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[bioontology-support] UBERON in Annotator

Ray Fergerson ray.fergerson at stanford.edu
Fri Apr 26 17:31:26 PDT 2013


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 lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of James
Malone
Sent: Thursday, April 25, 2013 7:39 AM
To: support at bioontology.org 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: http://jamesmaloneebi.blogspot.co.uk/

European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Cambridge, CB10 1SD,
United Kingdom
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Fax: + 44 (0) 1223 494 468

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