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RE: Ontology Working Group Proposal Draft

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Sat, 4 Feb 2006 21:18:33 -0500
Message-ID: <2BF18EC866AF0448816CDB62ADF6538102BF57F6@PHSXMB11.partners.org>
To: "Miller, Michael D \(Rosetta\)" <Michael_Miller@Rosettabio.com>, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Cc: "John Madden" <john.madden@duke.edu>, "Vinay K. Chaudhri" <Vinay.Chaudhri@sri.com>, <wangxiao@musc.edu>, <duncan.hull@cs.man.ac.uk>, "Robert Stevens" <robert.stevens@manchester.ac.uk>, "Amit Sheth @ LSDIS" <amit@cs.uga.edu>, "Alfredo Morales" <Alfredo.Morales@cerebra.com>, "Ullman-Cullere, Mollie" <MULLMANCULLERE@PARTNERS.ORG>, <ray.hookway@hp.com>, "Mark Musen" <musen@stanford.edu>


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:
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> > > >R&amp;D<o:p></o:p></span></font></p>
> > > >
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Received on Sunday, 5 February 2006 02:18:40 GMT

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