Querying KEGG RDF graph Comparing to WikiPathways RDF "schema"
0
1
Entering edit mode
8.1 years ago

I want to get all interactions between Metabolites and Gene Products in the KEGG database. I've done this before querying WikiPathways with the below SPARQL query. I can't seem to "break into" KEGG's SPARQL "schema" to translate this query in such a way that probes KEGG for the same information.

Particularly, I am having a hard time finding a predicate that is analogous to WikiPathway's http://vocabularies.wikipathways.org/wp#Interaction predicate. I need this predicate to connect both Metabolite-Metabolite interactions, GeneProduct-GeneProduct interactions and Metabolite-GeneProduct interactions, ideally.

PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
PREFIX rdfs:  <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX dc:  <http://purl.org/dc/elements/1.1/>
SELECT distinct ?src ?src_label ?src_type ?dest ?dest_label ?dest_type
WHERE {
  ?p a wp:Interaction .
  ?p wp:source ?src . 
  ?p wp:target ?dest .
  ?src rdfs:label ?src_label .
  ?dest rdfs:label ?dest_label .
  ?src a ?src_type .
  ?dest a ?dest_type .
  FILTER ((?src_type != wp:GeneProduct || ?src_type != wp:Metabolite) && (?dest_type != wp:GeneProduct || ?dest_type != wp:Metabolite)) .
  FILTER (?src_type != wp:DataNode && ?dest_type != wp:DataNode) .
  FILTER (?src_type != wp:Protein && ?dest_type != wp:Protein) .
  FILTER (?src_type != wp:Rna && ?dest_type != wp:Rna) .
  FILTER (?src_type != wp:Complex && ?dest_type != wp:Complex)
}

Can anyone help me "break into" KEGG by helping me see how the query for WikiPathways can be translated to the same query against KEGG? Any advice/insights would be invaluable!

KEGG WikiPathways RDF semantic web SPARQL • 2.0k views
ADD COMMENT
0
Entering edit mode

Against which KEGG SPARQL endpoint are you running your query?

ADD REPLY

Login before adding your answer.

Traffic: 849 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6