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

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 15:49:03 UTC