[MOBY-l] DAML/OIl editor for viewing MyGrid ontology

[Simon Twigger]

Hi Phil,

Many thanks for your comments, I was hoping someone from MyGrid would  
catch this. At the MOBY developers meeting this weekend we decided it  
was time to expand the MOBY service ontology and the existing MyGrid  
ontology seemed like a great place to start. I completely agree that we  
should endeavor to keep things in sync where ever possible.

I've been looking through the list of pubs from MyGrid and it looks  
like Chris Wroe's paper in Int. J. Cooperative Info. Systems. Vol. 12,  
No. 2 (2003) 197-224 on "DAML+OIL ontologies to describe bioinformatics  
web services and data"would be a good place for me to start reading  
about how this ontology came together. If there are other docs that you  
would recommend please let me know. Once I've got a better feel for  
things I'll probably pester you for more information if thats Ok.

Thanks for the info on Protege  at http://www.co-ode.org/, I found an  
OWL plugin already but the graph drawing plugin looks handy so I'll  
give that a go too.

Cheers,

Simon.


On Apr 5, 2004, at 5:59 AM, Phillip Lord wrote:

>
>>>>>> "Simon" == Twigger, Simon <simont at mcw.edu> writes:
>
>   Simon> After some hacking around online whilst waiting in the scenic
>   Simon> Concourse B at La Guardia airport, I found a DAML/Oil editor
>   Simon> that I could get to work on my Mac and that accepted the
>   Simon> MyGrid ontology files:
>
>   Simon> I tried the Protege editor which looked really nice but I
>   Simon> couldnt find a way to get DAML/Oil into the app from the flat
>   Simon> file, the DAML/Oil plugin is out of date and doesnt work with
>   Simon> the latest version of protege
>   Simon> (http://protege.stanford.edu). It looks good and has an Owl
>   Simon> plugin but I dont have Owl files to play with to test it out.
>
> OWL support for protege certainly exists. As well as the OWL plugin
> you might want to look at...
>
> http://www.co-ode.org/
>
> which is starting to build some quite nifty support for OWL editing
> into protege.
>
>
>   Simon> OilEd : http://oiled.man.ac.uk/ (java app)
>
>   Simon> The MyGrid ontology files can be found here:
>
>   Simon>  
> http://cvs.mygrid.org.uk/cgi-bin/viewcvs.cgi/mygrid/ontology-server/ 
> etc/onto
>   Simon> logy/
>
>   Simon> I used the mygrid.daml file in OilEd and its working nicely.
>
> It would be depressing if oiled could not load mygrid.daml. It was
> written with oiled, at least initially. And later it was generated
> with the oiled code base.
>
> One thing which is worth mentioning is that the file you are looking
> at has not been reasoned over. So many of the is-a links that you
> might expect to see are not there; they will magically appear if you
> use the reasoner. Sadly at the moment the reasoner will not run on a
> mac, although we have a new version that should do.
>
>
>>> From preliminary review, it looks like the branches of interest
>>> for the MOBY
>   Simon> service ontology might be:
>
>   Simon> top:domain_concept#1:process#1:generic_process#1
>
>   Simon> This has things like: aligning, calculating, filtering,
>   Simon> grouping, parsing, retrieving, etc. and is along the same
>   Simon> lines as we have right now in MOBY, there are 17 terms in
>   Simon> this brank with only aligning having any children.  I'll look
>   Simon> more at this and go from there.
>
> I think that it would be nice if we can try and keep the meanings of
> the different properties in sync in so far as that is possible between
> the mygrid ontology and the moby one. Ontologies are, after all, only
> useful in so far as they are shared.
>
> Cheers
>
> Phil
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>
>
--

Simon N. Twigger, Ph.D.
Assistant Professor, Department of Physiology
Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, USA
tel: 414-456-8802
fax: 414-456-6595