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

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: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of kei cheung
> Sent: Tuesday, June 06, 2006 9:52 AM
> To: Alan Ruttenberg
> Cc: donald.doherty@brainstage.com; 
> wilbanks@creativecommons.org; '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
> >
> >
> 
> 
> 
> 
>

Received on Tuesday, 6 June 2006 17:07:01 UTC