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[bioontology-support] Mappings with SNOMED

Lotay, Vaneet vaneet.lotay at
Thu Feb 28 08:11:57 PST 2013


I was using the SPARQL service to query some mappings between ontologies and for the most part it works great, I just noticed something odd in the results for some mappings.  I've been primarily running this query to get the mapping between 2 ontologies and then output the results in XML:

PREFIX map: <>

SELECT ?m ?source ?target WHERE {
      ?m map:source_ontology <> .
      ?m map:target_ontology  <> .
      ?m map:source ?source .
      ?m map:target ?target .

For some results, most often when there is a large number of mappings between 2 ontologies (>5000) the XML results get cut off, they do not get fully outputted:

      <binding name="m"><uri></uri></binding>
      <binding name="source"><uri></uri></binding>
      <binding name="target"><uri></uri></binding>
      <binding name="m"><uri></u<>

It looks like the file size can never grow beyond 1MB exactly (1,048,576B), so in turn I don't get the full results.  Is there a limit on how much can be outputted from the service, can you tell me how I can prevent this cutoff from happening?



Vaneet Lotay
Genomics Informaticist/Programmer
Institute of Personalized Medicine
Mount Sinai Medical Center
1 Gustave L. Levy Place
New York, NY 10029-6574

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