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[bioontology-support] Mappings with SNOMED

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


Hello,

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: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#>

SELECT ?m ?source ?target WHERE {
      ?m map:source_ontology <http://bioportal.bioontology.org/ontologies/1504> .
      ?m map:target_ontology  <http://bioportal.bioontology.org/ontologies/1423> .
      ?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>http://purl.bioontology.org/mapping/umls_cui/11d7feda746c5f63cc5702fdf62c99cd</uri></binding>
      <binding name="source"><uri>http://purl.bioontology.org/ontology/LNC/MTHU004551</uri></binding>
      <binding name="target"><uri>http://purl.bioontology.org/ontology/SNOMEDCT/72165005</uri></binding>
    </result>
    <result>
      <binding name="m"><uri>http://purl.bioontology.org/mapping/loom/4120f522e89acfebcd522b7a0d6c8d7d</u<http://purl.bioontology.org/mapping/loom/4120f522e89acfebcd522b7a0d6c8d7d%3c/u>
END OF FILE

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?

Thanks,

Vaneet

Vaneet Lotay
Genomics Informaticist/Programmer
Institute of Personalized Medicine
Mount Sinai Medical Center
1 Gustave L. Levy Place
New York, NY 10029-6574
646-438-0231


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