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[bioontology-support] REST access to Plant Structure ontology

Trish Whetzel whetzel at stanford.edu
Tue Nov 24 07:54:57 PST 2009


Hi Tomasz,

In the REST call to list all versions of an ontology by virtual id (http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_all_versions_of_an_ontology_from_a_virtual_ontology_id 
) there is an element "isRemote" with boolean values to indicate  
whether the ontology is local to BioPortal. For example, the value for  
isRemote for http://rest.bioontology.org/bioportal/ontologies/versions/1108?email=example@example.org 
  for the most recent version (40892) of the ontology is 1.

In addition, there are also some items that I would like to discuss  
with Misha regarding ontologies that were once listed as local to  
BioPortal that become listed as remote and will follow-up with you  
pending that discussion.

Trish


On Nov 24, 2009, at 2:33 AM, Tomasz Adamusiak wrote:

> 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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