Federated query between WikiPathways and Wikidata, listing SMILES for substrate and product for metabolic conversions.

query.rq

PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>

SELECT DISTINCT ?sourceWD ?sourceWDLabel ?sourceSMILEScan ?sourceSMILESiso ?targetWD ?targetWDLabel ?targetSMILEScan ?targetSMILESiso WITH {
  SELECT ?sourceWD ?targetWD WHERE {
    SERVICE <http://sparql.wikipathways.org/> {
      ?pathway a wp:Pathway . 
      ?interaction dcterms:isPartOf ?pathway .
      ?interaction a wp:Interaction, wp:Conversion .
      ?interaction wp:source ?source . ?source a wp:Metabolite; wp:bdbWikidata ?sourceWD .
      ?interaction wp:target ?target . ?target a wp:Metabolite; wp:bdbWikidata ?targetWD .
    }
  }
} AS %results WHERE {
  INCLUDE %results
  OPTIONAL { ?sourceWD wdt:P233 ?sourceSMILEScan }
  OPTIONAL { ?targetWD wdt:P233 ?targetSMILEScan }
  OPTIONAL { ?sourceWD wdt:P2017 ?sourceSMILESiso }
  OPTIONAL { ?targetWD wdt:P2017 ?targetSMILESiso }
  SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
}