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[bioontology-support] obsolete terms

Tomasz Adamusiak tomasz.adamusiak at ebi.ac.uk
Fri Dec 17 00:09:51 PST 2010


Hi Trish,

Thanks!

Tomasz

On 17/12/2010 05:07, Trish Whetzel wrote:
> 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 Thus there is no way today to tell if the term is obsolete.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
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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>



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