Example4-2_Additional_file_8.rq

# Example 4-2 with 2 subqueries (AD) [> 5 mins/100 rows]
PREFIX brso: <http://purl.jp/bio/10/brso/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX lscr: <http://purl.org/lscr#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX orth: <http://purl.org/net/orth#>
PREFIX genex: <http://purl.org/genex#>
PREFIX umls: <http://linkedlifedata.com/resource/umls/id/>
SELECT distinct ?mouse ?ensembl2 ?exprLevel
WHERE {
  SERVICE <https://bgee.org/sparql/> {
      ?oma_gene2 a orth:Gene .
      ?oma_gene2 lscr:xrefEnsemblGene ?ensembl2 .
      ?oma_gene2 orth:organism/obo:RO_0002162 taxon:9606 . # human
      ?oma_gene2 genex:isExpressedIn ?cond .
      ?cond genex:hasAnatomicalEntity obo:UBERON_0002097 . # skin of body
      ?cond genex:hasSex "any" .
      ?expr genex:hasExpressionCondition ?cond .
      ?expr genex:hasSequenceUnit ?oma_gene2 .
      ?expr a genex:Expression .
      ?expr genex:hasConfidenceLevel obo:CIO_0000029 . # high confidence level
      ?expr genex:hasExpressionLevel ?exprLevel .
#      FILTER (?exprLevel > 99)
    }
    {
        SELECT distinct ?mouse ?ensembl2 WHERE {
            GRAPH <http://metadb.riken.jp/db/omaRDF> {
              ?cluster a orth:OrthologsCluster .
              ?cluster orth:hasHomologousMember ?node1 .
              ?cluster orth:hasHomologousMember ?node2 .
              FILTER (?node1 != ?node2)
              ?node1 orth:hasHomologousMember* ?protein1 .
              ?node2 orth:hasHomologousMember* ?protein2 .
              ?protein1 sio:SIO_010079 ?oma_gene1 . # sio:SIO_010079 (is encoded by)
              ?oma_gene1 lscr:xrefEnsemblGene ?ensembl1 .
              ?oma_gene1 lscr:xrefNCBIGene ?ncbi1 .
             ?protein2 lscr:xrefUniprot ?uniprot2. ### 
              ?protein2 sio:SIO_010079 ?oma_gene2 .
              ?protein2 orth:organism ?oma_organism2 .
              ?oma_organism2 obo:RO_0002162 taxon:9606 .
              ?oma_gene2 lscr:xrefNCBIGene ?ncbi2 .
              ?oma_gene2 lscr:xrefEnsemblGene ?ensembl2 .
            }
            GRAPH <http://metadb.riken.jp/db/mouse_rdfEnsemblMouseGene> {
              ?mouse <http://purl.org/rbrc/resource/relatedGene> ?ensembl1 .
            }
           {        
               SELECT distinct ?uniprot2 WHERE {
               GRAPH <http://metadb.riken.jp/db/uniprot_ncbigene> {
                 ?uniprot2 rdfs:seeAlso ?ncbi2 .
                 ?uniprot2 rdfs:seeAlso ?identifiers_ncbi2 .
                 FILTER (?ncbi2 != ?identifiers_ncbi2)
               }
               GRAPH <http://metadb.riken.jp/db/gda_score_05> {
                 ?gda sio:SIO_000628 ?identifiers_ncbi2 .
                 ?gda sio:SIO_000628 ?umls .
                 VALUES (?umls) { (umls:C0025202) } # Melanoma
                 FILTER (?identifiers_ncbi2 != ?umls)
               }
        } 
      }
    }
  }
}
# LIMIT 100 OFFSET 0