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[bioontology-support] REST access to Plant Structure ontology

Natasha Noy noy at stanford.edu
Mon Nov 23 11:05:53 PST 2009


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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