Re: Versioning system for ontologies

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.


> 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.

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
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>>
>>>> (•`'·.¸(`'·.¸(•)¸.·'´)¸.·'´•) .,.,
>>>>
>>>
>>
>>
>> --
>>
>>
>> (•`'·.¸(`'·.¸(•)¸.·'´)¸.·'´•) .,.,
>>
>
>


-- 


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