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188_batch_gene_symbol_to_uniprot_and_ensembl

rq turtle/ttl

Given a batch of human gene symbols (TP53, BRCA1, EGFR), resolve each to its Ensembl gene ID and reviewed UniProt accession in one federated query - the closest direct analogue to biomaRt's getBM() across two live SPARQL endpoints instead of one local database. Gene symbols and the Ensembl gene resource itself only exist in Ensembl's own RDF, so the symbol-to-gene match happens inside the SERVICE clause; restricting to human (RO_0002162, in-taxon) avoids matching the same symbol used for orthologous genes in other species, and the up:reviewed true filter (evaluated locally, since ?protein is already bound to a UniProt IRI) keeps one canonical accession per gene rather than every isoform

Use at

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX ensembl: <http://rdf.ebi.ac.uk/terms/ensembl/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT
  ?symbol
  ?ensemblGeneId
  ?protein
WHERE {
  SERVICE <https://rdfportal.org/ebi/sparql> {
    VALUES ?symbol { "TP53" "BRCA1" "EGFR" }
    ?gene a ensembl:EnsemblGene ;
      rdfs:label ?symbol ;
      dcterms:identifier ?ensemblGeneId ;
      obo:RO_0002162 <http://identifiers.org/taxonomy/9606> ;
      rdfs:seeAlso ?protein .
    FILTER(STRSTARTS(STR(?protein), "http://purl.uniprot.org/uniprot/"))
  }
  ?protein up:reviewed true .
}
ORDER BY ?symbol

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v4("?ensemblGeneId"):::projected 
  v3("?gene")
  v2("?protein"):::projected 
  v3("?symbol"):::projected 
  c8([http://identifiers.org/taxonomy/9606]):::iri 
  c11(["true^^xsd:boolean"]):::literal 
  c4([http://rdf.ebi.ac.uk/terms/ensembl/EnsemblGene]):::iri 
  subgraph s1["https://rdfportal.org/ebi/sparql"]
    style s1 stroke-width:4px;
    f0[["starts-with(str(?protein),'http://purl.uniprot.org/uniprot/')"]]
    f0 --> v2
    bind1[/VALUES ?symbol/]
    bind1-->v3
    bind10(["TP53"])
    bind10 --> bind1
    bind11(["BRCA1"])
    bind11 --> bind1
    bind12(["EGFR"])
    bind12 --> bind1
    v3 --"a"-->  c4
    v3 --"rdfs:label"-->  v3
    v3 --"dcterms:identifier"-->  v4
    v3 --"obo:RO_0002162"-->  c8
    v3 --"rdfs:seeAlso"-->  v2
  end
  v2 --"up:reviewed"-->  c11