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[bioontology-support] [BioPortal] Feedback from Justin Sluka

Paul R Alexander palexander at
Mon Aug 6 10:59:11 PDT 2012


Can you give me a sample URL for a call you are making that fails? I 
would expect using "includedefinitions" to be slow in most cases as it 
requires an additional lookup per result. You can try setting the 
pagesize to something smaller and paging through the results or calling 
the term service for each of the results to get the definition.

Paul R Alexander
Senior Software Engineer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

On Mon Aug  6 10:52:19 2012, support at wrote:
> Name: Justin Sluka
> Email: Jsluka at
> Location:
> Comment:
> I'm a webdev with the Biocomplexity Institute at Indiana University, and I've got an issue with the BioPortal lookup service.
> My issue specifically comes from the use of the tag 'includededefinitions=true'. This causes the lookup service to take an extremely long time to return with the results, and often times just responds with an error.
> The error states:
> <errorStatus>
> <accessedResource>/bioportal/search/</accessedResource>
> <accessDate>2012-08-06 10:43:38.612 PDT</accessDate>
> <shortMessage>Internal Server Error</shortMessage>
> <longMessage>
> Transaction rolled back because it has been marked as rollback-only
> </longMessage>
> <errorCode>500</errorCode>
> </errorStatus>
> Can anyone help me figure this out?
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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