Question: Querying KEGG RDF graph Comparing to WikiPathways RDF "schema"
gravatar for areyoujokingme
4.2 years ago by
United States
areyoujokingme70 wrote:

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 predicate. I need this predicate to connect both Metabolite-Metabolite interactions, GeneProduct-GeneProduct interactions and Metabolite-GeneProduct interactions, ideally.

PREFIX wp: <>
PREFIX rdfs:  <> 
PREFIX dc:  <>
SELECT distinct ?src ?src_label ?src_type ?dest ?dest_label ?dest_type
  ?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!

ADD COMMENTlink written 4.2 years ago by areyoujokingme70

Against which KEGG SPARQL endpoint are you running your query?

ADD REPLYlink written 4.0 years ago by Egon Willighagen5.3k
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