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kozo2/uniprot-sparql.py

Last active June 13, 2016 12:45
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uniprot-sparql.py
from SPARQLWrapper import SPARQLWrapper, JSON
#sparql = SPARQLWrapper("http://sparql.uniprot.org/")
sparql = SPARQLWrapper("http://sparql.uniprot.org/sparql/")
sparql.setQuery("""
PREFIX up:<http://purl.uniprot.org/core/>
SELECT ?taxon
FROM <http://sparql.uniprot.org/taxonomy/>
WHERE
{
?taxon a up:Taxon .
}
""")
sparql.setReturnFormat(JSON)
results = sparql.query().convert()
print(results['results']['bindings'])
@kozo2

kozo2 commented Jun 12, 2016

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@JervenBolleman Thank you for you advice.
I had the same response again.

@JervenBolleman

JervenBolleman commented Jun 13, 2016

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Could you try

sparql = SPARQLWrapper("http://sparql.uniprot.org/sparql/")

From logs SPARQLWrapper not following a redirect to the real endpoint.

@kozo2

kozo2 commented Jun 13, 2016

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@JervenBolleman Sorry my reply is late.
Thank you very much.
New endpoint works well for Python SPARQLWrapper package.
I replaced
"http://sparql.uniprot.org/" to "http://sparql.uniprot.org/sparql/"

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