[obs] OBOE master file

[Shawn Bowers]

Hi --

> thanks for the information. Are the latest oboe files under version control
> somewhere?

Yep, they are under version control.

> I have a real concern here that people who are interested in exploring this
> for their own use are frustrated unnecessarily by being led down wrong paths
> simply due to lack of documentation and by abandoned versions having been
> kept alive.

Yeah, I understand. Having a webpage that links to the "official"
versions is probably the way to go ...

> "when it is finished" sounds like rather open-ended to me -
> based on my experience in ontology development, an ontology that is in
> active use in science is never finished.

I think you misunderstood what I said. I was saying when the
*documentation* is finished, not the ontologies per se. We started
writing up an "oboe guide" but it was shelved for some time because of
various reasons. Once the guide is finished, the plan is to put this
on the web.

> Are there are hurdles to disabling the outdated links (cvs remove, svn
> remove anyone?), or to putting up a one-page documentation on the Semtools
> or SONet site, using pretty much what you say below?

I think the best thing to do for now is as you say ... put up a
one-page document on the site that links to these ...

Thanks,
Shawn

>
>        -hilmar
>
> On Oct 27, 2010, at 11:39 AM, Shawn Bowers wrote:
>
>> Hi Hilmar,
>>
>> (I guess I'd be the "whoever" :-). Most of the "hits" you are finding
>> in your searches are to (older) cvs and/or svn repositories. The one
>> in the bioportal is the most recent, which can be found here:
>>
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl
>>
>> The ontologies under oboe.1.0 always contains the most recent versions.
>>
>> The ontology is split into a number of different files and some
>> extensions (which are also under oboe.1.0). They are:
>>
>>
>> 1). The basic, or core oboe classes:
>>
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl
>>
>>
>> 2). An extension for asserting context relationships as part of
>> measurement (e.g., that an observation was made of an entity when that
>> entity was "located in", was a "part of", etc., some other entity).
>> Oboe-core allows one to say that one observation/measurement was made
>> within the context of another, whereas oboe-context allows one to
>> assign a specific relationship to the contextualization.
>>
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe-context.owl
>>
>>
>> 3). The main extension to core, which includes structures for defining
>> measurement standards (e.g., units), etc. This should be the main
>> starting point for most oboe-compatible ontologies (although core
>> could be used as well)
>>
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl
>>
>>
>> 4). Various unit definitions are available in oboe-units:
>>
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe-units.owl
>>
>> This one has many units (including the SI units) and corresponding
>> top-level characteristics/dimensions (i.e., where a characteristic is
>> similar to what EQ calls "attributes"), but the list of units is not
>> complete (although it has the typical units used in many domains).
>>
>>
>> 5). Some experimental domain ontologies. These are still work in
>> progress and are currently being developed:
>>
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe-chemistry.owl
>> http://ecoinformatics.org/oboe/oboe.1.0/oboe-sbc.owl
>>
>> The oboe sbc ontology is targeted at common measurements taken at the
>> SBC LTER site. This ontology is being used for annotating SBC
>> datasets.
>>
>> 6). There are some plant-trait ontologies we've developed (for
>> annotating plant trait measurements, like specific leaf area, etc.)
>> These are not yet available via oboe.1.0 but I'm assuming they will be
>> soon ...
>>
>>
>> We're hoping to have formal documentation soon for all of the above,
>> and will make it public, etc., when it is finished (in a publishable
>> state).
>>
>> If anyone has any additional questions about oboe, how we use it, best
>> practices, etc., I'm more than happy to help!
>>
>>
>> Shawn
>>
>>
>> On Wed, Oct 27, 2010 at 7:56 AM, Hilmar Lapp <hlapp at nescent.org> wrote:
>>>
>>> Mark or Matt or whoever else happens to know: Where can I find the latest
>>> OWL master file of the OBOE ontology, and is there a project home page?
>>>
>>> What I was able to find (using Google) is this:
>>>
>>> -
>>>
>>> http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/seek/projects/kr-sms/kr/ontologies/OBOE/Observation.owl?content-type=text/xml
>>>
>>>       CVS, with last commit Jan 30, 2008
>>>
>>> - https://sonet.ecoinformatics.org/semtools-svn/oboe/
>>>
>>>       presumably SVN, but the link to oboe.owl returns a page not found
>>>
>>> - https://semtools.ecoinformatics.org/repository/dev/oboe/oboe.owl
>>>
>>>       which is linked to from Semtools:
>>>       https://semtools.ecoinformatics.org/repository/dev/oboe
>>>
>>>       Apparently last svn commit also from Jan 30, 2008. This advertises
>>> itself under namespace http://ecoinformatics.org/oboe/oboe.0.9
>>>
>>> - http://bioportal.bioontology.org/ontologies/44258
>>>
>>>       This advertises itself as "Version 1.0 pre-release" and namespace
>>>       http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl
>>>
>>>       The Bioportal page gives the Semtools page as homepage, but the two
>>> ontology versions actually differ quite a bit from browsing through it in
>>> Protege.
>>>
>>> So, which one is the master, and where is it documented clearly what the
>>> master is? Also, any plans in taking down those versions that are no
>>> longer
>>> developed?
>>>
>>> (And Cam, which version are you using?)
>>>
>>>       -hilmar
>>> --
>>> ===========================================================
>>> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
>>> ===========================================================
>>>
>>>
>>>
>>> _______________________________________________
>>> obs mailing list
>>> obs at ecoinformatics.org
>>> http://lists.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/obs
>>>
>
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
>
>