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[bioontology-support] missing provisional classes

Jim Balhoff balhoff at nescent.org
Mon Aug 18 12:34:51 PDT 2014


Hi Ray,

I have some more information about this problem. When my colleague sent me the missing ID, he only sent the UUID portion. Now I realize that we have many provisional term IDs like this:

http://purl.bioontology.org/ontology/provisional/ac7bb99b-47cb-4249-8ddc-46d361a07209

If I do a GET on that ID, I get an error response. If I change the beginning part to 'http://data.bioontology.org/provisional_classes/' I get a 404. Is it possible that some provisional terms were lost in migrating to the new API? I can replace the URIs with the new prefix in our data, but it seems like some are missing.

Thank you,
Jim


On Aug 15, 2014, at 1:51 PM, Jim Balhoff <balhoff at nescent.org> wrote:

> Hi Ray,
> 
> Unfortunately it's kind of hard to piece this together now; he requested new terms and replaced some of his missing ones. The creator for any of them should have been 'http://data.bioontology.org/users/phenoscape'
> 
> I am pretty sure some are missing because I can't imagine how he got those IDs into his data file otherwise. As far as I know there isn't any way to stop anyone from deleting a term, which has made me a little nervous. So anyone could have issued a DELETE request.
> 
> I wonder if it would work for you to disable DELETE for provisional terms, but instead add a field 'deprecated' that could be set to true, or something like that?
> 
> Thanks,
> Jim
> 
> 
> On Aug 14, 2014, at 8:25 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
> 
>> Do you know when this provisional class was created? Can you provide any
>> more information about the class (proposed name, parents, ontology, etc).
>> It is not obvious where this went to...
>> 
>> Ray
>> 
>> -----Original Message-----
>> From: bioontology-support
>> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Jim
>> Balhoff
>> Sent: Thursday, August 14, 2014 1:22 PM
>> To: bioontology-support at lists.stanford.edu
>> Subject: [bioontology-support] missing provisional classes
>> 
>> Hi,
>> 
>> One of our users is missing several provisional classes he created via the
>> API. One of them should be:
>> 
>> http://data.bioontology.org/provisional_classes/2423f93d-e225-48cb-838d-ee
>> e016b99632b
>> 
>> Is there a way to view provisional classes that may have been deleted (or
>> can you see these)? I am trying to figure out what may have happened to
>> this user's terms.
>> 
>> Thank you,
>> Jim
>> 
>> 
>> ____________________________________________
>> James P. Balhoff, Ph.D.
>> National Evolutionary Synthesis Center
>> 2024 West Main St., Suite A200
>> Durham, NC 27705
>> USA
>> 
>> 
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> 
> 



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