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[bioontology-support] UBERON in Annotator

James Malone malone at
Fri Apr 26 23:31:58 PDT 2013

Hi Ray,

I don't think the ontology has had substantial restructuring in a way 
that would cause your issues below to disappear. OK, thanks for the 
explanation. I'll speak to Chris to see if we can perhaps produce a 
stripped down version omitting one axis of classification for annotator 



On 27/04/2013 01:31, Ray Fergerson wrote:
> James,
> We have a lot of trouble with this ontology and have removed it from
> processing with the current annotator. The problem that we noted was that
> many or most terms have two parents (one is-a and one part-of). Thus a
> calculation of "paths to root" blows up. (Unfortunately the current
> annotation system precalculates all possible paths to root.) Our most
> recent attempt to load it (about a month ago) resulted in a table for this
> single ontology which was about 8x the size of the table for the entire
> rest of all of the ontologies in BioPortal. This size increase caused
> memory problems, particularly thrashing. It is pretty surprising that such
> a small ontology of only 8000 terms could do this... Nevertheless,
> removing the ontology caused the database size to return to normal and
> everything else worked as before.
> The new backend has a new annotation system that does not calculate these
> paths and should work much better for this case. Unfortunately it is not
> ready for prime time. In the mean time we can only load it if the ontology
> is modified (hacked) in some way (perhaps by excluding the part-of
> relationships).
> I also note that there are several newer versions of uberon that have been
> submitted since we tried to use it. Are these substantially different than
> the older versions? We could try it again and monitor it closely if we
> think that it may work better now.
> Ray
> -----Original Message-----
> From: bioontology-support-bounces at
> [mailto:bioontology-support-bounces at] On Behalf Of James
> Malone
> Sent: Thursday, April 25, 2013 7:39 AM
> To: support at Support
> Subject: [bioontology-support] UBERON in Annotator
> Hi,
> Is it possible we could have UBERON indexed by Annotator please? The
> ontology is already in BioPortal.
> Thanks in advance.
> James
> --
> Blog:
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Cambridge, CB10 1SD,
> United Kingdom
> Tel: + 44 (0) 1223 494 676
> Fax: + 44 (0) 1223 494 468
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European Bioinformatics Institute,
Wellcome Trust Genome Campus,
CB10 1SD,
United Kingdom
Tel: + 44 (0) 1223 494 676
Fax: + 44 (0) 1223 492 468

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