From pj37 at cornell.edu  Tue Sep  3 17:41:33 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 03 Sep 2002 17:41:33 -0400
Subject: protein kinase CK2
Message-ID: <3D752C8D.78C85895@cornell.edu>


Hi Midori,

I figured out 4 existing terms for casein kinase II
1	casein kinase II
2	casein kinase II complex
3	casein kinase II catalyst
4	casein kinase II regulator ( comment: do we mean regulator of CK2 or CK2
acting as a regulator)

all four had the same DBXref

the molecule CK2 is a heterotetrameric in structure with 2 catalytic alpha sub
units and two regulatory beta sub units. I suppose that is what the DAG means by
having 3 AND 4 as a PARTOF 1. 

I think they should be rephrased to 

%casein kinase II ; synonym:protein kinase CK2 ; Synonym:protein kinase CKII
 <casein kinase II alpha sub unit  or say   protein kinase CK2 catalytic sub
unit
 <casein kinase II beta sub unit ; or say   protein kinase CK2 regulatory sub
unit

Also having it as a complex creates a confusion. I think it should remain as an
enzyme and not as part of component ontology. This is a real tricky thing to put
the same thing with two different attributes just to have it as instances of two
ontologies. I still believe all the enzymes that have assembled in a complex for
their activity should be instances of function only and NOT as component. It
generally creates a lot of confusion. Its the same case with ATPases and lots of
other enzymes

casein kinase II and casein kinase II complex is the same thing. Merely defining
it in a different way does not mean that they are two different terms such as 

casein kinase II : Catalysis of the reaction: casein + ATP = phosphocasein +
ADP.
casein kinase II complex : An enzyme that catalyzes the phosphorylation of
casein.

You may consider revising the definitions of casein kinase II and casein kinase
II complex by suggesting its action on a generic substrate.

Please refer the article : PMID: 7896000
Protein kinase CK2 is a ubiquitous eukaryotic ser/thr protein kinase present in
the nucleus and cytoplasm. CK2 is known to phosphorylate more than 100
substrates, many of which are involved in the control of cell division and in
signal transduction.

Another reference is from IUBMB:
http://www.chem.qmw.ac.uk/iubmb/enzyme/EC2/7/1/37.html

Cheers

Pankaj


From midori at ebi.ac.uk  Wed Sep  4 08:16:46 2002
From: midori at ebi.ac.uk (Midori Harris)
Date: Wed, 4 Sep 2002 13:16:46 +0100 (BST)
Subject: protein kinase CK2
In-Reply-To: <E17mY1Q-00025j-00@ma11.gen.cam.ac.uk>
Message-ID: <Pine.LNX.4.10.10209041315460.4322-100000@pigeon.ebi.ac.uk>

I've just made the definition of 'casein kinase II complex' (GO:0005956)
consistent with the guidelines we came up with for enzyme complex defs.

midori

On Wed, 4 Sep 2002, Michael Ashburner wrote:

> I agree that the defn of the complex could be better written, but
> otherwise I disagree with you.
> 
> Michael
> 



From ma11 at gen.cam.ac.uk  Wed Sep  4 07:08:32 2002
From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics))
Date: Wed, 4 Sep 2002 12:08:32 +0100
Subject: protein kinase CK2
Message-ID: <E17mY1Q-00025j-00@ma11.gen.cam.ac.uk>

I agree that the defn of the complex could be better written, but
otherwise I disagree with you.

Michael

> From owner-go at genome.stanford.edu Tue Sep 03 23:40:52 2002
> Envelope-to: ma11 at gen.cam.ac.uk
> Delivery-date: Tue, 3 Sep 2002 23:40:52 +0100
> X-Authentication-Warning: alberich.Stanford.EDU: majordom set sender to owner-go at genome-mail.stanford.edu using -f
> Date: Tue, 03 Sep 2002 17:41:33 -0400
> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Organization: Cornell University
> X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U)
> X-Accept-Language: en,Hindi
> MIME-Version: 1.0
> To: "go at geneontology.org" <go at genome.Stanford.EDU>,
>         brie <gramene at brie.cshl.org>
> Subject: protein kinase CK2
> Content-Transfer-Encoding: 7bit
> Sender: owner-go at genome.stanford.edu
> 
> 
> Hi Midori,
> 
> I figured out 4 existing terms for casein kinase II
> 1	casein kinase II
> 2	casein kinase II complex
> 3	casein kinase II catalyst
> 4	casein kinase II regulator ( comment: do we mean regulator of CK2 or CK2
> acting as a regulator)
> 
> all four had the same DBXref
> 
> the molecule CK2 is a heterotetrameric in structure with 2 catalytic alpha sub
> units and two regulatory beta sub units. I suppose that is what the DAG means by
> having 3 AND 4 as a PARTOF 1. 
> 
> I think they should be rephrased to 
> 
> %casein kinase II ; synonym:protein kinase CK2 ; Synonym:protein kinase CKII
>  <casein kinase II alpha sub unit  or say   protein kinase CK2 catalytic sub
> unit
>  <casein kinase II beta sub unit ; or say   protein kinase CK2 regulatory sub
> unit
> 
> Also having it as a complex creates a confusion. I think it should remain as an
> enzyme and not as part of component ontology. This is a real tricky thing to put
> the same thing with two different attributes just to have it as instances of two
> ontologies. I still believe all the enzymes that have assembled in a complex for
> their activity should be instances of function only and NOT as component. It
> generally creates a lot of confusion. Its the same case with ATPases and lots of
> other enzymes
> 
> casein kinase II and casein kinase II complex is the same thing. Merely defining
> it in a different way does not mean that they are two different terms such as 
> 
> casein kinase II : Catalysis of the reaction: casein + ATP = phosphocasein +
> ADP.
> casein kinase II complex : An enzyme that catalyzes the phosphorylation of
> casein.
> 
> You may consider revising the definitions of casein kinase II and casein kinase
> II complex by suggesting its action on a generic substrate.
> 
> Please refer the article : PMID: 7896000
> Protein kinase CK2 is a ubiquitous eukaryotic ser/thr protein kinase present in
> the nucleus and cytoplasm. CK2 is known to phosphorylate more than 100
> substrates, many of which are involved in the control of cell division and in
> signal transduction.
> 
> Another reference is from IUBMB:
> http://www.chem.qmw.ac.uk/iubmb/enzyme/EC2/7/1/37.html
> 
> Cheers
> 
> Pankaj
> 


From pj37 at cornell.edu  Wed Sep  4 10:13:31 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 04 Sep 2002 10:13:31 -0400
Subject: protein kinase CK2
References: <Pine.LNX.4.10.10209041315460.4322-100000@pigeon.ebi.ac.uk>
Message-ID: <3D76150B.A52F5771@cornell.edu>

The new definition and the comment makes it clear. 
Do you think the alpha and beta subunits should also go in as part of casein
kinase II complex.
If I am not wrong presently these two terms (alpha and beta subunits) are
present as part of enzyme under function and not for complex  

casein kinase II catalyst
casein kinase II regulator 


suggested definitions:

term:casein kinase II catalyst
definitions : catalytic part of the casein kinase II complex comprised of alpha
subunit dimer

term:casein kinase II regulator
definitions : regulatory part of the casein kinase II complex comprised of beta
subunit dimer

you may want to rephrase them for function.

Pankaj

Midori Harris wrote:
> 
> I've just made the definition of 'casein kinase II complex' (GO:0005956)
> consistent with the guidelines we came up with for enzyme complex defs.
> 
> midori
> 
> On Wed, 4 Sep 2002, Michael Ashburner wrote:
> 
> > I agree that the defn of the complex could be better written, but
> > otherwise I disagree with you.
> >
> > Michael
> >

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From midori at ebi.ac.uk  Wed Sep  4 10:16:56 2002
From: midori at ebi.ac.uk (Midori Harris)
Date: Wed, 4 Sep 2002 15:16:56 +0100 (BST)
Subject: protein kinase CK2
In-Reply-To: <3D76150B.A52F5771@cornell.edu>
Message-ID: <Pine.LNX.4.10.10209041516260.4322-100000@pigeon.ebi.ac.uk>

I think the alpha and beta subunits would be gene products, so they
wouldn't get GO terms.

On Wed, 4 Sep 2002, Pankaj Jaiswal wrote:

> The new definition and the comment makes it clear. 
> Do you think the alpha and beta subunits should also go in as part of casein
> kinase II complex.
> If I am not wrong presently these two terms (alpha and beta subunits) are
> present as part of enzyme under function and not for complex  
> 
> casein kinase II catalyst
> casein kinase II regulator 
> 
> 
> suggested definitions:
> 
> term:casein kinase II catalyst
> definitions : catalytic part of the casein kinase II complex comprised of alpha
> subunit dimer
> 
> term:casein kinase II regulator
> definitions : regulatory part of the casein kinase II complex comprised of beta
> subunit dimer
> 
> you may want to rephrase them for function.
> 
> Pankaj
> 
> Midori Harris wrote:
> > 
> > I've just made the definition of 'casein kinase II complex' (GO:0005956)
> > consistent with the guidelines we came up with for enzyme complex defs.
> > 
> > midori
> > 
> > On Wed, 4 Sep 2002, Michael Ashburner wrote:
> > 
> > > I agree that the defn of the complex could be better written, but
> > > otherwise I disagree with you.
> > >
> > > Michael
> > >
> 
> -- 
> 
> ******************************************
> Pankaj Jaiswal, Ph.D.                                   
> Postdoctoral Associate
> Dept. of Plant Breeding                             
> Cornell University                                   
> Ithaca, NY-14853, USA   
> 
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org   
> ******************************************
> 



From pj37 at cornell.edu  Wed Sep  4 10:31:53 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 04 Sep 2002 10:31:53 -0400
Subject: protein kinase CK2
References: <Pine.LNX.4.10.10209041516260.4322-100000@pigeon.ebi.ac.uk>
Message-ID: <3D761959.4DECC252@cornell.edu>

Well I agree these are gene products but they also have a function which is CK2
kinase activity and CK2 regualtion. You may want to have something similar to
subunits of G-proteins

[i] GTPase (GO:0003924) 
	[i] heterotrimeric G-protein GTPase (GO:0003927) 
		[p] heterotrimeric G-protein GTPase, alpha-subunit (GO:0000263) 
		[p] heterotrimeric G-protein GTPase, beta-subunit (GO:0000264) 
		[p] heterotrimeric G-protein GTPase, gamma-subunit (GO:0000265) 

Midori Harris wrote:
> 
> I think the alpha and beta subunits would be gene products, so they
> wouldn't get GO terms.
> 
> On Wed, 4 Sep 2002, Pankaj Jaiswal wrote:
> 
> > The new definition and the comment makes it clear.
> > Do you think the alpha and beta subunits should also go in as part of casein
> > kinase II complex.
> > If I am not wrong presently these two terms (alpha and beta subunits) are
> > present as part of enzyme under function and not for complex
> >
> > casein kinase II catalyst
> > casein kinase II regulator
> >
> >
> > suggested definitions:
> >
> > term:casein kinase II catalyst
> > definitions : catalytic part of the casein kinase II complex comprised of alpha
> > subunit dimer
> >
> > term:casein kinase II regulator
> > definitions : regulatory part of the casein kinase II complex comprised of beta
> > subunit dimer
> >
> > you may want to rephrase them for function.
> >
> > Pankaj
> >
> > Midori Harris wrote:
> > >
> > > I've just made the definition of 'casein kinase II complex' (GO:0005956)
> > > consistent with the guidelines we came up with for enzyme complex defs.
> > >
> > > midori
> > >
> > > On Wed, 4 Sep 2002, Michael Ashburner wrote:
> > >
> > > > I agree that the defn of the complex could be better written, but
> > > > otherwise I disagree with you.
> > > >
> > > > Michael
> > > >
> >
> > --
> >
> > ******************************************
> > Pankaj Jaiswal, Ph.D.
> > Postdoctoral Associate
> > Dept. of Plant Breeding
> > Cornell University
> > Ithaca, NY-14853, USA
> >
> > Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> > E mail: pj37 at cornell.edu
> > http://www.gramene.org
> > ******************************************
> >

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From pj37 at cornell.edu  Wed Sep  4 11:33:37 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 04 Sep 2002 11:33:37 -0400
Subject: GO:ATPase
Message-ID: <3D7627D1.340A0A17@cornell.edu>



Hi,

Please correct me if I am wrong, The following three terms as children of ATPase
seems wrong specially the chloroplast and mitochondroial. The functional
involvement of ATP in translocation of the proteins (while importing) into the
organelles is limited to the folding/unfolding of the protein before it is
imported. Also it may be dependent on the potential across the membranes caused
by the activities of ATP translocator and the ATPsynthase as well as some other
proteins such as 14-3-3. 

ATPase (GO:0016887)
	[i] protein-transporting ATPase (GO:0015462)
	     [i] chloroplast protein-transporting ATPase (GO:0016464) 
	     [i] mitochondrial protein-transporting ATPase (GO:0008566) 

Ref. PMID: 11750663
The action of the Toc/Tic apparatus requires the hydrolysis of ATP and GTP at
different levels, indicating energetic requirements and regulatory properties of
the import process.


Also we need to have the terms for various subunits for H+-ATPases similar to 

[i] GTPase (GO:0003924) 
        [i] heterotrimeric G-protein GTPase (GO:0003927) 
                [p] heterotrimeric G-protein GTPase, alpha-subunit (GO:0000263) 
                [p] heterotrimeric G-protein GTPase, beta-subunit (GO:0000264) 
                [p] heterotrimeric G-protein GTPase, gamma-subunit (GO:0000265) 

since all these subunits though are gene products have specific functions.


From pj37 at cornell.edu  Fri Sep  6 11:07:38 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 06 Sep 2002 11:07:38 -0400
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
References: <Pine.GSO.4.44.0209041614510.1358-100000@acoma.Stanford.EDU>
Message-ID: <3D78C4BA.FE0253E@cornell.edu>

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





> On Wed, 4 Sep 2002, Pankaj Jaiswal wrote:
> 
> > Hi Sue,
> >
> > I went to the Deep Gene meeting at Wisconsin last month and introduced the
> > ontologies to the group of Brent and his colleagues.
> > It seems they are going to hold their next workshop at PAG this time. Though I
> > am not so sure if he said anything on holding a joint session with Ontology
> > workshop.
> >
> > Pankaj
> >
> > Sue Rhee wrote:
> > >
> > > Hi, Richard
> > >
> > > Yes, I could do that, if I can go to the meeting. Do you know what the
> > > dates are? Also, Brent Mishler <bmishler at socrates.Berkeley.EDU> from the
> > > Deep Green project was deeply interested in holding a joint 'ontologies'
> > > session, but I am not sure if anyone from the POC has been responsive
> > > enough to organize this with him. Would you be willing to communicate with
> > > him and see if his group would be interested in contributing a talk in
> > > your session please?
> > >
> > > CHeers,
> > > Sue
> > >
> > > On Wed, 4 Sep 2002, Bruskiewich, Richard wrote:
> > >
> > > > Sue,
> > > >
> > > > Would you like to talk about the TAIR interface this year at PAMG-XI? I'd be
> > > > more than pleased to slot you in.  Can Pankaj/Tanya coordinate a report on
> > > > the plant ontology development efforts?
> > > >
> > > > Cheers,
> > > > Richard
> > > >
> > > > -----Original Message-----
> > > > From: Vincent, Leszek [mailto:Leszek at missouri.edu]
> > > > Sent: Thursday, September 05, 2002 6:13 AM
> > > > To: Sue Rhee
> > > > Cc: lreiser at acoma.Stanford.EDU; pj37 at cornell.edu; srm4 at cornell.edu;
> > > > R.BRUSKIEWICH at CGIAR.ORG; tberardi at acoma.Stanford.EDU
> > > > Subject: RE: Invitation to a Meeting to discuss Ontologies for
> > > > Phenotypes
> > > >
> > > >
> > > > Hi Sue,
> > > >
> > > > Thanks for your reply & helpful input in all the points of your
> > > > contribution. Let's see what gets put into the email 'melting pot' during
> > > > the next few weeks as others contribute their comments/suggestions. Having a
> > > > coherent perspective amongst us plant-based folk would be very helpful for
> > > > us & a good constructive contribution to the meeting.
> > > >
> > > > I understand that Graham McLaren (IRRI) will be attending. I'll contact him
> > > > separately about this dialogue.
> > > >
> > > > - Leszek
> > > >
> > > > > -----Original Message-----
> > > > > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > > > Sent: Tuesday, September 03, 2002 3:14 PM
> > > > > To: Vincent, Leszek
> > > > > Cc: lreiser at acoma.Stanford.EDU; pj37 at cornell.edu; srm4 at cornell.edu;
> > > > > R.BRUSKIEWICH at CGIAR.ORG; tberardi at acoma.Stanford.EDU
> > > > > Subject: RE: Invitation to a Meeting to discuss Ontologies for
> > > > > Phenotypes
> > > > >
> > > > >
> > > > > Hi, all
> > > > >
> > > > > Sorry for the delay.
> > > > >
> > > > > On Wed, 28 Aug 2002, Vincent, Leszek wrote:
> > > > >
> > > > > > Dear colleagues,
> > > > > >
> > > > > > Michael Ashburner sent an invite recently: "the purpose of
> > > > > this meeting
> > > > > > is to discuss schema for the representation of phenotype
> > > > > and trait data
> > > > > > in model organism databases (plant, animal and microbial),
> > > > > and an agreed
> > > > > > mechanism for how to proceed from there."
> > > > > >
> > > > > > Regarding Michael's invite I have several comments:
> > > > > >
> > > > > > 1. I think it would be important for at least one
> > > > > representative from
> > > > > > each research group (Gramene, IRRI, MaizeDB & TAIR) to be present at
> > > > > > this meeting. That would mean 4 out of 30 people would be
> > > > > plant folk -
> > > > > > still only ~13% but an important 13% for such a
> > > > > 'grassroots' meeting.
> > > > > > Will it be possible for someone from each of the above groups to
> > > > > > participate in the meeting??
> > > > >
> > > > > Yes. TAIR will send two people: Sue Rhee and Tanya Beradini.
> > > > >
> > > > > > 2. I suspect that the challenges being experienced by
> > > > > non-plant people
> > > > > > regarding the representation of phenotypic data will be/ are fairly
> > > > > > similar/'identical' to ours - comments/thoughts??
> > > > >
> > > > > Yes. At least we should focus on the commonality and not the
> > > > > differences.
> > > > > Fundamentally the large issues of describing phenotypes should be the
> > > > > same, hense the coming together of the groups.
> > > > >
> > > > > > 3. I note that Michael is going to call for papers to be distributed
> > > > > > before the meeting. Would you like to 'brainstorm' this
> > > > > topic via email
> > > > > > (or phone conf call) - to help us each perceive the 'issues' more
> > > > > > clearly. I know I could benefit from some form of
> > > > > provocation/nucleating
> > > > > > thoughts in this area. This dialogue could contribute to either
> > > > > > providing individual 'papers' to Michael for distribution
> > > > > or a synthesis
> > > > > > of our views into a single brief doc. - I'd be happy to
> > > > > co-ordinate this
> > > > > > dialogue etc. What are your thoughts - comments??
> > > > >
> > > > > Sounds like a great idea. It would be great if the plant
> > > > > groups could come
> > > > > up with a coherent perspective. I wonder if we could all come up with
> > > > > issues/questions we want to bring out and perhaps after the
> > > > > discussions
> > > > > via email have brewed up some, we could talk over the phone?
> > > > >
> > > > > Here are a few questions I had:
> > > > >
> > > > > 1. What is/should be the distinction between a biological
> > > > > process and a
> > > > > phenotype?
> > > > >
> > > > > 2. Does the description of phenotype require several
> > > > > ontologies or should
> > > > > it be one ontology?
> > > > >
> > > > > 3. What is the difference between a trait and a phenotype?
> > > > >
> > > > > In responding to these, it would be great to include references and
> > > > > examples. I think it's less productive to have the dicussions
> > > > > at the level
> > > > > of personal feelings. At least, that is my 2 cents.
> > > > >
> > > > > Cheers!
> > > > > Sue
> > > > >
> > > > >
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > - Leszek
> > > > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > > > P. Leszek D. Vincent Ph.D., FLS
> > > > > > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> > > > > > University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
> > > > > > Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
> > > > > > Ph/Fax (Home): (573) 441-1228;
> > > > > > Email: Leszek at missouri.edu
> > > > > > Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> > > > > > (http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
> > > > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > > >
> > > > > > =======================
> > > > > > > -----Original Message-----
> > > > > > > From: Michael Ashburner (Genetics) [mailto:ma11 at gen.cam.ac.uk]
> > > > > > > Sent: Friday, August 23, 2002 1:12 PM
> > > > > > > To: <snip>
> > > > > >
> > > > > > > Subject: Invitation to a Meeting to discuss Ontologies
> > > > > for Phenotypes
> > > > > > >
> > > > > > >
> > > > > > > Cambridge August 23 2002.
> > > > > > >
> > > > > > > Dear colleague,
> > > > > > >
> > > > > > > A short working meeting to discuss the representation of
> > > > > phenotypic
> > > > > > > data in genomic/genetic databases will be held Dec 6 - 8,
> > > > > 2002 (See
> > > > > > > my email of May 16 2002; let me know if you have lost it or
> > > > > > > never received
> > > > > > > it).
> > > > > > >
> > > > > > > The meeting will be hosted by The Institute of Genomic
> > > > > > > Research (TIGR):
> > > > > > >
> > > > > > > The Institute for Genomic Research
> > > > > > > 9712 Medical Center Drive
> > > > > > > Rockville, MD 20850
> > > > > > > 301-838-0200
> > > > > > >
> > > > > > > I am very grateful to Owen White and Jennifer Wortman of TIGR for
> > > > > > > facilitating this and for the offer of facilities.
> > > > > > >
> > > > > > > The meeting will start at 8.30 am on Saturday December 7
> > > > > and finish
> > > > > > > after lunch on Sunday December 8.  We will have a group
> > > > > dinner at a
> > > > > > > local hostelry on the evening of Saturday; TIGR have very
> > > > > generously
> > > > > > > offered provide lunch and refreshments in the meeting room.
> > > > > > >
> > > > > > > We are strictly limited to 30 people.  I attach a list of
> > > > > > > those to whom
> > > > > > > this email is being sent.  If there are any very obvious
> > > > > ommissions
> > > > > > > please let me know.
> > > > > >
> > > > > > > <snip>
> > > > > >
> > > > > > > To repeat, the purpose of this meeting is to discuss
> > > > > schema for the
> > > > > > > representation of phenotype and trait data in model
> > > > > organism databases
> > > > > > > (plant, animal and microbial), and an agreed mechanism for
> > > > > > > how to proceed
> > > > > > > from  there.
> > > > > > >
> > > > > > > Please let me know if you will attend.
> > > > > > >
> > > > > > > I thank Jennifer Wortmann and Owen White of TIGR for their help.
> > > > > > >
> > > > > > > Best wishes,
> > > > > > >
> > > > > > > Michael Ashburner
> > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > > > > >
> > > > > > <snip>
> > > > > >
> > > > >
> > > > > --------------------------------------------------------------
> > > > > ---------------
> > > > > 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.
> > > > > --------------------------------------------------------------
> > > > > ---------------
> > > > >
> > > > >
> > > >
> > >
> > > -----------------------------------------------------------------------------
> > > 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.
> > > -----------------------------------------------------------------------------
> >
> > --
> >
> > ******************************************
> > Pankaj Jaiswal, Ph.D.
> > Postdoctoral Associate
> > Dept. of Plant Breeding
> > Cornell University
> > Ithaca, NY-14853, USA
> >
> > Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> > E mail: pj37 at cornell.edu
> > http://www.gramene.org
> > ******************************************
> >
> 
> -----------------------------------------------------------------------------
> 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.
> -----------------------------------------------------------------------------

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From jingyu at dnalandmarks.ca  Fri Sep 13 15:33:02 2002
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Fri, 13 Sep 2002 15:33:02 -0400
Subject: ftp from Gramene
Message-ID: <OF095806E6.2B830CF3-ON85256C33.0069D7F2@dnalandmarks.ca>

Noel,

> I think you want the file called final_markers_contigs_020502.dat.gz

Regarding to the file "final_markers_contigs_020502.dat.gz", could you add
one more colume in it to give chromosome number?  Thanks in advance.

- Jing



From bmishler at socrates.Berkeley.EDU  Sat Sep 14 01:15:09 2002
From: bmishler at socrates.Berkeley.EDU (Brent Mishler)
Date: Fri, 13 Sep 2002 22:15:09 -0700
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
In-Reply-To: <3D78C4BA.FE0253E@cornell.edu>
References: <Pine.GSO.4.44.0209041614510.1358-100000@acoma.Stanford.EDU>
 <3D78C4BA.FE0253E@cornell.edu>
Message-ID: <p05100326b9a873dd9b74@[202.3.240.224]>

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
**********************************************************



From teytelma at cshl.edu  Sun Sep 15 20:01:09 2002
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Sun, 15 Sep 2002 20:01:09 -0400 (EDT)
Subject: ftp from Gramene
In-Reply-To: <OF095806E6.2B830CF3-ON85256C33.0069D7F2@dnalandmarks.ca>
Message-ID: <Pine.GSO.4.05.10209151959580.28092-100000@phage.cshl.org>

Absolutely.

Lenny

> Noel,
> 
> > I think you want the file called final_markers_contigs_020502.dat.gz
> 
> Regarding to the file "final_markers_contigs_020502.dat.gz", could you add
> one more colume in it to give chromosome number?  Thanks in advance.
> 
> - Jing
> 
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From bagherinadali at yahoo.com  Tue Sep 17 06:45:58 2002
From: bagherinadali at yahoo.com (nadali bagheri)
Date: Tue, 17 Sep 2002 03:45:58 -0700 (PDT)
Subject: apomictic rice
Message-ID: <20020917104558.47098.qmail@web21108.mail.yahoo.com>


Dear my friend

Hello

I am Nadali bagheri, faculty of Mazandaran University, Iran.

Please, send me e.mail and information abaut "apomictic rice".

thank you

Nadali Bagheri 

 



---------------------------------
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Yahoo! News - Today's headlines
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From nnpanj at yahoo.com  Tue Sep 17 07:15:21 2002
From: nnpanj at yahoo.com (Paul Njiru)
Date: Tue, 17 Sep 2002 04:15:21 -0700 (PDT)
Subject: RM primer prices
Message-ID: <20020917111521.71232.qmail@web11003.mail.yahoo.com>


 

The person in charge

International Rice Microsatellite Initiative 

 Re: RM primer prices.

I am a Kenyan (foreign) student at Zhejiang University China researching on rice genetics. I wish to inquire on how I can acquire RM primers for my research work. So price tell the information regarding  their synthesis and prices. I am a final year PhD candidate and my work has been stopped because I can not get primer supplies.

Please vanish me with this information and how the consignment can me delivered in good time. I am due to graduate in  May / June 2003.

 Sincerely yours,

 Paul Njiru Nthakanio

Zhejiang University

Huajia chi Campus 

Foreign students building Room 422

Postal code 310029.

Hangzhou China

 

 



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Yahoo! News - Today's headlines
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From a.chandel at cgiar.org  Wed Sep 18 19:42:55 2002
From: a.chandel at cgiar.org (Chandel, Amaresh)
Date: Wed, 18 Sep 2002 16:42:55 -0700
Subject: Google Search apomictic rice
Message-ID: <3EA5C75212CDD511B74100508BE09576033819B1@mail.irri.cgiar.org>

 <<Google Search apomictic rice.htm>> Dear Nadali

please browse thru following information in attachment and u will get lot of
information on apomictic rice. anyway if you need more, just mail me back.

Bye and best of luck

amaresh chandel

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From shibo at nature.Berkeley.EDU  Mon Sep 23 14:04:29 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Mon, 23 Sep 2002 11:04:29 -0700 (PDT)
Subject: corn_EST db
Message-ID: <Pine.GSO.4.44.0209231102130.21340-100000@nature.Berkeley.EDU>

Dear,


There is an error in BLAST:

FATAL:  Could not open the database:  Corn_EST

EXIT CODE 18


Thanks,

shibo



From rhee at acoma.Stanford.EDU  Thu Sep 26 17:34:33 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Thu, 26 Sep 2002 14:34:33 -0700 (PDT)
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
In-Reply-To: <p05100326b9a873dd9b74@[202.3.240.224]>
Message-ID: <Pine.GSO.4.44.0209261424520.28427-100000@acoma.Stanford.EDU>

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
> **********************************************************
>
>

-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------




From R.BRUSKIEWICH at cgiar.org  Sun Sep 29 07:46:22 2002
From: R.BRUSKIEWICH at cgiar.org (Bruskiewich, Richard)
Date: Sun, 29 Sep 2002 04:46:22 -0700
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
Message-ID: <3EA5C75212CDD511B74100508BE095760388993C@mail.irri.cgiar.org>

Hi Brent & Sue,

Midori Harris will be reporting on SOFG in my workshop.

Cheers
Richard

-----Original Message-----
From: Brent Mishler [mailto:bmishler at socrates.Berkeley.EDU]
Sent: Saturday, September 28, 2002 7:57 AM
To: Sue Rhee
Cc: Pankaj Jaiswal; Bruskiewich, Richard; lreiser at acoma.Stanford.EDU;
tberardi at acoma.Stanford.EDU; Susan McCouch; Vincent Leszek; brie
Subject: Re: Invitation to a Meeting to discuss Ontologies for
Phenotypes


Hi Sue,

Sorry I won't see you at PAG in San Diego.  Those are good ideas you 
have for meetings to connect with.  It would be great if there could 
be reports at PAG on SOFG and the TIGR workshop.  We don't have final 
plans yet for what is happening at PAG, but let's put those reports 
on the agenda for sure.

You could also perhaps say something about Deep Gene and the 
interests of phylogenetic systematists at SOFG and the TIGR workshop. 
I think it would help those groups as well to consider the 
overarching role that history can play in classification.

I also really like your idea of a meeting in the Bay Area in the 
spring, and will have Deep Gene funds to pitch into that.  March is a 
good time for back-easterners to get away to California anyway!  So 
please go ahead and look into that and let me know what would be the 
best plan.

All the best,

Brent


At 2:34pm -0700 9/26/02, Sue Rhee wrote:
>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

-- 

**********************************************************
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
**********************************************************


From rhee at acoma.Stanford.EDU  Sat Sep 28 09:20:29 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Sat, 28 Sep 2002 06:20:29 -0700 (PDT)
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
In-Reply-To: <p0510031cb9ba9d9335a1@[202.3.231.111]>
Message-ID: <Pine.GSO.4.44.0209280619370.4948-100000@acoma.Stanford.EDU>

Hi, Brent,

On Fri, 27 Sep 2002, Brent Mishler wrote:

> Hi Sue,
>
> Sorry I won't see you at PAG in San Diego.  Those are good ideas you
> have for meetings to connect with.  It would be great if there could
> be reports at PAG on SOFG and the TIGR workshop.  We don't have final
> plans yet for what is happening at PAG, but let's put those reports
> on the agenda for sure.
>
> You could also perhaps say something about Deep Gene and the
> interests of phylogenetic systematists at SOFG and the TIGR workshop.
> I think it would help those groups as well to consider the
> overarching role that history can play in classification.

Sure, will do!

> I also really like your idea of a meeting in the Bay Area in the
> spring, and will have Deep Gene funds to pitch into that.  March is a
> good time for back-easterners to get away to California anyway!  So
> please go ahead and look into that and let me know what would be the
> best plan.

Will do!

>
> All the best,
>
> Brent
>
>
> At 2:34pm -0700 9/26/02, Sue Rhee wrote:
> >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
>
> --
>
> **********************************************************
> 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
> **********************************************************
>
>

-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------



From bmishler at socrates.Berkeley.EDU  Fri Sep 27 19:56:42 2002
From: bmishler at socrates.Berkeley.EDU (Brent Mishler)
Date: Fri, 27 Sep 2002 16:56:42 -0700
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
In-Reply-To: <Pine.GSO.4.44.0209261424520.28427-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0209261424520.28427-100000@acoma.Stanford.EDU>
Message-ID: <p0510031cb9ba9d9335a1@[202.3.231.111]>

Hi Sue,

Sorry I won't see you at PAG in San Diego.  Those are good ideas you 
have for meetings to connect with.  It would be great if there could 
be reports at PAG on SOFG and the TIGR workshop.  We don't have final 
plans yet for what is happening at PAG, but let's put those reports 
on the agenda for sure.

You could also perhaps say something about Deep Gene and the 
interests of phylogenetic systematists at SOFG and the TIGR workshop. 
I think it would help those groups as well to consider the 
overarching role that history can play in classification.

I also really like your idea of a meeting in the Bay Area in the 
spring, and will have Deep Gene funds to pitch into that.  March is a 
good time for back-easterners to get away to California anyway!  So 
please go ahead and look into that and let me know what would be the 
best plan.

All the best,

Brent


At 2:34pm -0700 9/26/02, Sue Rhee wrote:
>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

-- 

**********************************************************
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
**********************************************************



From bmishler at socrates.Berkeley.EDU  Sun Sep 29 16:55:55 2002
From: bmishler at socrates.Berkeley.EDU (Brent Mishler)
Date: Sun, 29 Sep 2002 13:55:55 -0700
Subject: Invitation to a Meeting to discuss Ontologies for Phenotypes
In-Reply-To: <3EA5C75212CDD511B74100508BE095760388993C@mail.irri.cgiar.org>
References: <3EA5C75212CDD511B74100508BE095760388993C@mail.irri.cgiar.org>
Message-ID: <p05100338b9bd192b928d@[202.3.231.111]>

Thanks Richard!

Cheers,

Brent

At 4:46am -0700 9/29/02, Bruskiewich, Richard wrote:
>Hi Brent & Sue,
>
>Midori Harris will be reporting on SOFG in my workshop.
>
>Cheers
>Richard
>
>-----Original Message-----
>From: Brent Mishler [mailto:bmishler at socrates.Berkeley.EDU]
>Sent: Saturday, September 28, 2002 7:57 AM
>To: Sue Rhee
>Cc: Pankaj Jaiswal; Bruskiewich, Richard; lreiser at acoma.Stanford.EDU;
>tberardi at acoma.Stanford.EDU; Susan McCouch; Vincent Leszek; brie
>Subject: Re: Invitation to a Meeting to discuss Ontologies for
>Phenotypes
>
>
>Hi Sue,
>
>Sorry I won't see you at PAG in San Diego.  Those are good ideas you
>have for meetings to connect with.  It would be great if there could
>be reports at PAG on SOFG and the TIGR workshop.  We don't have final
>plans yet for what is happening at PAG, but let's put those reports
>on the agenda for sure.
>
>You could also perhaps say something about Deep Gene and the
>interests of phylogenetic systematists at SOFG and the TIGR workshop.
>I think it would help those groups as well to consider the
>overarching role that history can play in classification.
>
>I also really like your idea of a meeting in the Bay Area in the
>spring, and will have Deep Gene funds to pitch into that.  March is a
>good time for back-easterners to get away to California anyway!  So
>please go ahead and look into that and let me know what would be the
>best plan.
>
>All the best,
>
>Brent
>
>
>At 2:34pm -0700 9/26/02, Sue Rhee wrote:
>>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
>
>--
>
>**********************************************************
>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
>**********************************************************


-- 

**********************************************************
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
**********************************************************



