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[bioontology-support] NCBO Virtual Applicance: Internal Server Error

Ray Fergerson rayferg at stanford.edu
Fri Aug 14 14:09:27 PDT 2015


This is a known problem for branches of very large ontologies. We have designed a fix but it will take some time to implement. Currently the only workaround is to get all the search results and then prune them yourselves. Our proposed fix will be much better (faster) than this but it will take a while to get to it.

Ray

-----Original Message-----
From: bioontology-support [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of mikayla-grace at studio.urban-warrior.org
Sent: Thursday, August 13, 2015 10:21 AM
To: support at bioontology.org
Subject: [bioontology-support] NCBO Virtual Applicance: Internal Server Error

We're using the NCBO Virtual Appliance v2.4.  It fails if we use the subtree_root_id parameter with a high level term (such as C7057 – Disease, Disorder or Finding, which represents a big branch of terms).

Success:

   http://bioontology.virginimage.org:8080/search?q=biology&ontology=NCIT&require_exact_match=true&apikey=***

   http://bioontology.virginimage.org:8080/search?q=biology&ontology=NCIT&require_exact_match=true&apikey=***&subtree_root_id=C77140

C77140 is a much narrower term.

Fail:

   http://bioontology.virginimage.org:8080/search?q=biology&ontology=NCIT&require_exact_match=true&apikey=***&subtree_root_id=C7057

With this URl, we consistently receive an "Internal Server Error".  The same URI works fine with the bioportal.bioontology.org server.

Any chance this can be fixed?

Thanks,
Mikayla Grace
bio-ontology at virginimage.org
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