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Contents
require 'sparql/client'
module TogoStanza::Stanza
module Querying
MAPPINGS = {
togogenome: 'http://ep.dbcls.jp/sparql7',
uniprot: 'http://ep.dbcls.jp/sparql7',
go: 'http://ep.dbcls.jp/sparql7'
}
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
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
end
end
Version data entries
30 entries across 30 versions & 1 rubygems