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[bioontology-support] obsolete terms

Tomasz Adamusiak tomasz at ebi.ac.uk
Fri Dec 10 02:25:47 PST 2010


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 Thus there is no way today to tell if the term is obsolete.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