Module: TogoStanza::Stanza::Querying

Included in:
Base
Defined in:
lib/togostanza/stanza/querying.rb

Constant Summary collapse

MAPPINGS = 
{
  togogenome: 'http://ep.dbcls.jp/sparql7',
  uniprot:    'http://ep.dbcls.jp/sparql7',
  go:         'http://ep.dbcls.jp/sparql7'
}

Instance Method Summary collapse

Instance Method Details

#query(endpoint, sparql) ⇒ Object 



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# File 'lib/togostanza/stanza/querying.rb', line 11

def query(endpoint, sparql)
  client = SPARQL::Client.new(MAPPINGS[endpoint] || endpoint)

  #Rails.logger.debug "SPARQL QUERY: \n#{sparql}"

  client.query(sparql).map {|binding|
    binding.each_with_object({}) {|(name, term), hash|
      hash[name] = term.to_s
    }
  }
end

#uniprot_url_from_togogenome(gene_id) ⇒ Object 



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# File 'lib/togostanza/stanza/querying.rb', line 23

def uniprot_url_from_togogenome(gene_id)
  # refseq の UniProt
  # slr1311 の時 "http://purl.uniprot.org/refseq/NP_439906.1"
  query(:togogenome, <<-SPARQL).first[:up]
  PREFIX insdc: <http://insdc.org/owl/>
  PREFIX idorg: <http://rdf.identifiers.org/database/>

  SELECT DISTINCT ?up
  FROM <http://togogenome.org/graph/refseq/>
  WHERE {
      ?s insdc:feature_locus_tag "#{gene_id}" .
      ?s rdfs:seeAlso ?np .
      ?s rdfs:seeAlso ?xref .
      ?np rdf:type idorg:Protein .
      BIND (STRAFTER(STR(?np), "ncbiprotein/") AS ?npid)
      BIND (IRI(CONCAT("http://purl.uniprot.org/refseq/", ?npid)) AS ?up)
  }
  SPARQL
end