Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] REST access to Plant Structure ontology

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

Hi Tomasz,

In the REST call to list all versions of an ontology by virtual 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 
  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.


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:
>> 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.:
>>>> Searching works though:
>>>> Cheers
>>>> Tomasz
>>>> --
>>>> Tomasz Adamusiak, MD, PhD
>>>> European Bioinformatics Institute
>>>> +44 (0) 1223 492 562
>>>> tomasz.adamusiak at
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at

More information about the bioontology-support mailing list