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[bioontology-support] missing provisional classes

Ray Fergerson ray.fergerson at stanford.edu
Tue Aug 19 13:46:04 PDT 2014


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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