Invitation to a Meeting to discuss Ontologies for Phenotypes

[Brent Mishler]

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

-- 

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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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