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[bioontology-support] obsolete terms

Trish Whetzel whetzel at stanford.edu
Thu Dec 16 21:07:16 PST 2010


Hi Tomasz,

The new release is out. The obsolete tag is located under the <relations> XML element and is formatted as:
<entry>
<string>is_obsolete</string>
<string>true</string>
</entry>

Trish


On Dec 10, 2010, at 2:25 AM, Tomasz Adamusiak wrote:

> Hi Ray,
> 
> Many thanks. Looking forward to the new release.
> 
> Tomasz
> 
> On 09/12/2010 01:22, Ray Fergerson wrote:
>> 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 Thus there is no way today to tell if the term is obsolete.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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>> bioontology-support at lists.stanford.edu
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