[obs] OBOE master file

[Hilmar Lapp]

Hi Shawn -

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

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. "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.

Are there are hurdles to disabling the outdated links (cvs remove, svn  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?

	-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 :
>> ===========================================================
>>
>>
>>
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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