Invitation to a Meeting to discuss Ontologies for Phenotypes

[Sue Rhee]

Brent,

That's great to hear. I am unfortunately not going to be attending the PAG
meeting as it overlaps with another meeting I'm comitted to.

There are two meetings relating to gene/phenotype ontologies occuring in
the near future that I (and members from Gramene, IRRI, and MaizeDB) will
be attending. One is SOFG (Standards and Ontologies in Functional
Genomics) in Hinxton UK in November 17-21
(http://www.ebi.ac.uk/microarray/General/Events/SOFG/SOFG.html) and the
other is a small workshop on phenotype ontologies organized by Michael
Ashburner and hosted at TIGR on Dec 6 - 8, 2002 (no URL, but if you are
interested, I could forward you the invitation message from Ashburner).

I wonder if somone who's attending these meetings (Pankaj or Leszek or
Tanya) could give an update at the PAG Deep Green or Ontologies workshop

and then have a short meeting in the bay area between POC and Deep Green
to set out some specific working plan and/or action items? I would be
happy to organize such a meeting at Carnegie if people are interested. Say
sometime in March or April...

Sue

On Fri, 13 Sep 2002, Brent Mishler wrote:

> Hi all,
>
> Sorry for the short delay.  I was just getting ready to head off to
> the South Pacific with my class when this came.  But we are settled
> in now, in our tropical paradise, and I'm trying to catch up.
>
> It was great that Pankaj came to our meeting in August; he did a fine
> job and the Deep Gene group got very interested in the potential
> overlaps between your efforts and ours.  I hope we could get together
> a joint workshop soon, and the idea of having it at the next PAG is a
> good one.  I'll be there myself, and we are having a Deep Gene
> sponsored symposium and workshop on "geneomics of plant reproduction"
> so there will be a good pool of people there with broad interests.
>
> Would anybody like to be the organizer of a session on gene/phenotype
> ontologies in relation to phlogenetics?
>
> Cheers,
>
> Brent
>
> At 11:07am -0400 9/6/02, Pankaj Jaiswal wrote:
> >Sue Rhee wrote:
> >>
> >>  That's great that you were able to do it. Did you introduce both GO and
> >>  POC? What was the response/reaction like?
> >>
> >>  Sue
> >>
> >
> >First of all there was a session on Gene Ontology (Gene Ontology: how should
> >genes be named?  How can they be compared between genomes?  Homology versus
> >function.) in which mainly Dina Mandoli (by way of Mark Wilkinson's
> >presentation) and Daphne Preuss introduced the GO concepts, in a generic way.
> >Then I made a small presentation on application of ontologies, by giving a
> >couple of examples and tried to initiate a discussion on how ontologies are
> >becoming important in the curation work. I presented both the GO and
> >POC (PO and
> >TO). As far as GO was concerned the reaction was its Okay to have a
> >GO-function/process/component defined for a gene product in the pair
> >wise terms
> >but it does not reflect the vision of a plant systematist on how
> >will it explain
> >the particular gene product's acquiring of these GO concepts (as part of its
> >biological role) in an organism on an evolutionary aspect. Though we have a
> >granularity at organismal level (sensu terms) for distinction but still on a
> >wider aspect it does not explain the phylogenetics.  This is important in
> >understanding the basic difference in genetic variation. Also Most of the
> >variation does not come from the coding regions (curated by GO) but
> >from the non
> >coding, inter or intra genic genic regions, which the GO does not handle.
> >Therefore the PO can infact jump into this wagon to take care of the variation
> >atleast at the level of morphological/anatomical variation resulting
> >due to the
> >various factors such as  genetic/epigenetic/enviroment. The concept of PO and
> >its DAG structure was appreciated since it helps in making multiple
> >relationships of derived and children terms. We (POC) need to have a
> >very smart
> >idea on how are we going to handle the micro organisms where there is no
> >anatomy. There were some concerns raised by the group on how we define
> >morphology and anatomy, should we have them separate or have it
> >combined form as
> >of now. I think we need to convince the community on this issue
> >before we go on
> >to have something concrete on this, because a
> >taxonomist/paleontologist/systematist views it is a different
> >perspective than a
> >biochemist/molecular biologist. I had a good discussion with Andrew
> >Doust (from
> >Toby Kellogg's group) and  Geeta Bharathan and was able to convince them to an
> >extent on POC concepts, but it still needs more exposure and some
> >good examples
> >to convince.
> >
> >After coming back Susan and myself presented an overview of the ontology work
> >(GO and PO) as well as Gramene to Andrew Doust and Toby over a conference call
> >while sharing the desktop. We are yet to hear their comments though they were
> >excited about the work.
> >
> >At the deep Gene workshop, everyone felt that this is the right time
> >to have the
> >ontologies working specially the PO and TO, otherwise its going to be too late
> >since a lot of high throughput projects on plants will start (some
> >have already
> >started) churning out the mutant collections and it will be really hard to go
> >back and score the phenotypes again. As far as pairwise similarity is there GO
> >is doing a fine job.
> >
> >May be Brent can comment more on this, I am copying the mail to him.
> >
> >Pankaj
>
> --
>
> **********************************************************
> Brent D. Mishler
>       Professor, Department of Integrative Biology
>       Director, University and Jepson Herbaria
>       Associate Director, California Biodiversity Center
>    Mailing address:
>       UNIVERSITY OF CALIFORNIA, BERKELEY
>       UNIVERSITY AND JEPSON HERBARIA
>       1001 VALLEY LIFE SCIENCES BLDG # 2465
>       BERKELEY, CA  94720-2465  USA
>    Phone:  (510) 642-6810
>    FAX:    (510) 643-5390
>    E-mail: bmishler at socrates.berkeley.edu
>    WWW:    http://ucjeps.berkeley.edu/people/mishler.html
> **********************************************************
>
>

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Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
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