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[bioontology-support] REST access to Plant Structure ontology

Tomasz Adamusiak tomasz at ebi.ac.uk
Tue Nov 24 02:33:33 PST 2009


Hi Natasha,

Many thanks for clarifying. If I understand correctly, basically any 
ontology could become remote to BP and its virtual ID would then stop 
resolving to the latest non-remote version. In that case, for every 
ontology I'm querying, I will have to iterate through all the versions 
first to find the latest non-remote one. Could there be perhaps an extra 
field added in there somewhere indicating which one is that?

Though frankly as a BioPortal user I shouldn't really be concerned about 
all that and would be quite happy if the virtual ID just pointed to the 
latest non-remote version :)

Thanks
Tomasz

Natasha Noy wrote, On 2009-11-23 19:05:
> Hi Tomasz,
>
> Here is what's going on: the ontology is no longer in the OBO Foundry
> CVS, so it is now "remote" as far as BioPortal is concerned: for the
> ontologies that we pull from OBO Foundry site, we can download only the
> ones that are in their CVS. When it became remote (just recently, with
> BioPortal version 40892), we didn't wipe out the old version (40433)
> from the search index (actually, that's a bug) and that's why the search
> still works.
>
> But when you try to access the ontology by the virtual id as in your
> rest call for the concept, it resolves to the latest version (40892) and
> that one is not local to BioPortal.
>
> So, there are several ways to address this:
> 1. Have the developers of Plant structure ontology submit it directly to
> BioPortal (or ask us to do it any time a new version is published and
> we'll be happy to do it for them).
> 2. Have your REST call go to the latest version that *is* in BioPortal
> rather than fetch it by the virtual ID:
> http://rest.bioontology.org/bioportal/concepts/40433/PO:0000055
>
> We are working on having the pull enabled from other repositories -- not
> just the OBO Foundry CVS, but it is not quite there yet.
>
> I hope this helps.
>
> Natasha
>
>
> On Nov 23, 2009, at 8:13 AM, Trish Whetzel wrote:
>
>> Hi Tomasz,
>>
>> I looked into this, however am not sure what is causing the problem.
>> I'll pass this along to the developers to look into further.
>>
>> Trish
>>
>>
>> On Nov 23, 2009, at 4:54 AM, Tomasz Adamusiak wrote:
>>
>>> Hi,
>>>
>>> I can't access PO concepts through web services any more, e.g.:
>>> http://rest.bioontology.org/bioportal/virtual/ontology/1108/PO:0000055?email=example@example.org
>>>
>>>
>>> Searching works though:
>>> http://rest.bioontology.org/bioportal/search/PO:0000055/?ontologyids=1108&email=example@example.org
>>>
>>>
>>> Cheers
>>> 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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>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support



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