W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > February 2006

[OWG] Telecon

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Mon, 20 Feb 2006 12:04:02 -0500
Message-ID: <2BF18EC866AF0448816CDB62ADF65381033C2994@PHSXMB11.partners.org>
To: "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>, "Susie Stephens" <susie.stephens@oracle.com>, <helen.chen@agfa.com>, "Alan Rector" <rector@cs.man.ac.uk>


Hi,

Would like to schedule a teleconference to discuss the project plan and short
term/long term deliverables.

Would like to schedule it initially as a weekly call for an hour around 11am
Eastern (as this works very well for people on the West Coast and Europe) so
that we can make rapid progress. As things get finalized and stable, we can then
reduce the frequency of the calls.

Please let me know the days which will work for you guys (Tuesday - Friday).

Thanks and Regards,

---Vipul

> -----Original Message-----
> From: Kashyap, Vipul
> Sent: Monday, February 13, 2006 5:53 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'; 'Mark
> Musen'; 'Susie Stephens'; 'helen.chen@agfa.com'; 'Alan Rector'; Kashyap,
> Vipul
> Subject: RE: Ontology Working Group Proposal Draft
> 
> 
> Hi,
> 
> A revised version of the Ontology Task Force Proposal is attached with
> this proposal. A list of proposed tasks with proposed task coordinators is
> as follows. Please let me know if you would rather coordinate other tasks.
> These is just an initial proposal and I have tried to accommodate
> everyone!
> Collaborators of other collaborating task groups have also been
> identified.
> 
> 1. Use Cases Document (3 months):
>    Task Coordinators: Vipul Kashyap, Mollie Ullman-Cullere
>    Collaborating Task Coordinators: Susie Stephens?, Helen Chen?
> 
> 2. Ontology Definitions and Best Practices White Paper (1 year):
>    Task Coordinators: Alfredo Morales, Wangxiao, Robert Stevens
>    Collaborating Task Coordinators: Alan Rector?, Helen Chen
> 
> 3. Ontology Access and Usage Best Practices Report (6 months):
>    Task Coordinators: Duncan Hall, Ray Hookaway
>    Collaborating Task Coordinators: Mark Musen?, Susie Stephens?,
>                                     Helen Chen?
> 
> 4. Creation of Wikis for Collaborative Ontology Development (6 months):
>    Task Coordinators: John Madden, Wangxiao
>    Collaborating Task Coordinators: Mark Musen?
> 
> 5. Ontology Maintenance Report (18 months):
>    Task Coordinators: Mark Musen
>    Collaborating Task Coordinators: Vinay Chaudhri, Alan Rector
> 
> 6. Ontology Evaluation Report (18 months):
>    Task Coordinators: Mark Musen
>    Collaborating Task Coordinators: Amit Sheth, Alan Rector?
> 
> 7. Use Case Solution Design (2 years):
>    Task Coordinators: Vipul Kashyap, John Madden, Alfredo Morales
>    Collaborating Task Coordinators: Susie Stephens?
> 
> Please let me have your comments, feedback and suggestions on the task
> breakdown and assignments.
> 
> We also need to have our own teleconference, maybe the week after February
> 20th, say February 27th. Let me know if that day works for you guys.
> 
> Cheers,
> 
> ---Vipul
> 
> > -----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
> > >
> > > > -----Original Message-----
> > > > From: public-semweb-lifesci-request@w3.org
> > > [mailto:public-semweb-lifesci-
> > > > request@w3.org]
> > > > Sent: Wednesday, August 11, 2004 10:35 AM
> > > > To: Kashyap, Vipul
> > > > Subject: Re: subscribe
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> > > > >From: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>
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> > > > >
> > > > >====================================================
> > > > >
> > > > >Vipul Kashyap, PhD
> > > > >
> > > > >Senior Medical Informatician, Clinical Knowledge Management
> > > > >
> > > > >Partners HealthCare Systems, Clinical Informatics R&D
> > > > >
> > > > >Work: (781)416-9254
> > > > >
> > > > >Mobile: (617)943-7120
> > > > >
> > > > >Fax: (781)416-8913
> > > > >
> > > > >Email: vkashyap1@partners.org <mailto:vkashyap1@partners.org>
> > > > >
> > > > >Web: http://www.partners.org/cird/staff.asp?stAb=vik
> > > > ><http://www.partners.org/cird/staff.asp?stAb=vik>
> > > > >
> > > > >
> > > > >
> > > > >
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> > > > >
> > > > ><head>
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> > > > ><meta name=3DGenerator content=3D"Microsoft Word 11
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> > > > > p.MsoNormal, li.MsoNormal, div.MsoNormal
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> > > Roman"><span =
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> > > >10.0pt'>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3
> > > D=3D=3D=3D=3
> > > > D=
> > > >
> > > >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
> > > 3D=3D=3D=3D=
> > > > >=3D=3D=3D=3D=3D=3D<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'>Vipul Kashyap, PhD<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'>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>
> > > > >
> > > > ><p class=3DMsoNormal><font size=3D2 face=3D"Times New
> > > Roman"><span =
> > > > >style=3D'font-size:
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> > > t1:place><f=
> > > > >ont
> > > > >size=3D2><span style=3D'font-size:10.0pt'>: =
> > > > >(617)943-7120<o:p></o:p></span></font></p>
> > > > >
> > > > ><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'>Email: <a =
> > > > >href=3D"mailto:vkashyap1@partners.org">vkashyap1@partners.org</a>
> > > > ></span></font><o:p></o:p></p>
> > > > >
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> > > >
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> > > > >rtners.org/cird/staff.asp?stAb=3Dvik</a>
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> > > > >
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Received on Monday, 20 February 2006 17:26:19 GMT

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