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

Hi Kei,

Not surprising that Gavin is involved there.  I'm not sure of his main
priorities but he might be interested.  You can give it a shot.

cheers,
Michael

> -----Original Message-----
> From: kei cheung [mailto:kei.cheung@yale.edu] 
> Sent: Tuesday, June 06, 2006 10:18 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 and Larry,
> 
> As I understand it, Gavin Sherlock who is a member of MGED is 
> involved 
> in the ontological/informatic aspect of  the NIH Neuroscience 
> Microarray 
> Consortium. I'm also involved in the informatic aspect of this 
> Consortium. Should we contact Gavin to see if he is also 
> interested in 
> this? Since all of us are very busy and I'm a believer of 
> incrementality, we probably should aim at something small and 
> simple to 
> begin with and work our way up.
> 
> Cheers,
> 
> -Kei
> 
> Miller, Michael D (Rosetta) wrote:
> 
> >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 18:57:20 UTC