Re: Versioning system for ontologies

On Fri, Apr 19, 2013 at 1:17 PM, Ali SH <asaegyn+out@gmail.com> wrote:

> Dear Alan,
>
> On Fri, Apr 19, 2013 at 1:08 PM, Alan Ruttenberg <alanruttenberg@gmail.com
> > wrote:
>
>> What you say is certainly of interest. But I would call that change
>> tracking and provenance maintenance rather than version control.
>>
>
> I suspect then we may differ in that I interpret version control as a
> component part of change tracking and provenance. I'm interested in
> ensuring that the ontologies I (my group) have developed satisfy a set of
> test cases and audit suites (e.g. competency questions, time
> limits) through each version.
>
> I suppose for other use cases, vanilla version control may suffice, but i
> would personally be curious about the quality of said ontologies.
>

I've very much for paying attention to ontology quality, and in my own
practice have processes in place such as those you suggest. Let's say I'm
pleasantly surprised the topic comes up, as it doesn't often enough ;-)


>
>
>> As I said, whatever solution you take, don't forget about publishing your
>> ontology according to the spec. There is a tendency, when using such
>> systems, to forget about the basics and therefore reduce the network
>> effects that accrue from using what we have sweated to specify, in favor of
>> using ad-hoc, albeit proximally useful, systems.
>>
>
> Absolutely! Though of course, one can interpret the above as complementary
> additions, as opposed to ad hoc or proximally useful :P. It depends on the
> intended ontology usage and requirements.
>

Both those terms are descriptive, not pejorative. I don't think we disagree.


>
> Best,
> Ali
>
>
>> -Alan
>>
>>
>>
>> On Fri, Apr 19, 2013 at 1:05 PM, Ali SH <asaegyn+out@gmail.com> wrote:
>>
>>> Hi Alan,
>>>
>>> What you suggest certainly provides a way of handling versioning, but in
>>> many environments, the additional repository features seem to be
>>> requirements. You almost always want to know who made a change, what the
>>> change was, alongside other provenance information - and of course, make
>>> this information machine readable (as opposed to a text note) seems
>>> desirable for this community :P.
>>>
>>> As I'm sure you're aware, when considering the quality and evaluation of
>>> ontologies, identifying the state of an ontology throughout its lifecycle
>>> also becomes quite important. Rafael S. Goncalves, Maria Copeland and their
>>> colleagues provide an interesting set of analyses on how ontologies differ
>>> through multiple versions [1] [2] [3].
>>>
>>> Of tangential (but closely related) interest to versioning, people might
>>> want to take a look at this year's Ontology Summit 2013 which focuses on
>>> "Ontology Evaluation Across the Ontology Lifecycle" [4]. Of particular
>>> interest may be the talk on the lifecycle stages (and from that one can
>>> extrapolate requirements for versioning that would faciliatae higher
>>> quality ontologies) - particularly Hanz Polzer and Mary Balboni's
>>> contributions [5].
>>>
>>> PS - Thanks for the response, will follow up offlist :D!
>>> [1]
>>> http://owl.cs.manchester.ac.uk/research/topics/ncit/regression-%20analysis/
>>> [2] http://ceur-ws.org/Vol-745/paper_40.pdf
>>> [3]
>>> http://ontolog.cim3.net/file/work/OntologySummit2013/2013-03-07_OntologySummit2013_OntologyEvaluation-IntrinsicAspects-2/OntologySummit2013_ontology-regression-testing--MariaCopeland_20130307.pdf
>>> [4] http://ontolog.cim3.net/OntologySummit/2013/
>>> [5] http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2013_01_24
>>>
>>>
>>> On Fri, Apr 19, 2013 at 12:49 PM, Alan Ruttenberg <
>>> alanruttenberg@gmail.com> wrote:
>>>
>>>> Don't forget about OWL's versionIRI, which gives a way to express that
>>>> different versions are of a single ontology. The most basic version control
>>>> is to periodically save a file, put it at a location, and make the
>>>> versionIRI point to it. Keep the ontologyIRI the same thoughtout. Use
>>>> import with the version you care load. At the ontologyIRI put either the
>>>> most recent version or the most recent version you release.
>>>>
>>>> There is no need for additional repository infrastructure, though that
>>>> may add useful features. Whatever you do, make sure that at a minimum you
>>>> version using vanilla specifications, given that they can support that.
>>>>
>>>> I generally recommend you do not change IRIs of terms as you change
>>>> versions. Rather,  try to ensure that the referents of your URIs refer to
>>>> the same intended entities, and obsolete them if they no longer refer well.
>>>>
>>>> Happy to discuss this offlist if you are interested in my experiences.
>>>>
>>>> Best,
>>>> Alan
>>>>
>>>> On Friday, April 19, 2013, Ali SH wrote:
>>>>
>>>>> I'm also very interested in hearing answers to this.
>>>>>
>>>>> As Stephen mentions, treating an ontology analogously to source code
>>>>> (which is close enough) means that you can use services such as github (or
>>>>> google code). The downside is that an ontology lifecycle management is
>>>>> *not* equivalent to source code management. Barring a native solution
>>>>> for ontologies, they do come quite close.
>>>>>
>>>>> You might also be interested in following the development of the Open
>>>>> Ontology Repository [1]
>>>>> (a fork of the BioPortal platform), which among other things will be
>>>>> addressing this issue as well.
>>>>>
>>>>> [1] http://ontolog.cim3.net/cgi-bin/wiki.pl?OpenOntologyRepository
>>>>>
>>>>> On Fri, Apr 19, 2013 at 11:57 AM, Stephen D. Williams <sdw@lig.net>wrote:
>>>>>
>>>>>>  Do you want to version it like source code?  Everyone has, is, or
>>>>>> will move to Git for that.
>>>>>> Or maintain the history of changes for reasoning and/or historical
>>>>>> queries?  This is probably more needed for actual statements, but could
>>>>>> make sense here too: "Answer this query based on the ontology at time X."
>>>>>>
>>>>>> Stephen
>>>>>>
>>>>>>
>>>>>> On 4/19/13 7:05 AM, Prateek wrote:
>>>>>>
>>>>>>  Hello all,
>>>>>>
>>>>>>  I am trying to identify a system which will provide versioning and
>>>>>> revision control capabilities specifically for ontologies. Does anyone have
>>>>>> any experience and idea about which systems can help out or if systems like
>>>>>> SVN, CVS can do the job?
>>>>>>
>>>>>>  Regards
>>>>>>
>>>>>>  Prateek
>>>>>>
>>>>>>  --
>>>>>>
>>>>>> - - - - - - - - - - - - - - - - - - -
>>>>>> Prateek Jain, Ph. D.
>>>>>> RSM
>>>>>> IBM T.J. Watson Research Center
>>>>>> 1101 Kitchawan Road, 37-244
>>>>>> Yorktown Heights, NY 10598
>>>>>> Linkedin: http://www.linkedin.com/in/prateekj
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Stephen D. Williams sdw@lig.net stephendwilliams@gmail.com LinkedIn: http://sdw.st/in
>>>>>> V:650-450-UNIX (8649) V:866.SDW.UNIX V:703.371.9362 F:703.995.0407AIM:sdw Skype:StephenDWilliams Yahoo:sdwlignet Resume: http://sdw.st/gres
>>>>>> Personal: http://sdw.st facebook.com/sdwlig twitter.com/scienteer
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>>
>>>>> (•`'·.¸(`'·.¸(•)¸.·'´)¸.·'´•) .,.,
>>>>>
>>>>
>>>
>>>
>>> --
>>>
>>>
>>> (•`'·.¸(`'·.¸(•)¸.·'´)¸.·'´•) .,.,
>>>
>>
>>
>
>
> --
>
>
> (•`'·.¸(`'·.¸(•)¸.·'´)¸.·'´•) .,.,
>