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[bioontology-support] Mappings with SNOMED

Lotay, Vaneet vaneet.lotay at mountsinai.org
Fri Mar 1 09:25:40 PST 2013


Thanks for the tip.  It doesn't seem to be affecting the JSON output only XML.

Vaneet

From: manuelso [mailto:manuelso at stanford.edu]
Sent: Friday, March 01, 2013 12:24 PM
To: Lotay, Vaneet
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Mappings with SNOMED

Hi Lotay,

Thanks for reporting this issue.

I will look into it, our SPARQL proxy must have some kind of size limit. While it gets fixed you can use LIMIT and OFFSET to paginate over the results and be able to retrieve all the results.

Manuel


On Feb 28, 2013, at 8:11 AM, "Lotay, Vaneet" <vaneet.lotay at mountsinai.org<mailto:vaneet.lotay at mountsinai.org>> wrote:


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#<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><http://purl.bioontology.org/mapping/umls_cui/11d7feda746c5f63cc5702fdf62c99cd%3c/uri%3e%3c/binding%3e>
      <binding name="source"><uri>http://purl.bioontology.org/ontology/LNC/MTHU004551</uri></binding><http://purl.bioontology.org/ontology/LNC/MTHU004551%3c/uri%3e%3c/binding%3e>
      <binding name="target"><uri>http://purl.bioontology.org/ontology/SNOMEDCT/72165005</uri></binding><http://purl.bioontology.org/ontology/SNOMEDCT/72165005%3c/uri%3e%3c/binding%3e>
    </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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