.org wikipathways content is replicated. Currently this SPARQL endpoint is being developed, with very irregular updates.
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)
| http://sparqlbin.com/#f123c99388d62965e9c96de98c03f718
|
Datasource oriented queries
| Get all datasource currently captured in WikiPathways
| select distinct ?datasource count(?datasource) as ?numberEntries
WHERE {
?concept dc:source ?datasource
}
| Execute
|
| Get the number of entries per datasource in WikiPathways
| SELECT DISTINCT ?datasource
WHERE {
?concept dc:source ?datasource
}
| 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
