RE: Ontology Working Group Proposal Draft

Michael,

Thanks for the feedback. The type of ontologies you mention will be incorporated
into the ontology working group proposal.

Look forward to your participation and feedback.

Cheers,

---Vipul

=======================================
Vipul Kashyap, Ph.D.
Senior Medical Informatician
Clinical Informatics R&D, Partners HealthCare System
Phone: (781)416-9254
Cell: (617)943-7120
http://www.partners.org/cird/staff.asp?stAb=vik 
 
To keep up you need the right answers; to get ahead you need the right questions
---John Browning and Spencer Reiss, Wired 6.04.95

> -----Original Message-----
> From: Miller, Michael D (Rosetta) [mailto:Michael_Miller@Rosettabio.com]
> Sent: Friday, February 03, 2006 6:13 PM
> To: Kashyap, Vipul; public-semweb-lifesci
> Cc: John Madden; Vinay K. Chaudhri; wangxiao@musc.edu;
> duncan.hull@cs.man.ac.uk; Robert Stevens; Amit Sheth @ LSDIS; Alfredo
> Morales; Ullman-Cullere, Mollie; ray.hookway@hp.com; Mark Musen
> Subject: RE: Ontology Working Group Proposal Draft
> 
> Hi All,
> 
> Overall, it looks like a nice formulation.  I especially like the
> emphasis in practical usage.
> 
> For point 2, there is an additional class of ontologies for annotating
> life science studies/investigations/experiments for purposes of
> publication and reproducibility.
> 
> For microarray experiments, several major scientific journals, including
> the Nature group, The Lancet, Cell and EMBO journal adopted MIAME
> recommendations and submission of the experiment to a repository (GEO or
> ArrayExpress) as a requirement for publication of microarray
> experiments.
> 
> MAGE-OM and MAGE-ML, the OMG Gene Expression specification
> (http://www.omg.org/technology/documents/formal/gene_expression.htm),
> were developed as a format for describing a microarray experiment and
> the MGED Ontology (http://mged.sourceforge.net/ontologies/index.php) was
> developed for use in annotating MAGE-ML documents.  It is actually
> getting used a great deal.
> 
> There is a follow-up effort, FuGE-OM and FuGE-ML (functional genomic
> experiments) that is currently being developed, to broaden the base to
> proteomics, genotyping, various -omics, etc. which is also having a
> similar ontology developed.
> 
> cheers,
> Michael
> 
> Michael Miller
> Lead Software Developer
> Rosetta Biosoftware Business Unit
> www.rosettabio.com
> 
> 
> > -----Original Message-----
> > From: public-semweb-lifesci-request@w3.org
> > [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of
> > Kashyap, Vipul
> > Sent: Friday, February 03, 2006 2:27 PM
> > To: public-semweb-lifesci
> > Cc: John Madden; Vinay K. Chaudhri; wangxiao@musc.edu;
> > duncan.hull@cs.man.ac.uk; Robert Stevens; Amit Sheth @ LSDIS;
> > Alfredo Morales; Ullman-Cullere, Mollie; ray.hookway@hp.com;
> > Kashyap, Vipul; Mark Musen
> > Subject: Ontology Working Group Proposal Draft
> >
> >
> >
> > Hi,
> >
> > The draft proposal for the Ontology Working Sub-Group is
> > attached with this
> > e-mail.
> >
> > I recognize that this might need to be scoped down a little
> > bit. Have tried to
> > identify collaboration points with the other sub-groups. The
> > proposal identifies
> > "lead" parties for each of the deliverables.
> >
> > This is a draft and any feedback and suggestions are most welcome.
> >
> > Cheers,
> >
> > ---Vipul
> >
> > =======================================
> > Vipul Kashyap, Ph.D.
> > Senior Medical Informatician
> > Clinical Informatics R&D, Partners HealthCare System
> > Phone: (781)416-9254
> > Cell: (617)943-7120
> > http://www.partners.org/cird/staff.asp?stAb=vik
> >
> > To keep up you need the right answers; to get ahead you need
> > the right questions
> > ---John Browning and Spencer Reiss, Wired 6.04.95
> >
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> > > ><p class=3DMsoNormal><font size=3D2 face=3D"Times New
> > Roman"><span =
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> > > >
> > > ><p class=3DMsoNormal><font size=3D2 face=3D"Times New
> > Roman"><span =
> > > >style=3D'font-size:
> > > >10.0pt'>Senior Medical Informatician, Clinical Knowledge =
> > > >Management<o:p></o:p></span></font></p>
> > > >
> > > ><p class=3DMsoNormal><font size=3D2 face=3D"Times New
> > Roman"><span =
> > > >style=3D'font-size:
> > > >10.0pt'>Partners HealthCare Systems, Clinical Informatics =
> > > >R&amp;D<o:p></o:p></span></font></p>
> > > >
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Received on Sunday, 5 February 2006 02:18:40 UTC