PRA3006-SPARQL

lipidPathways.rq

Database	WikiPathways
SPARQl endpoint	https://sparql.wikipathways.org/sparql
License	CCZero

Code examples: curl

SPARQL

#Pathways describing the biology of oxygenated hydrocarbons (LMFA12)
PREFIX chebi: <http://purl.obolibrary.org/obo/chebi/>

SELECT ?lipid ?name ?formula ?lmid (GROUP_CONCAT(?wpid_;separator=", ") AS ?pathway)
WHERE {
  SERVICE <https://lipidmaps.org/sparql> {
    VALUES ?category { <https://www.lipidmaps.org/rdf/category/112> <https://www.lipidmaps.org/rdf/category/11200> } 
    ?lipidmaps rdfs:label ?name ;
      rdfs:subClassOf* ?category ;
      chebi:formula ?formula .
  }
  BIND (IRI(CONCAT("https://identifiers.org/lipidmaps/",
               SUBSTR(STR(?lipidmaps), 31))) AS ?lmid)
  ?lipid wp:bdbLipidMaps ?lmid ;
         dcterms:isPartOf ?pathway .
  ?pathway a wp:Pathway ; dcterms:identifier ?wpid_ .
}

Run or Edit

Output

lipid	name	formula	lmid	pathway
https://identifiers.org/chebi/CHEBI:28398	Butan-2-one	C4H8O	https://identifiers.org/lipidmaps/LMFA12000043	WP4838
https://identifiers.org/kegg.compound/C00207	Propan-2-one	C3H6O	https://identifiers.org/lipidmaps/LMFA12000057	WP3602
https://identifiers.org/chebi/CHEBI:15347	Propan-2-one	C3H6O	https://identifiers.org/lipidmaps/LMFA12000057	WP4742, WP5175

Code examples

curl

curl -o lipidPathways.rq https://raw.githubusercontent.com/BiGCAT-UM/PRA3006-SPARQL/master/sparql/lipidPathways.rq
curl -H "Accept: text/tab-separated-values" -G https://sparql.wikipathways.org/sparql --data-urlencode query@lipidPathways.rq

This SPARQL query is available under CCZero.

This site is open source. Improve this page.