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:[EMAIL PROTECTED]
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:[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
