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[bioontology-support] obsolete terms
ray.fergerson at stanford.edu
Wed Dec 8 17:22:21 PST 2010
Unfortunately the current release filters out the obo is_obsolete tag.
Thus there is no way today to tell if the term is obsolete. This tag will
no longer be filtered in the next release. We expect this new release to
go out next week. I hope that you can wait until then.
Get-term should work fine for virtual ontology ids.
From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Sent: Monday, December 06, 2010 4:02 AM
To: support at bioontology.org
Cc: Helen Parkinson
Subject: [bioontology-support] obsolete terms
Is there a way to to identify obsolete terms in the REST output?
mail=example at example.org
The OBO version of DO has an is_obsolete tag on this term, but I don't
see it in the BioPortal REST ouput. I could use a proxy of having no
relationships for the moment, but would be easier if some sort of flag
was set in there.
The problem for us here is that obsolete terms are returned in a search
query when we try to map user annotation values to external ontologies,
so looking for a way to filter those out.
Also once the obsolete term is identified the OBO consider/replaced_by
tags would really come in handy, as in this example
email=example at example.org
By the way, is the get term by virtual ontology id method being
deprecated? I just noticed it's no longer mentioned in the docs:
All help very much appreciated!
Tomasz Adamusiak, MD, PhD
European Bioinformatics Institute
+44 (0) 1223 492 562
tomasz.adamusiak at ebi.ac.uk
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