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[bioontology-support] obsolete terms

Tomasz Adamusiak tomasz at ebi.ac.uk
Mon Dec 6 04:01:38 PST 2010


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?email=example@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@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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