Federated query gives: "Usupported combination of subqueries and service invocations"

Question

[cleb]

I try to perform the following query on uniprot:

PREFIX rh:<http://rdf.rhea-db.org/>
PREFIX up:<http://purl.uniprot.org/core/>
PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT
       ?protein
       ?ecNumber
       ?reaction
       ?equation

WHERE {

    ?protein a up:Protein .
    ?protein up:reviewed true .
    ?taxon a up:Taxon .
    ?taxon up:scientificName ?name .
    VALUES ?taxonlist { taxon:83333 }
    {
        ?taxon rdfs:subClassOf ?taxonlist .
        ?protein up:organism ?taxon . 
    } UNION {
        ?protein up:organism ?taxonlist . 
    }

    ?protein up:enzyme|((up:component|up:domain)/up:enzyme) ?ecNumber .

  SERVICE <http://rdf.rhea-db.org/> {

    ?reaction rdfs:subClassOf rh:Reaction .
    ?reaction rh:status rh:Approved .
    ?reaction rh:equation ?equation .
    ?reaction rh:ec ?ecNumber .
  } 
}

which always results in the error:

VirtuosoException: SQ074: Line 36: SP031:
SPARQL compiler: Internal error: Usupported combination of subqueries and service invocations

When I remove the entire SERVICE part, it seems to work fine. Is there a way to perform a federated query from uniprot and if so, how?

Answer 1

[De]

Hi Cleb,

I just ran into the same issue, and with help of a colleague, we fixed the issue. Documentation link. We have implemented this approach in a different query, see example below.

I needed to add a SELECT within the SELECT clause, so the service query is executed after the initial request. Furthermore, adding double curly brackets after the first WHERE. Note that I executed this query in a Virtuoso powered SPARQL endpoint , and there is a difference for Blazegraph powered ones (see Wikidata example).

    SELECT DISTINCT ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) ((substr(str(?COMPOUND),46)) as ?PubChem) 
WHERE{ 
  {
  SELECT ?pathwayRes (str(?wpid) as ?pathway) (str(?title) as ?pathwayTitle) ((substr(str(?COMPOUND),46)) as ?PubChem) 
    WHERE{
  VALUES ?wpid {"WP4224"^^xsd:string "WP4225"^^xsd:string "WP4571"^^xsd:string}

  ?gene a wp:Metabolite ;
    dcterms:identifier ?id ;
    dcterms:isPartOf ?pathwayRes ;
    wp:bdbPubChem ?COMPOUND .

  ?pathwayRes a wp:Pathway ;
    wp:organismName "Homo sapiens"^^xsd:string ;
    dcterms:identifier ?wpid ;
    dc:title ?title .
     }
  }
  SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/molmedb> {
   <http://identifiers.org/molmedb/MM00431> skos:exactMatch ?COMPOUND.
  filter (strstarts(str(?COMPOUND), 'http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID'))

  } 
}