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
> >
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> > > ><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:
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> > > >R&amp;D<o:p></o:p></span></font></p>
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