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[bioontology-support] missing provisional classes

Jim Balhoff balhoff at nescent.org
Wed Aug 20 10:23:39 PDT 2014


Hi Ray,

Thank you for checking into this. It's very confusing because I can't really imagine how a non-existent ID would have gotten into the data. :-)

I think we can just resubmit the missing terms wherever we come across one. I am really glad to know about the URL for terms created by a particular user. I was wishing I could do filtering by user on the provisional classes query, looks like I can.

Best regards,
Jim


On Aug 19, 2014, at 4:46 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:

> Jim,
> 
> We cannot find this ID in the old system either.
> 
> Your purl below is strange in that there is no such purl in the server
> (ontology/provisional). Even if we lost the provisional terms (which we
> don't think that we did) the purl server (which is completely independent)
> should still have the purls - even if where they point to is broken. There
> isn't a way to delete a purl out of the server.
> 
> All of the provisional terms that we have in the system now created by
> phenoscape are available from:
> 
> http://data.bioontology.org/users/phenoscape/provisional_classes
> 
> There are quite a few there, but none that match your UUID.  We may just
> not be able to reconstruct what happened.
> 
> Ray
> 
> -----Original Message-----
> From: Jim Balhoff [mailto:balhoff at gmail.com] On Behalf Of Jim Balhoff
> Sent: Monday, August 18, 2014 12:35 PM
> To: Ray Fergerson
> Cc: bioontology-support at lists.stanford.edu
> Subject: Re: [bioontology-support] missing provisional classes
> 
> 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-4
> 6d361a07209
> 
> 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-83
>>> 8d-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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