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:[EMAIL PROTECTED]
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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Alan Ruttenberg
Sent: Tuesday, June 06, 2006 6:40 AM
To: kc28
Cc: [EMAIL PROTECTED];
[EMAIL PROTECTED]; '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
