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RE: Ontology Working Group Proposal Draft

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Fri, 3 Feb 2006 15:12:52 -0800
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, "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>
Message-ID: <E1F5A71-0007th-SW@maggie.w3.org>

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 
>  
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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:
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> > >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>
> > >
> > ><p class=3DMsoNormal><font size=3D2 face=3D"Times New 
> Roman"><span =
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> t1:place><f=
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> > 
> >href=3D"http://www.partners.org/cird/staff.asp?stAb=3Dvik">ht
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Received on Friday, 3 February 2006 23:13:11 GMT

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