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[bioontology-support] obsolete terms

Ray Fergerson ray.fergerson at stanford.edu
Wed Dec 8 17:22:21 PST 2010


Tomasz,

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Thus there is no way today to tell if the term is obsolete.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.

Ray

-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Tomasz Adamusiak
Sent: Monday, December 06, 2010 4:02 AM
To: support at bioontology.org
Cc: Helen Parkinson
Subject: [bioontology-support] obsolete terms

Hi,

Is there a way to to identify obsolete terms in the REST output?
Example:
http://rest.bioontology.org/bioportal/virtual/ontology/1009/DOID:0050326?e
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
http://rest.bioontology.org/bioportal/virtual/ontology/1015/FBbt:00005525?
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:
http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_term

All help very much appreciated!

Thanks
Tomasz




--
Tomasz Adamusiak, MD, PhD
European Bioinformatics Institute
+44 (0) 1223 492 562
tomasz.adamusiak at ebi.ac.uk
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