RE: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the UMLS presentation

Hi Kei and Larry,

Well, since I'm on the MGED board and principal editor of the OMG Gene
Expression (MAGE) specification, I'm probably good as anyone as a point
person.

What exactly do you envision that the MGED community can do and how we
can work together?  It's a grass-roots organization that in the last few
years became an official non-profit, so consortium is a bit too strong a
word.  It's an open community so anyone can participate, it is a matter
of having the time and desire.

One of my problems is that I'm typically very constrained for time, my
employees actually expect me to write code from time to time.  As such
I've typically just been listening in.  When I do participate, as
recently, it is as someone whose main focus is NOT ontologies or the
underpinnings of the semantic web but as someone for whom ontologies and
the semantic web are but two (important) considerations of the many
considerations for the application I work on.

cheers,
Michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com

> -----Original Message-----
> From: kei cheung [mailto:kei.cheung@yale.edu] 
> Sent: Tuesday, June 06, 2006 9:41 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for 
> the UMLS presentation
> 
> 
> Hi Michael,
> 
> Thanks for sharing your thoughts. MGED still has rooms for 
> ontological 
> improvement. As Larry suggested, we would have a better luck 
> if we can 
> work with the MGED consortium.
> 
> Cheers,
> 
> -Kei
> 
> Miller, Michael D (Rosetta) wrote:
> 
> >Hi Kei,
> >
> >  
> >
> >>Is there a converter available which can take existing datasets in 
> >>mage-ml format and convert them into mged-owl format?
> >>    
> >>
> >
> >You're asking the wrong person here, but not that I know of.
> >
> >The reason I am the wrong person is that I don't believe that MAGE-OM
> >(from which MAGE-ML, MAGEJava and MAGEPerl is generated) is best
> >represented as an ontology.  I believe there is much that 
> ontologies can
> >do but the best way to capture the process of performing microarray
> >experiment is to call out the actual pipeline process of wet lab
> >biologist processing samples, bench technicians performing the
> >hybridization and scans, the bioinformaticists interpreting the scan
> >data and the overall design of the experiment.  The way 
> these different
> >steps relate to each other does not, to my mind, fit best into an
> >ontology model, that by calling them out as first class 
> objects in the
> >UML model and modeling their specific associations/relationships, all
> >different from each other and specific to the object).
> >
> >To be able to annotate all these objects with ontology terms is
> >definitely needed but to me a separate piece.
> >
> >Granted, if you, or anyone, wish to generate an OWL model 
> from MAGE-OM,
> >it should be possible and I would certainly be interested in 
> the result.
> >The current code to generate the MAGE-ML, MAGEJava and 
> MAGEPerl provide
> >good examples how to do this
> >(http://mged.sourceforge.net/software/index.php).
> >
> >But one could also generate a MAGECobol implementation.
> >
> >cheers,
> >Michael
> >
> >  
> >
> >>-----Original Message-----
> >>From: kei cheung [mailto:kei.cheung@yale.edu] 
> >>Sent: Tuesday, June 06, 2006 7:54 AM
> >>To: Miller, Michael D (Rosetta)
> >>Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
> >>Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for 
> >>the UMLS presentation
> >>
> >>
> >>Hi Michael et al,
> >>
> >>Is there a converter available which can take existing datasets in 
> >>mage-ml format and convert them into mged-owl format?
> >>
> >>Thanks,
> >>
> >>-Kei
> >>
> >>Miller, Michael D (Rosetta) wrote:
> >>
> >>    
> >>
> >>>Hi Alan and All,
> >>>
> >>>The MGED Ontology is now available as OWL.  There has been a recent
> >>>revision to correct some of the formal problems such an early
> >>>implementation has had.
> >>>
> >>>http://mged.sourceforge.net/ontologies/MGEDOntology.owl
> >>>
> >>>Also, the FuGO project would love any feedback, thanks for 
> >>>      
> >>>
> >>pointing out
> >>    
> >>
> >>>the upcoming workshop.
> >>>
> >>>cheers,
> >>>Michael
> >>>
> >>> 
> >>>
> >>>      
> >>>
> >>>>-----Original Message-----
> >>>>From: public-semweb-lifesci-request@w3.org 
> >>>>[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> >>>>Alan Ruttenberg
> >>>>Sent: Tuesday, June 06, 2006 6:40 AM
> >>>>To: kc28
> >>>>Cc: donald.doherty@brainstage.com; 
> >>>>wilbanks@creativecommons.org; 'Daniel Rubin'; 
> >>>>public-semweb-lifesci@w3.org; 'Matthew Cockerill'
> >>>>Subject: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for the 
> >>>>UMLS presentation
> >>>>
> >>>>
> >>>>
> >>>>On Jun 5, 2006, at 9:15 PM, kc28 wrote:
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>>>>It might be time to think about how to convert mged ontology or 
> >>>>>mage-ml into RDF/OWL. The following are two related articles:
> >>>>>
> >>>>>http://www.nature.com/msb/journal/v2/n1/full/msb4100052.html
> >>>>>http://www.nature.com/nbt/journal/v23/n9/full/nbt0905-1095.html
> >>>>>
> >>>>>Cheers,
> >>>>>
> >>>>>-Kei
> >>>>>     
> >>>>>
> >>>>>          
> >>>>>
> >>>>As I understand it, this is the nature of the FuGO project: 
> >>>>http://fugo.sourceforge.net/
> >>>>They have an upcoming workshop
> >>>>http://www.ebi.ac.uk/microarray/General/Events/FuGO2006/index.html
> >>>>
> >>>>-Alan
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>> 
> >>>
> >>>      
> >>>
> >>
> >>
> >>    
> >>
> >
> >
> >  
> >
> 
> 
> 
>

Received on Tuesday, 6 June 2006 16:52:20 UTC