Hi Michael et al.,
Karen Skinner (of NIDA) has once pointed me to the following public
microarray experiment related to the study of Parkinson's Disease
http://arrayconsortium.tgen.org/np2/viewProject.do?action=viewProject&projectId=61
My question is that can we use FuGO or FuGO-OM or other ontologies
(MGED-OWL) to describe this experiment (or part of it)? This might also
serve as a Parkinson use case study for the ontology working group.
Cheers,
-Kei
Miller, Michael D (Rosetta) wrote:
Hi All,
Thanks for pointing us to FuGO. To me, it seems like that the FuGO
community is currently defining an upper ontology that can be
universally used to describe different types of genomic/proteomic
experiments including microarray experiments.
This, I believe, is their goal.
but
there is no
example use for microarray experiments.
To actually describe microarray experiments (and proteomics, etc.), it
is expected that this will be done through extensions of FuGE-OM, a UML
model that takes experiences from MAGEv1 and PEDRo (and others) to
create an object model that describes what is basic to all biological
based experiments. MAGEv2 will extend this model.
One goal of FuGO is:
"The purpose of this ontology is to support the consistent annotation of
functional genomics experiments, regardless of the particular field of
study."
So it is unlikely at this point that there will be a class
"Hybridization" or "FeatureExtraction" in the ontology but there is
likely to be terms that describe particular ways of doing a
hybridization or feature extraction.
FuGO is still at an early stage, see http://fugo.sourceforge.net/ for
how someone can contribute.
cheers,
Michael
-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of kei cheung
Sent: Tuesday, June 06, 2006 9:52 AM
To: Alan Ruttenberg
Cc: [EMAIL PROTECTED];
[EMAIL PROTECTED]; 'Daniel Rubin';
public-semweb-lifesci@w3.org; 'Matthew Cockerill'
Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
the UMLS presentation
Hi Alan,
Thanks for pointing us to FuGO. To me, it seems like that the FuGO
community is currently defining an upper ontology that can be
universally used to describe different types of genomic/proteomic
experiments including microarray experiments. There is a draft OWL
version of FuGO
(http://fugo.sourceforge.net/ontology/FuGO.owl). A list
of use case uses is also shown at:
http://fugo.sourceforge.net/ontologyInfo/ontology.php, but
there is no
example use for microarray experiments. So it might be worthwhile to
take a look at how FuGO can be used to describe microarray
experiments
(at least at a high level).
Cheers,
-Kei
Alan Ruttenberg wrote:
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
