From pj37 at cornell.edu  Thu Oct  2 12:08:33 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 02 Oct 2003 12:08:33 -0400
Subject: POC poster abstract for  PAG
Message-ID: <3F7C4D81.3040803@cornell.edu>


Hi Everyone,

Please go through the abstract for the PAG 2004 and make your suggestions. The 
deadline for submission is tomorrow and I would like to have the final version 
ready by tonight.

I am sorry for asking this at the last minute.

Many thanks
Pankaj

Title: The Plant Ontology Consortium

Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,  Doreen 
Ware,  Peter Stevens,  Pankaj Jaiswal,  Leonore Reiser,  Peter Stevens, Leszek 
Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.

The goals of the Plant Ontology Consortium are to develop a common set of 
controlled vocabulary terms to describe anatomic and developmental stage terms 
in both experimental and agronomically important plants.  We have started with 
Arabidopsis and cereals such as rice and maize, and later extend this ontology 
to encompass legumes, Solanaceae, and other plant families.  Concurrently, these 
terms will be applied to the task of describing the genes and mutants that are 
contained within the plant specific databases maintained by the participating 
institutions, thereby simultaneously refining the ontologies, and providing 
points of reference with which to compare the genes and mutants across these 
species. The broader impact of this project is that it will provide a framework 
of plant development to allow researchers to make meaningful cross database 
queries across the various species specific resources such as Gramene, TAIR, 
MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and 
dissimilarities involved in plant development. For example, researchers will be 
able to obtain a definitive list of genes whose action affects plant stem 
development.  The development and implementation of plant ontology will allow 
the fruits of research in one plant species to be more easily used in the study 
of other species, leading to a greater understanding of plant biology.
The project is supported by National Science Foundation grant No. 0321666 to the 
Plant Ontology Consortium.




From lreiser at acoma.Stanford.EDU  Thu Oct  2 12:15:05 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Thu, 2 Oct 2003 09:15:05 -0700 (PDT)
Subject: po-dev-digest V1 #12
In-Reply-To: <200310021608.h92G8ZeE003260@brie4.cshl.org>
Message-ID: <Pine.GSO.4.44.0310020914540.17565-100000@acoma.Stanford.EDU>

I received the email

On Thu, 2 Oct 2003, po-dev-digest wrote:

>
> po-dev-digest        Thursday, October 2 2003        Volume 01 : Number 012
>
>
>
> Gramene Software Development Digest: test po-dev at plantontology.org
> Gramene Software Development Digest: test
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test
> Gramene Software Development Digest: RE: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: RE: test po-dev at plantontology.org
> Gramene Software Development Digest: RE: test po-dev at plantontology.org
> Gramene Software Development Digest: POC poster abstract for  PAG
>
> ----------------------------------------------------------------------
>
> Date: Tue, 23 Sep 2003 19:19:55 -0400
> From: Shuly <shuly at cshl.org>
> Subject: test po-dev at plantontology.org
>
> This is a test,
> please let me know if you got this email.
> Thanks,
> Shuly.
>
> ------------------------------
>
> Date: Tue, 23 Sep 2003 19:25:43 -0400
> From: Shuly <shuly at cshl.org>
> Subject: test
>
> test
>
> ------------------------------
>
> Date: Tue, 23 Sep 2003 19:27:27 -0400
> From: Shuly <shuly at cshl.org>
> Subject: Re: test po-dev at plantontology.org
>
> I got it!
>
> Shuly wrote:
>
> > This is a test,
> > please let me know if you got this email.
> > Thanks,
> > Shuly.
> >
>
> ------------------------------
>
> Date: Tue, 23 Sep 2003 16:34:53 -0700 (PDT)
> From: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> Subject: Re: test po-dev at plantontology.org
>
> yes
> _leonore
> On Tue, 23 Sep 2003, Shuly wrote:
>
> > This is a test,
> > please let me know if you got this email.
> > Thanks,
> > Shuly.
> >
>
> - -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> - -------------------------------------------------------------------------------
>
> ------------------------------
>
> Date: Tue, 23 Sep 2003 18:49:14 -0500
> From: Felipe Zapata <fzqhd at studentmail.umsl.edu>
> Subject: Re: test po-dev at plantontology.org
>
> Got it!!
>
> Felipe
>
>
> Quoting Shuly <shuly at cshl.org>:
>
> > This is a test,
> > please let me know if you got this email.
> > Thanks,
> > Shuly.
> >
> >
>
>
> _____________
> Felipe Zapata
> University of Missouri-St.Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis MO, 63121
> Phone: (314) 516-6200
> Fax: (314) 516-6233
>
> ------------------------------
>
> Date: Tue, 23 Sep 2003 21:08:26 -0500
> From: "Leszek Vincent" <Leszek at missouri.edu>
> Subject: Re: test po-dev at plantontology.org
>
> Email received - Leszek
>
> - ----- Original Message -----
> From: "Shuly" <shuly at cshl.org>
> To: <po-dev at plantontology.org>
> Sent: Tuesday, September 23, 2003 6:19 PM
> Subject: test po-dev at plantontology.org
>
>
> > This is a test,
> > please let me know if you got this email.
> > Thanks,
> > Shuly.
> >
> >
>
> ------------------------------
>
> Date: Tue, 23 Sep 2003 21:08:42 -0500
> From: "Leszek Vincent" <Leszek at missouri.edu>
> Subject: Re: test
>
> Email received - Leszek
>
> - ----- Original Message -----
> From: "Shuly" <shuly at cshl.org>
> To: <po-dev at brie4.cshl.org>
> Sent: Tuesday, September 23, 2003 6:25 PM
> Subject: test
>
>
> > test
> >
> >
>
> ------------------------------
>
> Date: Wed, 24 Sep 2003 07:35:07 -0400
> From: "Ware, Doreen" <ware at cshl.edu>
> Subject: RE: test po-dev at plantontology.org
>
> worked!
>
> - -----Original Message-----
> From: Shuly [mailto:shuly at cshl.org]
> Sent: Tuesday, September 23, 2003 7:20 PM
> To: po-dev at plantontology.org
> Subject: test po-dev at plantontology.org
>
>
> This is a test,
> please let me know if you got this email.
> Thanks,
> Shuly.
>
> ------------------------------
>
> Date: Wed, 24 Sep 2003 13:28:57 -0400
> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Subject: Re: test po-dev at plantontology.org
>
> I got it. great job.
> Pankaj
>
> Shuly wrote:
>
> > This is a test,
> > please let me know if you got this email.
> > Thanks,
> > Shuly.
>
> ------------------------------
>
> Date: Wed, 24 Sep 2003 15:53:35 -0400
> From: "Ware, Doreen" <ware at cshl.edu>
> Subject: RE: test po-dev at plantontology.org
>
> This is a test of the system.
>
>
> doreen
>
> - -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Wednesday, September 24, 2003 1:29 PM
> To: po-dev at plantontology.org
> Subject: Re: test po-dev at plantontology.org
>
>
> I got it. great job.
> Pankaj
>
> Shuly wrote:
>
> > This is a test,
> > please let me know if you got this email.
> > Thanks,
> > Shuly.
>
> ------------------------------
>
> Date: Wed, 24 Sep 2003 15:51:08 -0500
> From: Toby Kellogg <kellogge at msx.umsl.edu>
> Subject: RE: test po-dev at plantontology.org
>
> HI Doreen -
>   Can't remember if I replied to this particular address or not - in any
> case, it works.  It was great to see you at the Banbury meeting.
> Toby
>
> >This is a test of the system.
> >
> >
> >doreen
> >
> >-----Original Message-----
> >From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> >Sent: Wednesday, September 24, 2003 1:29 PM
> >To: po-dev at plantontology.org
> >Subject: Re: test po-dev at plantontology.org
> >
> >
> >I got it. great job.
> >Pankaj
> >
> >Shuly wrote:
> >
> >> This is a test,
> >> please let me know if you got this email.
> >> Thanks,
> >> Shuly.
>
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
> ------------------------------
>
> Date: Thu, 02 Oct 2003 12:08:33 -0400
> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Subject: POC poster abstract for  PAG
>
> Hi Everyone,
>
> Please go through the abstract for the PAG 2004 and make your suggestions. The
> deadline for submission is tomorrow and I would like to have the final version
> ready by tonight.
>
> I am sorry for asking this at the last minute.
>
> Many thanks
> Pankaj
>
> Title: The Plant Ontology Consortium
>
> Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,  Doreen
> Ware,  Peter Stevens,  Pankaj Jaiswal,  Leonore Reiser,  Peter Stevens, Leszek
> Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.
>
> The goals of the Plant Ontology Consortium are to develop a common set of
> controlled vocabulary terms to describe anatomic and developmental stage terms
> in both experimental and agronomically important plants.  We have started with
> Arabidopsis and cereals such as rice and maize, and later extend this ontology
> to encompass legumes, Solanaceae, and other plant families.  Concurrently, these
> terms will be applied to the task of describing the genes and mutants that are
> contained within the plant specific databases maintained by the participating
> institutions, thereby simultaneously refining the ontologies, and providing
> points of reference with which to compare the genes and mutants across these
> species. The broader impact of this project is that it will provide a framework
> of plant development to allow researchers to make meaningful cross database
> queries across the various species specific resources such as Gramene, TAIR,
> MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and
> dissimilarities involved in plant development. For example, researchers will be
> able to obtain a definitive list of genes whose action affects plant stem
> development.  The development and implementation of plant ontology will allow
> the fruits of research in one plant species to be more easily used in the study
> of other species, leading to a greater understanding of plant biology.
> The project is supported by National Science Foundation grant No. 0321666 to the
> Plant Ontology Consortium.
>
> ------------------------------
>
> End of po-dev-digest V1 #12
> ***************************
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Thu Oct  2 12:17:28 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 02 Oct 2003 12:17:28 -0400
Subject: po-dev-digest V1 #12
In-Reply-To: <200310021608.h92G8ZeE003260@brie4.cshl.org>
References: <200310021608.h92G8ZeE003260@brie4.cshl.org>
Message-ID: <3F7C4F98.3050001@cornell.edu>

I got this.
Pankaj

BTW, I just now sent a mail to the po-dev. can you approve it. Also it did not 
accept my MS word attachment. Are you running a filter on it.



po-dev-digest wrote:

> po-dev-digest        Thursday, October 2 2003        Volume 01 : Number 012
> 
> 
> 
> Gramene Software Development Digest: test po-dev at plantontology.org
> Gramene Software Development Digest: test
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test
> Gramene Software Development Digest: RE: test po-dev at plantontology.org
> Gramene Software Development Digest: Re: test po-dev at plantontology.org
> Gramene Software Development Digest: RE: test po-dev at plantontology.org
> Gramene Software Development Digest: RE: test po-dev at plantontology.org
> Gramene Software Development Digest: POC poster abstract for  PAG
> 
> ----------------------------------------------------------------------
> 
> Date: Tue, 23 Sep 2003 19:19:55 -0400
> From: Shuly <shuly at cshl.org>
> Subject: test po-dev at plantontology.org
> 
> This is a test,
> please let me know if you got this email.
> Thanks,
> Shuly.
> 
> ------------------------------
> 
> Date: Tue, 23 Sep 2003 19:25:43 -0400
> From: Shuly <shuly at cshl.org>
> Subject: test
> 
> test
> 
> ------------------------------
> 
> Date: Tue, 23 Sep 2003 19:27:27 -0400
> From: Shuly <shuly at cshl.org>
> Subject: Re: test po-dev at plantontology.org
> 
> I got it!
> 
> Shuly wrote:
> 
> 
>>This is a test,
>>please let me know if you got this email.
>>Thanks,
>>Shuly.
>>
> 
> 
> ------------------------------
> 
> Date: Tue, 23 Sep 2003 16:34:53 -0700 (PDT)
> From: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> Subject: Re: test po-dev at plantontology.org
> 
> yes
> _leonore
> On Tue, 23 Sep 2003, Shuly wrote:
> 
> 
>>This is a test,
>>please let me know if you got this email.
>>Thanks,
>>Shuly.
>>
> 
> 
> - -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> - -------------------------------------------------------------------------------
> 
> ------------------------------
> 
> Date: Tue, 23 Sep 2003 18:49:14 -0500
> From: Felipe Zapata <fzqhd at studentmail.umsl.edu>
> Subject: Re: test po-dev at plantontology.org
> 
> Got it!!
> 
> Felipe
> 
> 
> Quoting Shuly <shuly at cshl.org>:
> 
> 
>>This is a test,
>>please let me know if you got this email.
>>Thanks,
>>Shuly.
>>
>>
> 
> 
> 
> _____________
> Felipe Zapata
> University of Missouri-St.Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis MO, 63121
> Phone: (314) 516-6200
> Fax: (314) 516-6233
> 
> ------------------------------
> 
> Date: Tue, 23 Sep 2003 21:08:26 -0500
> From: "Leszek Vincent" <Leszek at missouri.edu>
> Subject: Re: test po-dev at plantontology.org
> 
> Email received - Leszek
> 
> - ----- Original Message ----- 
> From: "Shuly" <shuly at cshl.org>
> To: <po-dev at plantontology.org>
> Sent: Tuesday, September 23, 2003 6:19 PM
> Subject: test po-dev at plantontology.org
> 
> 
> 
>>This is a test,
>>please let me know if you got this email.
>>Thanks,
>>Shuly.
>>
>>
> 
> 
> ------------------------------
> 
> Date: Tue, 23 Sep 2003 21:08:42 -0500
> From: "Leszek Vincent" <Leszek at missouri.edu>
> Subject: Re: test
> 
> Email received - Leszek
> 
> - ----- Original Message ----- 
> From: "Shuly" <shuly at cshl.org>
> To: <po-dev at brie4.cshl.org>
> Sent: Tuesday, September 23, 2003 6:25 PM
> Subject: test
> 
> 
> 
>>test
>>
>>
> 
> 
> ------------------------------
> 
> Date: Wed, 24 Sep 2003 07:35:07 -0400
> From: "Ware, Doreen" <ware at cshl.edu>
> Subject: RE: test po-dev at plantontology.org
> 
> worked!
> 
> - -----Original Message-----
> From: Shuly [mailto:shuly at cshl.org]
> Sent: Tuesday, September 23, 2003 7:20 PM
> To: po-dev at plantontology.org
> Subject: test po-dev at plantontology.org
> 
> 
> This is a test,
> please let me know if you got this email.
> Thanks,
> Shuly.
> 
> ------------------------------
> 
> Date: Wed, 24 Sep 2003 13:28:57 -0400
> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Subject: Re: test po-dev at plantontology.org
> 
> I got it. great job.
> Pankaj
> 
> Shuly wrote:
> 
> 
>>This is a test,
>>please let me know if you got this email.
>>Thanks,
>>Shuly.
> 
> 
> ------------------------------
> 
> Date: Wed, 24 Sep 2003 15:53:35 -0400
> From: "Ware, Doreen" <ware at cshl.edu>
> Subject: RE: test po-dev at plantontology.org
> 
> This is a test of the system.
> 
> 
> doreen
> 
> - -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Wednesday, September 24, 2003 1:29 PM
> To: po-dev at plantontology.org
> Subject: Re: test po-dev at plantontology.org
> 
> 
> I got it. great job.
> Pankaj
> 
> Shuly wrote:
> 
> 
>>This is a test,
>>please let me know if you got this email.
>>Thanks,
>>Shuly.
> 
> 
> ------------------------------
> 
> Date: Wed, 24 Sep 2003 15:51:08 -0500
> From: Toby Kellogg <kellogge at msx.umsl.edu>
> Subject: RE: test po-dev at plantontology.org
> 
> HI Doreen -
>   Can't remember if I replied to this particular address or not - in any
> case, it works.  It was great to see you at the Banbury meeting.
> Toby
> 
> 
>>This is a test of the system.
>>
>>
>>doreen
>>
>>-----Original Message-----
>>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
>>Sent: Wednesday, September 24, 2003 1:29 PM
>>To: po-dev at plantontology.org
>>Subject: Re: test po-dev at plantontology.org
>>
>>
>>I got it. great job.
>>Pankaj
>>
>>Shuly wrote:
>>
>>
>>>This is a test,
>>>please let me know if you got this email.
>>>Thanks,
>>>Shuly.
> 
> 
> 
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> 
> ------------------------------
> 
> Date: Thu, 02 Oct 2003 12:08:33 -0400
> From: Pankaj Jaiswal <pj37 at cornell.edu>
> Subject: POC poster abstract for  PAG
> 
> Hi Everyone,
> 
> Please go through the abstract for the PAG 2004 and make your suggestions. The 
> deadline for submission is tomorrow and I would like to have the final version 
> ready by tonight.
> 
> I am sorry for asking this at the last minute.
> 
> Many thanks
> Pankaj
> 
> Title: The Plant Ontology Consortium
> 
> Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,  Doreen 
> Ware,  Peter Stevens,  Pankaj Jaiswal,  Leonore Reiser,  Peter Stevens, Leszek 
> Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.
> 
> The goals of the Plant Ontology Consortium are to develop a common set of 
> controlled vocabulary terms to describe anatomic and developmental stage terms 
> in both experimental and agronomically important plants.  We have started with 
> Arabidopsis and cereals such as rice and maize, and later extend this ontology 
> to encompass legumes, Solanaceae, and other plant families.  Concurrently, these 
> terms will be applied to the task of describing the genes and mutants that are 
> contained within the plant specific databases maintained by the participating 
> institutions, thereby simultaneously refining the ontologies, and providing 
> points of reference with which to compare the genes and mutants across these 
> species. The broader impact of this project is that it will provide a framework 
> of plant development to allow researchers to make meaningful cross database 
> queries across the various species specific resources such as Gramene, TAIR, 
> MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and 
> dissimilarities involved in plant development. For example, researchers will be 
> able to obtain a definitive list of genes whose action affects plant stem 
> development.  The development and implementation of plant ontology will allow 
> the fruits of research in one plant species to be more easily used in the study 
> of other species, leading to a greater understanding of plant biology.
> The project is supported by National Science Foundation grant No. 0321666 to the 
> Plant Ontology Consortium.
> 
> ------------------------------
> 
> End of po-dev-digest V1 #12
> ***************************
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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  Thu Oct  2 12:27:53 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 02 Oct 2003 12:27:53 -0400
Subject: POC poster abstract for  PAG
Message-ID: <3F7C5209.5050005@cornell.edu>


Hi Everyone,

Please go through the abstract for the PAG 2004 and make your suggestions. The
deadline for submission is tomorrow and I would like to have the final version
ready by tonight.

I am sorry for asking this at the last minute.

Many thanks
Pankaj

Title: The Plant Ontology Consortium

Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,  Doreen
Ware,  Pankaj Jaiswal,  Peter Stevens, Leonore Reiser,  Leszek
Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.

The goals of the Plant Ontology Consortium are to develop a common set of
controlled vocabulary terms to describe anatomic and developmental stage terms
in both experimental and agronomically important plants.  We have started with
Arabidopsis and cereals such as rice and maize, and later extend this ontology
to encompass legumes, Solanaceae, and other plant families.  Concurrently, these
terms will be applied to the task of describing the genes and mutants that are
contained within the plant specific databases maintained by the participating
institutions, thereby simultaneously refining the ontologies, and providing
points of reference with which to compare the genes and mutants across these
species. The broader impact of this project is that it will provide a framework
of plant development to allow researchers to make meaningful cross database
queries across the various species specific resources such as Gramene, TAIR,
MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and
dissimilarities involved in plant development. For example, researchers will be
able to obtain a definitive list of genes whose action affects plant stem
development.  The development and implementation of plant ontology will allow
the fruits of research in one plant species to be more easily used in the study
of other species, leading to a greater understanding of plant biology.
The project is supported by National Science Foundation grant No. 0321666 to the
Plant Ontology Consortium.






From rhee at acoma.Stanford.EDU  Thu Oct  2 12:38:33 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Thu, 2 Oct 2003 09:38:33 -0700 (PDT)
Subject: POC poster abstract for  PAG
In-Reply-To: <3F7C4D81.3040803@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310020930480.18147-100000@acoma.Stanford.EDU>

Pankaj,

Looks great. Thanks for doing it. My suggestions below. By the way, the
po-dev seems to be working for me so please don't cc to my other emails. I
got the same message three times.

> Title: The Plant Ontology Consortium
>
> Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,  Doreen

Seung Y. Rhee for my name

> Ware,  Peter Stevens,  Pankaj Jaiswal,  Leonore Reiser,  Peter Stevens, Leszek
> Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.
>
> The goals of the Plant Ontology Consortium are to develop a common set of
> controlled vocabulary terms to describe anatomic and developmental stage terms

anatomical rather than anatomic?

> in both experimental and agronomically important plants.  We have started with

experimentally rather than experimental

remove 'have' in have started

> Arabidopsis and cereals such as rice and maize, and later extend this ontology

replace 'later extend' with 'plan on extending'

> to encompass legumes, Solanaceae, and other plant families.  Concurrently, these
> terms will be applied to the task of describing the genes and mutants that are

remove 'the task of'

> contained within the plant specific databases maintained by the participating

remove 'specific'

> institutions, thereby simultaneously refining the ontologies, and providing
> points of reference with which to compare the genes and mutants across these
> species. The broader impact of this project is that it will provide a framework
> of plant development to allow researchers to make meaningful cross database

cross-database

> queries across the various species specific resources such as Gramene, TAIR,

species-specific

> MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and

I thought Gramene and PlantGDB were NOT species-specific. Also, it would
be nice to add URLs to these databases you are referring to.

> dissimilarities involved in plant development. For example, researchers will be
> able to obtain a definitive list of genes whose action affects plant stem
> development.  The development and implementation of plant ontology will allow
> the fruits of research in one plant species to be more easily used in the study
> of other species, leading to a greater understanding of plant biology.
> The project is supported by National Science Foundation grant No. 0321666 to the
> Plant Ontology Consortium.
>
>
>

-----------------------------------------------------------------------------
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 PolaccoM at missouri.edu  Thu Oct  2 13:39:20 2003
From: PolaccoM at missouri.edu (Mary Polacco)
Date: Thu, 02 Oct 2003 12:39:20 -0500
Subject: po-dev-digest V1 #12
In-Reply-To: <200310021608.h92G8ZeE003260@brie4.cshl.org>
Message-ID: <BBA1CCF8.943A%PolaccoM@missouri.edu>

Hi Pankaj,

You might also include agronomic traits in the listing below (line 6,7 of
the abstract.

-mary
On 10/2/03 11:08 AM, "po-dev-digest" <owner-po-dev-digest at plantontology.org>
wrote:

> of describing the genes and mutants that are
> contained within the plant specific databases



From kellogge at msx.umsl.edu  Thu Oct  2 14:32:03 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Thu, 2 Oct 2003 13:32:03 -0500
Subject: po-dev-digest V1 #12
In-Reply-To: <200310021608.h92G8ZeE003260@brie4.cshl.org>
Message-ID: <l03130301bba21f9cc960@[134.124.70.41]>

Got it -
T

>po-dev-digest        Thursday, October 2 2003        Volume 01 : Number 012
>
>
>
>Gramene Software Development Digest: test po-dev at plantontology.org
>Gramene Software Development Digest: test
>Gramene Software Development Digest: Re: test po-dev at plantontology.org
>Gramene Software Development Digest: Re: test po-dev at plantontology.org
>Gramene Software Development Digest: Re: test po-dev at plantontology.org
>Gramene Software Development Digest: Re: test po-dev at plantontology.org
>Gramene Software Development Digest: Re: test
>Gramene Software Development Digest: RE: test po-dev at plantontology.org
>Gramene Software Development Digest: Re: test po-dev at plantontology.org
>Gramene Software Development Digest: RE: test po-dev at plantontology.org
>Gramene Software Development Digest: RE: test po-dev at plantontology.org
>Gramene Software Development Digest: POC poster abstract for  PAG
>
>----------------------------------------------------------------------
>
>Date: Tue, 23 Sep 2003 19:19:55 -0400
>From: Shuly <shuly at cshl.org>
>Subject: test po-dev at plantontology.org
>
>This is a test,
>please let me know if you got this email.
>Thanks,
>Shuly.
>
>------------------------------
>
>Date: Tue, 23 Sep 2003 19:25:43 -0400
>From: Shuly <shuly at cshl.org>
>Subject: test
>
>test
>
>------------------------------
>
>Date: Tue, 23 Sep 2003 19:27:27 -0400
>From: Shuly <shuly at cshl.org>
>Subject: Re: test po-dev at plantontology.org
>
>I got it!
>
>Shuly wrote:
>
>> This is a test,
>> please let me know if you got this email.
>> Thanks,
>> Shuly.
>>
>
>------------------------------
>
>Date: Tue, 23 Sep 2003 16:34:53 -0700 (PDT)
>From: Leonore Reiser <lreiser at acoma.Stanford.EDU>
>Subject: Re: test po-dev at plantontology.org
>
>yes
>_leonore
>On Tue, 23 Sep 2003, Shuly wrote:
>
>> This is a test,
>> please let me know if you got this email.
>> Thanks,
>> Shuly.
>>
>
>-
>-------------------------------------------------------------------------------
>>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>The Arabidopsis Information Resource	FAX: (650) 325-6857
>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>Department of Plant Biology		URL: http://arabidopsis.org/
>260 Panama St.
>Stanford, CA 94305
>-
>-------------------------------------------------------------------------------
>>
>------------------------------
>
>Date: Tue, 23 Sep 2003 18:49:14 -0500
>From: Felipe Zapata <fzqhd at studentmail.umsl.edu>
>Subject: Re: test po-dev at plantontology.org
>
>Got it!!
>
>Felipe
>
>
>Quoting Shuly <shuly at cshl.org>:
>
>> This is a test,
>> please let me know if you got this email.
>> Thanks,
>> Shuly.
>>
>>
>
>
>_____________
>Felipe Zapata
>University of Missouri-St.Louis
>Department of Biology
>8001 Natural Bridge Rd.
>St. Louis MO, 63121
>Phone: (314) 516-6200
>Fax: (314) 516-6233
>
>------------------------------
>
>Date: Tue, 23 Sep 2003 21:08:26 -0500
>From: "Leszek Vincent" <Leszek at missouri.edu>
>Subject: Re: test po-dev at plantontology.org
>
>Email received - Leszek
>
>- ----- Original Message -----
>From: "Shuly" <shuly at cshl.org>
>To: <po-dev at plantontology.org>
>Sent: Tuesday, September 23, 2003 6:19 PM
>Subject: test po-dev at plantontology.org
>
>
>> This is a test,
>> please let me know if you got this email.
>> Thanks,
>> Shuly.
>>
>>
>
>------------------------------
>
>Date: Tue, 23 Sep 2003 21:08:42 -0500
>From: "Leszek Vincent" <Leszek at missouri.edu>
>Subject: Re: test
>
>Email received - Leszek
>
>- ----- Original Message -----
>From: "Shuly" <shuly at cshl.org>
>To: <po-dev at brie4.cshl.org>
>Sent: Tuesday, September 23, 2003 6:25 PM
>Subject: test
>
>
>> test
>>
>>
>
>------------------------------
>
>Date: Wed, 24 Sep 2003 07:35:07 -0400
>From: "Ware, Doreen" <ware at cshl.edu>
>Subject: RE: test po-dev at plantontology.org
>
>worked!
>
>- -----Original Message-----
>From: Shuly [mailto:shuly at cshl.org]
>Sent: Tuesday, September 23, 2003 7:20 PM
>To: po-dev at plantontology.org
>Subject: test po-dev at plantontology.org
>
>
>This is a test,
>please let me know if you got this email.
>Thanks,
>Shuly.
>
>------------------------------
>
>Date: Wed, 24 Sep 2003 13:28:57 -0400
>From: Pankaj Jaiswal <pj37 at cornell.edu>
>Subject: Re: test po-dev at plantontology.org
>
>I got it. great job.
>Pankaj
>
>Shuly wrote:
>
>> This is a test,
>> please let me know if you got this email.
>> Thanks,
>> Shuly.
>
>------------------------------
>
>Date: Wed, 24 Sep 2003 15:53:35 -0400
>From: "Ware, Doreen" <ware at cshl.edu>
>Subject: RE: test po-dev at plantontology.org
>
>This is a test of the system.
>
>
>doreen
>
>- -----Original Message-----
>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
>Sent: Wednesday, September 24, 2003 1:29 PM
>To: po-dev at plantontology.org
>Subject: Re: test po-dev at plantontology.org
>
>
>I got it. great job.
>Pankaj
>
>Shuly wrote:
>
>> This is a test,
>> please let me know if you got this email.
>> Thanks,
>> Shuly.
>
>------------------------------
>
>Date: Wed, 24 Sep 2003 15:51:08 -0500
>From: Toby Kellogg <kellogge at msx.umsl.edu>
>Subject: RE: test po-dev at plantontology.org
>
>HI Doreen -
>  Can't remember if I replied to this particular address or not - in any
>case, it works.  It was great to see you at the Banbury meeting.
>Toby
>
>>This is a test of the system.
>>
>>
>>doreen
>>
>>-----Original Message-----
>>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
>>Sent: Wednesday, September 24, 2003 1:29 PM
>>To: po-dev at plantontology.org
>>Subject: Re: test po-dev at plantontology.org
>>
>>
>>I got it. great job.
>>Pankaj
>>
>>Shuly wrote:
>>
>>> This is a test,
>>> please let me know if you got this email.
>>> Thanks,
>>> Shuly.
>
>
>Elizabeth A. Kellogg
>Department of Biology
>University of Missouri-St. Louis
>8001 Natural Bridge Road
>St. Louis, MO 63121
>phone: 314-516-6217
>fax: 314-516-6233
>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
>------------------------------
>
>Date: Thu, 02 Oct 2003 12:08:33 -0400
>From: Pankaj Jaiswal <pj37 at cornell.edu>
>Subject: POC poster abstract for  PAG
>
>Hi Everyone,
>
>Please go through the abstract for the PAG 2004 and make your suggestions.
>The
>deadline for submission is tomorrow and I would like to have the final
>version
>ready by tonight.
>
>I am sorry for asking this at the last minute.
>
>Many thanks
>Pankaj
>
>Title: The Plant Ontology Consortium
>
>Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,  Doreen
>Ware,  Peter Stevens,  Pankaj Jaiswal,  Leonore Reiser,  Peter Stevens,
>Leszek
>Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.
>
>The goals of the Plant Ontology Consortium are to develop a common set of
>controlled vocabulary terms to describe anatomic and developmental stage
>terms
>in both experimental and agronomically important plants.  We have started
>with
>Arabidopsis and cereals such as rice and maize, and later extend this
>ontology
>to encompass legumes, Solanaceae, and other plant families.  Concurrently,
>these
>terms will be applied to the task of describing the genes and mutants that
>are
>contained within the plant specific databases maintained by the participating
>institutions, thereby simultaneously refining the ontologies, and providing
>points of reference with which to compare the genes and mutants across these
>species. The broader impact of this project is that it will provide a
>framework
>of plant development to allow researchers to make meaningful cross database
>queries across the various species specific resources such as Gramene, TAIR,
>MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and
>dissimilarities involved in plant development. For example, researchers
>will be
>able to obtain a definitive list of genes whose action affects plant stem
>development.  The development and implementation of plant ontology will allow
>the fruits of research in one plant species to be more easily used in the
>study
>of other species, leading to a greater understanding of plant biology.
>The project is supported by National Science Foundation grant No. 0321666
>to the
>Plant Ontology Consortium.
>
>------------------------------
>
>End of po-dev-digest V1 #12
>***************************


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From kellogge at msx.umsl.edu  Thu Oct  2 14:45:29 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Thu, 2 Oct 2003 13:45:29 -0500
Subject: POC observations so far
Message-ID: <l03130302bba2218f3e82@[134.124.70.41]>

Hi all -
  Felipe has made great progress here downloading the various programs
necessary for viewing and manipulating the ontologies.  He's run into some
mechanical problems that he can sort out with Pankaj, the most critical
being trying to get two DagEdit windows open at the same time so two
ontologies can be viewed side by side.  In terms of the ontologies
themselves, we immediately found a number of terms that are not in common
use, or are in odd hierarchical relationships; these should be easy enough
to change.
  A more interesting and complex issue comes with species-specific terms.
An easy one is "silique" in Arabidopsis, which would be an instance of
"fruit" if one is working with multiple species.  A more difficult one is
"stigma", which is a part of "pistil", part of "gynoecium", part of
"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
tassels, because the gynoecium stops developing.  Similarly, "abscission
zone" is part of "silique" in Arabidopsis, and would end up being part of
"fruit" if "silique" were interpreted as an instance of "fruit".  However,
abscission zones do not form in the grass fruit so couldn't be a part of
fruit.  in both cases we end up violating the True Path Rule.  It may be
that this is inevitable, since the descriptors aren't strictly
hierarchical.   Obviously one can get around this somewhat by creating
species-specific bits of the hierarchy, and by making creative use of
"sensu"; this will probably work fine as long as the ontology only has to
apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
apply to all flowering plants, though, there may be a limit to how
species-specific we make the ontologies.   For example we could divide
fruits into indehiscent and dehiscent and then have abscission zone as part
of dehiscent fruits, which would be OK until we get to a fruit that forms
an abscission zone but doesn't dehisce.  Another possibility that Felipe
and I explored a little would be to add another category of connection,
such as "a process that can occur in"  - in addition to "is part of", "is
an instance of" and "develops from".  I suspect that another category might
create more problems than it solves, but it seemed worth considering.
  Any thoughts on this are welcome!
Toby

Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From schmidt at cshl.edu  Thu Oct  2 17:09:18 2003
From: schmidt at cshl.edu (Steven Schmidt)
Date: Thu, 02 Oct 2003 17:09:18 -0400
Subject: Word attachment
Message-ID: <200310021709.18829.schmidt@cshl.edu>

Hi Pankaj,

As a simple way to block viruses, the mail server that handles the Gramene and 
Plant Ontology lists does not accept .doc, .exe, .pif, .scr , etc.
You can save your document as .rtf (which cannot carry a virus) and send that.

-Steve
-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977



From pj37 at cornell.edu  Thu Oct  2 17:33:48 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 02 Oct 2003 17:33:48 -0400
Subject: Diversity of Flower Morphology
References: <Pine.GSO.4.44.0309231940090.22170-100000@acoma.Stanford.EDU>
Message-ID: <3F7C99BB.B15D5650@cornell.edu>

Hi Sue,

I am not sure what you are looking for. Toby and Peter might be able to help.

Pankaj

Sue Rhee wrote:

> Dear Colleagues,
>
> I am writing a review article on ontologies and shared vocabularies with a
> colleague working on mouse/human anatomy, Jonathan Bard, and we would love
> to have a composite figure illustrating the diversity of flower morphology
> in angiosperms.
>
> Do you have any pictures of flowers that you can share or know of anyone
> else that could help me?
>
> Cheers,
> Sue
> -----------------------------------------------------------------------------
> 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 fzqhd at studentmail.umsl.edu  Thu Oct  2 17:46:15 2003
From: fzqhd at studentmail.umsl.edu (Felipe Zapata)
Date: Thu,  2 Oct 2003 16:46:15 -0500
Subject: po-dev-digest V1 #12
In-Reply-To: <3F7C4F98.3050001@cornell.edu>
References: <200310021608.h92G8ZeE003260@brie4.cshl.org> <3F7C4F98.3050001@cornell.edu>
Message-ID: <1065131175.3f7c9ca77056f@studentmail.umsl.edu>

In addition to the comments proposed so far, I have attached an RTF file with 
just 2 comments.

Felipe


_____________
Felipe Zapata
University of Missouri-St.Louis
Department of Biology
8001 Natural Bridge Rd.
St. Louis MO, 63121
Phone: (314) 516-6200
Fax: (314) 516-6233
-------------- next part --------------
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Type: application/rtf
Size: 5527 bytes
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URL: <http://brie4.cshl.edu/pipermail/po-dev/attachments/20031002/ed0b8af1/attachment.rtf>

From rhee at acoma.Stanford.EDU  Thu Oct  2 21:14:50 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Thu, 2 Oct 2003 18:14:50 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <l03130302bba2218f3e82@[134.124.70.41]>
Message-ID: <Pine.GSO.4.44.0310021753250.29769-100000@acoma.Stanford.EDU>

Toby,

Great items for discussion. I agree that invoking another category will
make things more complex than desirable, at least in the beginning. Also,
the category you want to bring in (process that can occur in) can be a
good example of composite ontology use in the future (anatomy + process
ontologies).

I have to think about the stigma example more but regarding the abscission
zone, I believe there should be a generic abscission zone that should a
parent of silique abscission zone, pedicel abscission zone, and petiole
abscission zone. These children can then be children of silique, pedicel,
and petiole, respectively. Otherwise, we are going to violate true path
rule as soon as we have a gene that is specifically expressed in the
petiole abscission zone.

I totally agree that 'sensu' solution is something to be considered as a
last resort. Nonetheless, I think we should try to be economical in
brining in generic parental terms, in order to minimize complexity and
possibly to prevent getting into more sticky situation later. So I'm not
sure about the need to invoke indehiscent and dehiscent fruits. If we did
this, how many parts of fruits will have to be separated to go into
different branches of the fruit?

Sue

>   A more interesting and complex issue comes with species-specific terms.
> An easy one is "silique" in Arabidopsis, which would be an instance of
> "fruit" if one is working with multiple species.  A more difficult one is
> "stigma", which is a part of "pistil", part of "gynoecium", part of
> "floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> tassels, because the gynoecium stops developing.  Similarly, "abscission
> zone" is part of "silique" in Arabidopsis, and would end up being part of
> "fruit" if "silique" were interpreted as an instance of "fruit".  However,
> abscission zones do not form in the grass fruit so couldn't be a part of
> fruit.  in both cases we end up violating the True Path Rule.  It may be
> that this is inevitable, since the descriptors aren't strictly
> hierarchical.   Obviously one can get around this somewhat by creating
> species-specific bits of the hierarchy, and by making creative use of
> "sensu"; this will probably work fine as long as the ontology only has to
> apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> apply to all flowering plants, though, there may be a limit to how
> species-specific we make the ontologies.   For example we could divide
> fruits into indehiscent and dehiscent and then have abscission zone as part
> of dehiscent fruits, which would be OK until we get to a fruit that forms
> an abscission zone but doesn't dehisce.  Another possibility that Felipe
> and I explored a little would be to add another category of connection,
> such as "a process that can occur in"  - in addition to "is part of", "is
> an instance of" and "develops from".  I suspect that another category might
> create more problems than it solves, but it seemed worth considering.
>   Any thoughts on this are welcome!
> Toby
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
>
>

-----------------------------------------------------------------------------
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 ware at cshl.edu  Fri Oct  3 07:45:23 2003
From: ware at cshl.edu (Ware, Doreen)
Date: Fri, 3 Oct 2003 07:45:23 -0400 
Subject: POC poster abstract for  PAG
Message-ID: <39FDE54A4920D411AE0C0090274602F202D09FB3@exch01>

Hi Pankaj

In addition to the other comments... 

Remove the species-specific and change to one of the following "community"
or "plant"

add "Barleybase" to databases.

include URLs if you have not gone over the word limitation.

-----Original Message-----
From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
Sent: Thursday, October 02, 2003 12:39 PM
To: POC-dev
Subject: Re: POC poster abstract for PAG


Pankaj,

Looks great. Thanks for doing it. My suggestions below. By the way, the
po-dev seems to be working for me so please don't cc to my other emails. I
got the same message three times.

> Title: The Plant Ontology Consortium
>
> Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch,
Doreen

Seung Y. Rhee for my name

> Ware,  Peter Stevens,  Pankaj Jaiswal,  Leonore Reiser,  Peter Stevens,
Leszek
> Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.
>
> The goals of the Plant Ontology Consortium are to develop a common set of
> controlled vocabulary terms to describe anatomic and developmental stage
terms

anatomical rather than anatomic?

> in both experimental and agronomically important plants.  We have started
with

experimentally rather than experimental

remove 'have' in have started

> Arabidopsis and cereals such as rice and maize, and later extend this
ontology

replace 'later extend' with 'plan on extending'

> to encompass legumes, Solanaceae, and other plant families.  Concurrently,
these
> terms will be applied to the task of describing the genes and mutants that
are

remove 'the task of'

> contained within the plant specific databases maintained by the
participating

remove 'specific'

> institutions, thereby simultaneously refining the ontologies, and
providing
> points of reference with which to compare the genes and mutants across
these
> species. The broader impact of this project is that it will provide a
framework
> of plant development to allow researchers to make meaningful cross
database

cross-database

> queries across the various species specific resources such as Gramene,
TAIR,

species-specific

> MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and

I thought Gramene and PlantGDB were NOT species-specific. Also, it would
be nice to add URLs to these databases you are referring to.

> dissimilarities involved in plant development. For example, researchers
will be
> able to obtain a definitive list of genes whose action affects plant stem
> development.  The development and implementation of plant ontology will
allow
> the fruits of research in one plant species to be more easily used in the
study
> of other species, leading to a greater understanding of plant biology.
> The project is supported by National Science Foundation grant No. 0321666
to the
> Plant Ontology Consortium.
>
>
>

----------------------------------------------------------------------------
-
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 lstein at cshl.edu  Fri Oct  3 09:40:18 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri, 3 Oct 2003 09:40:18 -0400
Subject: POC poster abstract for  PAG
In-Reply-To: <3F7C5209.5050005@cornell.edu>
References: <3F7C5209.5050005@cornell.edu>
Message-ID: <200310030940.18119.lstein@cshl.edu>

> Authors: Lincoln Stein, Elizabeth Kellogg, Sue Rhee,  Susan McCouch, 
> Doreen Ware,  Pankaj Jaiswal,  Peter Stevens, Leonore Reiser,  Leszek
> Vincent, Mary Polacco, Marty Sachs, Filipe Zapata, Shuly Avraham.
>
> The goals of the Plant Ontology Consortium are to develop a common set of

controlled vocabulary (ontology) terms to describe anatomic and developmental 
stage

> terms in both experimental and agronomically important plants.  

Our first year goal is to create a unified vocabulary for the Arabidopsis 
dicot and the rice and maize monocots.  In later years we will extend this 
controlled vocabulary

>  to encompass legumes, Solanaceae, and other plant
> families.  Concurrently, these terms will be applied to the task of
> describing the genes and mutants that are contained within the plant
> specific databases maintained by the participating institutions, thereby
> simultaneously refining the ontologies, and providing points of reference
                                         ^vocabularies

> with which to compare the genes and mutants across these species. The
> broader impact of this project is that it will provide a framework of plant
> development to allow researchers to make meaningful cross database queries
> across the various species specific resources such as Gramene, TAIR,
> MaizeGDB, PlantGDB, etc. in order to discover patterns of similarities and
> dissimilarities involved in plant development. For example, researchers
> will be able to obtain a definitive list of genes whose action affects

a list of known genes whose action affects

> plant stem development.  The development and implementation of plant

plant stem development, under a consistent and unified definition of the term 
"plant stem development."  The development and implementation of the plant

> ontology will allow the fruits of research in one plant species to be more
> easily used in the study of other species, leading to a greater
> understanding of plant biology. The project is supported by National
> Science Foundation grant No. 0321666 to the Plant Ontology Consortium.

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From lstein at cshl.edu  Fri Oct  3 09:52:01 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri, 3 Oct 2003 09:52:01 -0400
Subject: POC observations so far
In-Reply-To: <l03130302bba2218f3e82@[134.124.70.41]>
References: <l03130302bba2218f3e82@[134.124.70.41]>
Message-ID: <200310030952.01419.lstein@cshl.edu>

Hi,

I'm not sure that the abscission zone problem represent a violation of the 
true path rule.  In the sequence ontology, we have introns being parts of 
primary transcripts, and it doesn't seem to matter that prokaryotes' 
transcripts don't have introns.  Some species will simply not have a 
particular part.

The stigma issue is harder and I suspect it represents an incorrect structure 
in the tassel->floret->gynoecium->pistil path.

Lincoln

On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> Hi all -
>   Felipe has made great progress here downloading the various programs
> necessary for viewing and manipulating the ontologies.  He's run into some
> mechanical problems that he can sort out with Pankaj, the most critical
> being trying to get two DagEdit windows open at the same time so two
> ontologies can be viewed side by side.  In terms of the ontologies
> themselves, we immediately found a number of terms that are not in common
> use, or are in odd hierarchical relationships; these should be easy enough
> to change.
>   A more interesting and complex issue comes with species-specific terms.
> An easy one is "silique" in Arabidopsis, which would be an instance of
> "fruit" if one is working with multiple species.  A more difficult one is
> "stigma", which is a part of "pistil", part of "gynoecium", part of
> "floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> tassels, because the gynoecium stops developing.  Similarly, "abscission
> zone" is part of "silique" in Arabidopsis, and would end up being part of
> "fruit" if "silique" were interpreted as an instance of "fruit".  However,
> abscission zones do not form in the grass fruit so couldn't be a part of
> fruit.  in both cases we end up violating the True Path Rule.  It may be
> that this is inevitable, since the descriptors aren't strictly
> hierarchical.   Obviously one can get around this somewhat by creating
> species-specific bits of the hierarchy, and by making creative use of
> "sensu"; this will probably work fine as long as the ontology only has to
> apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> apply to all flowering plants, though, there may be a limit to how
> species-specific we make the ontologies.   For example we could divide
> fruits into indehiscent and dehiscent and then have abscission zone as part
> of dehiscent fruits, which would be OK until we get to a fruit that forms
> an abscission zone but doesn't dehisce.  Another possibility that Felipe
> and I explored a little would be to add another category of connection,
> such as "a process that can occur in"  - in addition to "is part of", "is
> an instance of" and "develops from".  I suspect that another category might
> create more problems than it solves, but it seemed worth considering.
>   Any thoughts on this are welcome!
> Toby
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From pj37 at cornell.edu  Fri Oct  3 10:52:15 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Oct 2003 10:52:15 -0400
Subject: POC observations so far
In-Reply-To: <200310030952.01419.lstein@cshl.edu>
References: <l03130302bba2218f3e82@[134.124.70.41]> <200310030952.01419.lstein@cshl.edu>
Message-ID: <3F7D8D1F.1050706@cornell.edu>



Lincoln Stein wrote:

> The stigma issue is harder and I suspect it represents an incorrect structure 
> in the tassel->floret->gynoecium->pistil path.
> 

The problem with maize is often the male and female florets occur in the female 
and male inflorescences respectively. Though this is not a normal condition. I 
agree with Sue, when we have the implementation of slots/properties linking 
different anatomical terms at some point in future, we should be able to build 
the correct structures. Please let me know if the following structure works.

inflorescence
----%tassel
-------<staminate floret; synonym: male floret
----------<androecium
-------------<stamen
----------------<anther
----------------<stamen filament
----%spike
------%spike  (sensu zea); synonym:cob
-------<pistillate floret; synonym: female floret
----------<gynoecium
-------------<pistil
---------------<style
---------------<stigma
---------------<ovary
----%panicle
--------<perfect floret
----------<gynoecium
------------<pistil
--------------<style
--------------<stigma
--------------<ovary
----------<androecium
------------<stamen
--------------<anther
--------------<stamen filament
----%capitulum (sensu compositae)
--------<ray floret
--------<disc floret
----<floret
------%floret
--------%ray floret
--------%disc floret
------%floret (sensu Poaceae)
--------%perfect floret
----------<gynoecium
------------<pistil
--------------<style
--------------<stigma
--------------<ovary
----------<androecium
------------<stamen
--------------<anther
--------------<stamen filament
--------%imperfect floret
----------%staminate floret; synonym: male floret
-------------<androecium
---------------<stamen
---------------<anther
----------%pistillate floret; synonym: female floret
-------------<gynoecium
----------------<pistil
------------------<style
------------------<stigma
------------------<ovary




> Lincoln
> 
> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> 
>>Hi all -
>>  Felipe has made great progress here downloading the various programs
>>necessary for viewing and manipulating the ontologies.  He's run into some
>>mechanical problems that he can sort out with Pankaj, the most critical
>>being trying to get two DagEdit windows open at the same time so two
>>ontologies can be viewed side by side.  In terms of the ontologies
>>themselves, we immediately found a number of terms that are not in common
>>use, or are in odd hierarchical relationships; these should be easy enough
>>to change.
>>  A more interesting and complex issue comes with species-specific terms.
>>An easy one is "silique" in Arabidopsis, which would be an instance of
>>"fruit" if one is working with multiple species.  A more difficult one is
>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
>>abscission zones do not form in the grass fruit so couldn't be a part of
>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>>that this is inevitable, since the descriptors aren't strictly
>>hierarchical.   Obviously one can get around this somewhat by creating
>>species-specific bits of the hierarchy, and by making creative use of
>>"sensu"; this will probably work fine as long as the ontology only has to
>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>>apply to all flowering plants, though, there may be a limit to how
>>species-specific we make the ontologies.   For example we could divide
>>fruits into indehiscent and dehiscent and then have abscission zone as part
>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>>and I explored a little would be to add another category of connection,
>>such as "a process that can occur in"  - in addition to "is part of", "is
>>an instance of" and "develops from".  I suspect that another category might
>>create more problems than it solves, but it seemed worth considering.
>>  Any thoughts on this are welcome!
>>Toby
>>
>>Elizabeth A. Kellogg
>>Department of Biology
>>University of Missouri-St. Louis
>>8001 Natural Bridge Road
>>St. Louis, MO 63121
>>phone: 314-516-6217
>>fax: 314-516-6233
>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 fzqhd at studentmail.umsl.edu  Fri Oct  3 11:41:14 2003
From: fzqhd at studentmail.umsl.edu (Felipe Zapata)
Date: Fri,  3 Oct 2003 10:41:14 -0500
Subject: POC observations so far
In-Reply-To: <3F7D8D1F.1050706@cornell.edu>
References: <l03130302bba2218f3e82@[134.124.70.41]> <200310030952.01419.lstein@cshl.edu> <3F7D8D1F.1050706@cornell.edu>
Message-ID: <1065195674.3f7d989a864c6@studentmail.umsl.edu>

The structure that Pankaj suggests could work, however what happens when you 
querry the ontology? Let's say for example you querry for gynoecium.  You won't 
retrieve Tassel at all, even though there's a "gynoecium" (incomplet, imperfect) 
in tassels that simply stops developing.

Felipe


Quoting Pankaj Jaiswal <pj37 at cornell.edu>:

> 
> 
> Lincoln Stein wrote:
> 
> > The stigma issue is harder and I suspect it represents an incorrect
> structure 
> > in the tassel->floret->gynoecium->pistil path.
> > 
> 
> The problem with maize is often the male and female florets occur in the
> female 
> and male inflorescences respectively. Though this is not a normal condition.
> I 
> agree with Sue, when we have the implementation of slots/properties linking 
> different anatomical terms at some point in future, we should be able to
> build 
> the correct structures. Please let me know if the following structure works.
> 
> inflorescence
> ----%tassel
> -------<staminate floret; synonym: male floret
> ----------<androecium
> -------------<stamen
> ----------------<anther
> ----------------<stamen filament
> ----%spike
> ------%spike  (sensu zea); synonym:cob
> -------<pistillate floret; synonym: female floret
> ----------<gynoecium
> -------------<pistil
> ---------------<style
> ---------------<stigma
> ---------------<ovary
> ----%panicle
> --------<perfect floret
> ----------<gynoecium
> ------------<pistil
> --------------<style
> --------------<stigma
> --------------<ovary
> ----------<androecium
> ------------<stamen
> --------------<anther
> --------------<stamen filament
> ----%capitulum (sensu compositae)
> --------<ray floret
> --------<disc floret
> ----<floret
> ------%floret
> --------%ray floret
> --------%disc floret
> ------%floret (sensu Poaceae)
> --------%perfect floret
> ----------<gynoecium
> ------------<pistil
> --------------<style
> --------------<stigma
> --------------<ovary
> ----------<androecium
> ------------<stamen
> --------------<anther
> --------------<stamen filament
> --------%imperfect floret
> ----------%staminate floret; synonym: male floret
> -------------<androecium
> ---------------<stamen
> ---------------<anther
> ----------%pistillate floret; synonym: female floret
> -------------<gynoecium
> ----------------<pistil
> ------------------<style
> ------------------<stigma
> ------------------<ovary
> 
> 
> 
> 
> > Lincoln
> > 
> > On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> > 
> >>Hi all -
> >>  Felipe has made great progress here downloading the various programs
> >>necessary for viewing and manipulating the ontologies.  He's run into some
> >>mechanical problems that he can sort out with Pankaj, the most critical
> >>being trying to get two DagEdit windows open at the same time so two
> >>ontologies can be viewed side by side.  In terms of the ontologies
> >>themselves, we immediately found a number of terms that are not in common
> >>use, or are in odd hierarchical relationships; these should be easy enough
> >>to change.
> >>  A more interesting and complex issue comes with species-specific terms.
> >>An easy one is "silique" in Arabidopsis, which would be an instance of
> >>"fruit" if one is working with multiple species.  A more difficult one is
> >>"stigma", which is a part of "pistil", part of "gynoecium", part of
> >>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> >>tassels, because the gynoecium stops developing.  Similarly, "abscission
> >>zone" is part of "silique" in Arabidopsis, and would end up being part of
> >>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
> >>abscission zones do not form in the grass fruit so couldn't be a part of
> >>fruit.  in both cases we end up violating the True Path Rule.  It may be
> >>that this is inevitable, since the descriptors aren't strictly
> >>hierarchical.   Obviously one can get around this somewhat by creating
> >>species-specific bits of the hierarchy, and by making creative use of
> >>"sensu"; this will probably work fine as long as the ontology only has to
> >>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> >>apply to all flowering plants, though, there may be a limit to how
> >>species-specific we make the ontologies.   For example we could divide
> >>fruits into indehiscent and dehiscent and then have abscission zone as
> part
> >>of dehiscent fruits, which would be OK until we get to a fruit that forms
> >>an abscission zone but doesn't dehisce.  Another possibility that Felipe
> >>and I explored a little would be to add another category of connection,
> >>such as "a process that can occur in"  - in addition to "is part of", "is
> >>an instance of" and "develops from".  I suspect that another category
> might
> >>create more problems than it solves, but it seemed worth considering.
> >>  Any thoughts on this are welcome!
> >>Toby
> >>
> >>Elizabeth A. Kellogg
> >>Department of Biology
> >>University of Missouri-St. Louis
> >>8001 Natural Bridge Road
> >>St. Louis, MO 63121
> >>phone: 314-516-6217
> >>fax: 314-516-6233
> >>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > 
> > 
> 
> -- 
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Research 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
> ******************************************
> 
> 
> 


_____________
Felipe Zapata
University of Missouri-St.Louis
Department of Biology
8001 Natural Bridge Rd.
St. Louis MO, 63121
Phone: (314) 516-6200
Fax: (314) 516-6233


From kellogge at msx.umsl.edu  Fri Oct  3 11:50:00 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Fri, 3 Oct 2003 10:50:00 -0500
Subject: Diversity of Flower Morphology
In-Reply-To: <Pine.GSO.4.44.0310021454180.19014-100000@acoma.Stanford.EDU>
References:  <3D4AD7F06881FD42A720D33D8E399DF3AD5576@COL-EMAIL4.col.missouri.edu>
Message-ID: <l03130301bba349ad56d7@[134.124.70.41]>

Hi Sue -
  There are a lot of good illustrations in the book Plant Systematics: A
phylogenetic approach by Judd et al., published by Sinauer Associates.  I
think your library might have a copy.  Or you might see if David Ackerley
has one - he's at Stanford so must be somewhere within a couple of miles of
you.  The book includes multiple line drawings and also has a CD with lots
of color plates.
Toby

>No. not all angiosperms. just an 'example' that shows how diverse flower
>morphology can be in this taxa...
>
>I'm really looking for ~10 papers.
>
>Sue
>
>On Thu, 2 Oct 2003, Vincent, Leszek wrote:
>
>> Hi Sue - I'm catching up on an old email you sent.
>>
>> I've pondered your Q & can't propose any one figure (or even a few)
>> which could cope with representing the diversity of flower morphology in
>> the angiosperms. Are you really meaning all the angiosperms? - that's a
>> h-u-g-e spectrum of diversity (speaking from a plant systematics
>> perspective). Help me if I'm misunderstanding your Q.
>>
>> - Leszek
>> ????????????????????????????????????????????????????????????????????????
>> 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
>> Yahoo! Messenger: leszekvincent
>> Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
>> (http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
>> Associate Curator, Dunn-Palmer Herbarium (UMO)
>> Research Associate, Missouri Botanical Garden, USA
>>
>> ????????????????????????????????????????????????????????????????????????
>>
>> > -----Original Message-----
>> > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
>> > Sent: Tuesday, September 23, 2003 9:46 PM
>> > To: Pankaj Jaiswal
>> > Cc: Leonore Reiser; Kellogg, Elizabeth A.; Vincent, Leszek;
>> > Kellogg, Elizabeth A.; Polacco, Mary L.; Susan McCouch;
>> > jlbowman at ucdavis.edu; scholl.1 at osu.edu
>> > Subject: Diversity of Flower Morphology
>> >
>> >
>> > Dear Colleagues,
>> >
>> > I am writing a review article on ontologies and shared
>> > vocabularies with a colleague working on mouse/human anatomy,
>> > Jonathan Bard, and we would love to have a composite figure
>> > illustrating the diversity of flower morphology in angiosperms.
>> >
>> > Do you have any pictures of flowers that you can share or
>> > know of anyone else that could help me?
>> >
>> > Cheers,
>> > Sue
>> > --------------------------------------------------------------
>> > ---------------
>> > 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.
>-----------------------------------------------------------------------------

Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From pj37 at cornell.edu  Fri Oct  3 11:56:09 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Oct 2003 11:56:09 -0400
Subject: POC observations so far
In-Reply-To: <1065195674.3f7d989a864c6@studentmail.umsl.edu>
References: <l03130302bba2218f3e82@[134.124.70.41]> <200310030952.01419.lstein@cshl.edu> <3F7D8D1F.1050706@cornell.edu> <1065195674.3f7d989a864c6@studentmail.umsl.edu>
Message-ID: <3F7D9C19.3010302@cornell.edu>



Felipe Zapata wrote:
> The structure that Pankaj suggests could work, however what happens when you 
> querry the ontology? Let's say for example you querry for gynoecium.  You won't 
> retrieve Tassel at all, even though there's a "gynoecium" (incomplet, imperfect) 
> in tassels that simply stops developing.

I think as of this time we should consider making very explicit relationships. I 
don't know if its true or not, please correct me here, will anybody search for 
gynoecium in Tassel floret. I presume not. Incase they do then alternative would 
be to have "rudimentary gynoecium", but i have no clues if it has developed 
enough to have a proper pistil.

-%gynoecium
---%rudimentary gynoecium
---<pistil
------<stigma
------<style
------<ovary



----%tassel
-------<staminate floret; synonym: male floret
----------<androecium
-------------<stamen
----------------<anther
----------------<stamen filament
----------<rudimentary gynoecium

> 
> Felipe
> 
> 
> Quoting Pankaj Jaiswal <pj37 at cornell.edu>:
> 
> 
>>
>>Lincoln Stein wrote:
>>
>>
>>>The stigma issue is harder and I suspect it represents an incorrect
>>
>>structure 
>>
>>>in the tassel->floret->gynoecium->pistil path.
>>>
>>
>>The problem with maize is often the male and female florets occur in the
>>female 
>>and male inflorescences respectively. Though this is not a normal condition.
>>I 
>>agree with Sue, when we have the implementation of slots/properties linking 
>>different anatomical terms at some point in future, we should be able to
>>build 
>>the correct structures. Please let me know if the following structure works.
>>
>>inflorescence
>>----%tassel
>>-------<staminate floret; synonym: male floret
>>----------<androecium
>>-------------<stamen
>>----------------<anther
>>----------------<stamen filament
>>----%spike
>>------%spike  (sensu zea); synonym:cob
>>-------<pistillate floret; synonym: female floret
>>----------<gynoecium
>>-------------<pistil
>>---------------<style
>>---------------<stigma
>>---------------<ovary
>>----%panicle
>>--------<perfect floret
>>----------<gynoecium
>>------------<pistil
>>--------------<style
>>--------------<stigma
>>--------------<ovary
>>----------<androecium
>>------------<stamen
>>--------------<anther
>>--------------<stamen filament
>>----%capitulum (sensu compositae)
>>--------<ray floret
>>--------<disc floret
>>----<floret
>>------%floret
>>--------%ray floret
>>--------%disc floret
>>------%floret (sensu Poaceae)
>>--------%perfect floret
>>----------<gynoecium
>>------------<pistil
>>--------------<style
>>--------------<stigma
>>--------------<ovary
>>----------<androecium
>>------------<stamen
>>--------------<anther
>>--------------<stamen filament
>>--------%imperfect floret
>>----------%staminate floret; synonym: male floret
>>-------------<androecium
>>---------------<stamen
>>---------------<anther
>>----------%pistillate floret; synonym: female floret
>>-------------<gynoecium
>>----------------<pistil
>>------------------<style
>>------------------<stigma
>>------------------<ovary
>>
>>
>>
>>
>>
>>>Lincoln
>>>
>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>>>
>>>
>>>>Hi all -
>>>> Felipe has made great progress here downloading the various programs
>>>>necessary for viewing and manipulating the ontologies.  He's run into some
>>>>mechanical problems that he can sort out with Pankaj, the most critical
>>>>being trying to get two DagEdit windows open at the same time so two
>>>>ontologies can be viewed side by side.  In terms of the ontologies
>>>>themselves, we immediately found a number of terms that are not in common
>>>>use, or are in odd hierarchical relationships; these should be easy enough
>>>>to change.
>>>> A more interesting and complex issue comes with species-specific terms.
>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>>>>"fruit" if one is working with multiple species.  A more difficult one is
>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>>>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>>>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>>>>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
>>>>abscission zones do not form in the grass fruit so couldn't be a part of
>>>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>>>>that this is inevitable, since the descriptors aren't strictly
>>>>hierarchical.   Obviously one can get around this somewhat by creating
>>>>species-specific bits of the hierarchy, and by making creative use of
>>>>"sensu"; this will probably work fine as long as the ontology only has to
>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>>>>apply to all flowering plants, though, there may be a limit to how
>>>>species-specific we make the ontologies.   For example we could divide
>>>>fruits into indehiscent and dehiscent and then have abscission zone as
>>
>>part
>>
>>>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>>>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>>>>and I explored a little would be to add another category of connection,
>>>>such as "a process that can occur in"  - in addition to "is part of", "is
>>>>an instance of" and "develops from".  I suspect that another category
>>
>>might
>>
>>>>create more problems than it solves, but it seemed worth considering.
>>>> Any thoughts on this are welcome!
>>>>Toby
>>>>
>>>>Elizabeth A. Kellogg
>>>>Department of Biology
>>>>University of Missouri-St. Louis
>>>>8001 Natural Bridge Road
>>>>St. Louis, MO 63121
>>>>phone: 314-516-6217
>>>>fax: 314-516-6233
>>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>>
>>>
>>-- 
>>******************************************
>>Pankaj Jaiswal, Ph.D.
>>Research 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
>>******************************************
>>
>>
>>
> 
> 
> 
> _____________
> Felipe Zapata
> University of Missouri-St.Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis MO, 63121
> Phone: (314) 516-6200
> Fax: (314) 516-6233
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 kellogge at msx.umsl.edu  Fri Oct  3 12:17:08 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Fri, 3 Oct 2003 11:17:08 -0500
Subject: POC observations so far
In-Reply-To: <3F7D8D1F.1050706@cornell.edu>
References: <200310030952.01419.lstein@cshl.edu>
 <l03130302bba2218f3e82@[134.124.70.41]>
 <200310030952.01419.lstein@cshl.edu>
Message-ID: <l03130304bba34cc71189@[134.124.70.41]>

Just a simultaneous addition to Felipe's comment:
Unisexual flowers are pretty common in Poaceae and in angiosperms in
general.  Among model systems they occur in Populus, sugar beet, Silene,
and the outer florets of some sunflower relatives, so if we can solve the
problem for maize, we will have solved a number of similar problems.  The
difficulty is that in maize, as in many angiosperms, all flowers start
development as bisexual structures; in staminate florets, the pistil then
aborts.  This means that the structure:
>----%tassel
>-------<staminate floret; synonym: male floret
>----------<androecium
>-------------<stamen
>----------------<anther
>----------------<stamen filament
also should include gynoecium, pistil (and nucellus, ultimately), and
ovary, but not style and stigma.   As long as style and stigma are
daughters of pistil, there's a problem.  The gene tasselseed2 is expressed
in the young ovary of the staminate florets in the tassel, and we can't
describe its expression pattern accurately unless staminate flowers are
allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
gynoecium" certainly seems like a step in the right direction, as long as a
search on gynoecium will find the rudimentary ones as well.
toby

>Lincoln Stein wrote:
>
>> The stigma issue is harder and I suspect it represents an incorrect
>>structure
>> in the tassel->floret->gynoecium->pistil path.
>>
>
>The problem with maize is often the male and female florets occur in the
>female
>and male inflorescences respectively. Though this is not a normal
>condition. I
>agree with Sue, when we have the implementation of slots/properties linking
>different anatomical terms at some point in future, we should be able to
>build
>the correct structures. Please let me know if the following structure works.
>
>inflorescence
>----%tassel
>-------<staminate floret; synonym: male floret
>----------<androecium
>-------------<stamen
>----------------<anther
>----------------<stamen filament
>----%spike
>------%spike  (sensu zea); synonym:cob
>-------<pistillate floret; synonym: female floret
>----------<gynoecium
>-------------<pistil
>---------------<style
>---------------<stigma
>---------------<ovary
>----%panicle
>--------<perfect floret
>----------<gynoecium
>------------<pistil
>--------------<style
>--------------<stigma
>--------------<ovary
>----------<androecium
>------------<stamen
>--------------<anther
>--------------<stamen filament
>----%capitulum (sensu compositae)
>--------<ray floret
>--------<disc floret
>----<floret
>------%floret
>--------%ray floret
>--------%disc floret
>------%floret (sensu Poaceae)
>--------%perfect floret
>----------<gynoecium
>------------<pistil
>--------------<style
>--------------<stigma
>--------------<ovary
>----------<androecium
>------------<stamen
>--------------<anther
>--------------<stamen filament
>--------%imperfect floret
>----------%staminate floret; synonym: male floret
>-------------<androecium
>---------------<stamen
>---------------<anther
>----------%pistillate floret; synonym: female floret
>-------------<gynoecium
>----------------<pistil
>------------------<style
>------------------<stigma
>------------------<ovary
>
>
>
>
>> Lincoln
>>
>> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>>
>>>Hi all -
>>>  Felipe has made great progress here downloading the various programs
>>>necessary for viewing and manipulating the ontologies.  He's run into some
>>>mechanical problems that he can sort out with Pankaj, the most critical
>>>being trying to get two DagEdit windows open at the same time so two
>>>ontologies can be viewed side by side.  In terms of the ontologies
>>>themselves, we immediately found a number of terms that are not in common
>>>use, or are in odd hierarchical relationships; these should be easy enough
>>>to change.
>>>  A more interesting and complex issue comes with species-specific terms.
>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>>>"fruit" if one is working with multiple species.  A more difficult one is
>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>>>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
>>>abscission zones do not form in the grass fruit so couldn't be a part of
>>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>>>that this is inevitable, since the descriptors aren't strictly
>>>hierarchical.   Obviously one can get around this somewhat by creating
>>>species-specific bits of the hierarchy, and by making creative use of
>>>"sensu"; this will probably work fine as long as the ontology only has to
>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>>>apply to all flowering plants, though, there may be a limit to how
>>>species-specific we make the ontologies.   For example we could divide
>>>fruits into indehiscent and dehiscent and then have abscission zone as part
>>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>>>and I explored a little would be to add another category of connection,
>>>such as "a process that can occur in"  - in addition to "is part of", "is
>>>an instance of" and "develops from".  I suspect that another category might
>>>create more problems than it solves, but it seemed worth considering.
>>>  Any thoughts on this are welcome!
>>>Toby
>>>
>>>Elizabeth A. Kellogg
>>>Department of Biology
>>>University of Missouri-St. Louis
>>>8001 Natural Bridge Road
>>>St. Louis, MO 63121
>>>phone: 314-516-6217
>>>fax: 314-516-6233
>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>
>>
>
>--
>******************************************
>Pankaj Jaiswal, Ph.D.
>Research 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
>******************************************


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From lreiser at acoma.Stanford.EDU  Fri Oct  3 12:38:37 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Oct 2003 09:38:37 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <200310030952.01419.lstein@cshl.edu>
Message-ID: <Pine.GSO.4.44.0310030935520.4221-100000@acoma.Stanford.EDU>

My recollection with GO is that part if is CAN be a part of but not IS
always a part of.
Can the flower problem be resolved with perfect/imperfect/female/male??or
more appropriate morphological terms?


On Fri, 3 Oct 2003, Lincoln Stein wrote:

> Hi,
>
> I'm not sure that the abscission zone problem represent a violation of the
> true path rule.  In the sequence ontology, we have introns being parts of
> primary transcripts, and it doesn't seem to matter that prokaryotes'
> transcripts don't have introns.  Some species will simply not have a
> particular part.
>
> The stigma issue is harder and I suspect it represents an incorrect structure
> in the tassel->floret->gynoecium->pistil path.
>
> Lincoln
>
> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> > Hi all -
> >   Felipe has made great progress here downloading the various programs
> > necessary for viewing and manipulating the ontologies.  He's run into some
> > mechanical problems that he can sort out with Pankaj, the most critical
> > being trying to get two DagEdit windows open at the same time so two
> > ontologies can be viewed side by side.  In terms of the ontologies
> > themselves, we immediately found a number of terms that are not in common
> > use, or are in odd hierarchical relationships; these should be easy enough
> > to change.
> >   A more interesting and complex issue comes with species-specific terms.
> > An easy one is "silique" in Arabidopsis, which would be an instance of
> > "fruit" if one is working with multiple species.  A more difficult one is
> > "stigma", which is a part of "pistil", part of "gynoecium", part of
> > "floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> > tassels, because the gynoecium stops developing.  Similarly, "abscission
> > zone" is part of "silique" in Arabidopsis, and would end up being part of
> > "fruit" if "silique" were interpreted as an instance of "fruit".  However,
> > abscission zones do not form in the grass fruit so couldn't be a part of
> > fruit.  in both cases we end up violating the True Path Rule.  It may be
> > that this is inevitable, since the descriptors aren't strictly
> > hierarchical.   Obviously one can get around this somewhat by creating
> > species-specific bits of the hierarchy, and by making creative use of
> > "sensu"; this will probably work fine as long as the ontology only has to
> > apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> > apply to all flowering plants, though, there may be a limit to how
> > species-specific we make the ontologies.   For example we could divide
> > fruits into indehiscent and dehiscent and then have abscission zone as part
> > of dehiscent fruits, which would be OK until we get to a fruit that forms
> > an abscission zone but doesn't dehisce.  Another possibility that Felipe
> > and I explored a little would be to add another category of connection,
> > such as "a process that can occur in"  - in addition to "is part of", "is
> > an instance of" and "develops from".  I suspect that another category might
> > create more problems than it solves, but it seemed worth considering.
> >   Any thoughts on this are welcome!
> > Toby
> >
> > Elizabeth A. Kellogg
> > Department of Biology
> > University of Missouri-St. Louis
> > 8001 Natural Bridge Road
> > St. Louis, MO 63121
> > phone: 314-516-6217
> > fax: 314-516-6233
> > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
> --
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From kellogge at msx.umsl.edu  Fri Oct  3 12:52:18 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Fri, 3 Oct 2003 11:52:18 -0500
Subject: POC observations so far
In-Reply-To: <3F7D9C19.3010302@cornell.edu>
References: <1065195674.3f7d989a864c6@studentmail.umsl.edu>
 <l03130302bba2218f3e82@[134.124.70.41]>
 <200310030952.01419.lstein@cshl.edu> <3F7D8D1F.1050706@cornell.edu>
 <1065195674.3f7d989a864c6@studentmail.umsl.edu>
Message-ID: <l03130305bba351d14074@[134.124.70.41]>

Just a follow-up (messages crossing in the mail):
Unfortunately, people do search for gynoecia in tassel florets, and even
write papers about them.  (perhaps we have brain defects that make us do
these sorts of things...)  let's try the "rudimentary" solution for a while
and see how it plays out.  We'll want rudimentary stamens as well, although
that term will overlap with staminodia.
  On another subject, are we still planning a conference call on Monday?
if so, I'll have to shift the time of my lab meeting.
Toby

>Felipe Zapata wrote:
>> The structure that Pankaj suggests could work, however what happens when
>>you
>> querry the ontology? Let's say for example you querry for gynoecium.
>>You won't
>> retrieve Tassel at all, even though there's a "gynoecium" (incomplet,
>>imperfect)
>> in tassels that simply stops developing.
>
>I think as of this time we should consider making very explicit
>relationships. I
>don't know if its true or not, please correct me here, will anybody search
>for
>gynoecium in Tassel floret. I presume not. Incase they do then alternative
>would
>be to have "rudimentary gynoecium", but i have no clues if it has developed
>enough to have a proper pistil.
>
>-%gynoecium
>---%rudimentary gynoecium
>---<pistil
>------<stigma
>------<style
>------<ovary
>
>
>
>----%tassel
>-------<staminate floret; synonym: male floret
>----------<androecium
>-------------<stamen
>----------------<anther
>----------------<stamen filament
>----------<rudimentary gynoecium
>
>>
>> Felipe
>>
>>
>> Quoting Pankaj Jaiswal <pj37 at cornell.edu>:
>>
>>
>>>
>>>Lincoln Stein wrote:
>>>
>>>
>>>>The stigma issue is harder and I suspect it represents an incorrect
>>>
>>>structure
>>>
>>>>in the tassel->floret->gynoecium->pistil path.
>>>>
>>>
>>>The problem with maize is often the male and female florets occur in the
>>>female
>>>and male inflorescences respectively. Though this is not a normal condition.
>>>I
>>>agree with Sue, when we have the implementation of slots/properties linking
>>>different anatomical terms at some point in future, we should be able to
>>>build
>>>the correct structures. Please let me know if the following structure works.
>>>
>>>inflorescence
>>>----%tassel
>>>-------<staminate floret; synonym: male floret
>>>----------<androecium
>>>-------------<stamen
>>>----------------<anther
>>>----------------<stamen filament
>>>----%spike
>>>------%spike  (sensu zea); synonym:cob
>>>-------<pistillate floret; synonym: female floret
>>>----------<gynoecium
>>>-------------<pistil
>>>---------------<style
>>>---------------<stigma
>>>---------------<ovary
>>>----%panicle
>>>--------<perfect floret
>>>----------<gynoecium
>>>------------<pistil
>>>--------------<style
>>>--------------<stigma
>>>--------------<ovary
>>>----------<androecium
>>>------------<stamen
>>>--------------<anther
>>>--------------<stamen filament
>>>----%capitulum (sensu compositae)
>>>--------<ray floret
>>>--------<disc floret
>>>----<floret
>>>------%floret
>>>--------%ray floret
>>>--------%disc floret
>>>------%floret (sensu Poaceae)
>>>--------%perfect floret
>>>----------<gynoecium
>>>------------<pistil
>>>--------------<style
>>>--------------<stigma
>>>--------------<ovary
>>>----------<androecium
>>>------------<stamen
>>>--------------<anther
>>>--------------<stamen filament
>>>--------%imperfect floret
>>>----------%staminate floret; synonym: male floret
>>>-------------<androecium
>>>---------------<stamen
>>>---------------<anther
>>>----------%pistillate floret; synonym: female floret
>>>-------------<gynoecium
>>>----------------<pistil
>>>------------------<style
>>>------------------<stigma
>>>------------------<ovary
>>>
>>>
>>>
>>>
>>>
>>>>Lincoln
>>>>
>>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>>>>
>>>>
>>>>>Hi all -
>>>>> Felipe has made great progress here downloading the various programs
>>>>>necessary for viewing and manipulating the ontologies.  He's run into some
>>>>>mechanical problems that he can sort out with Pankaj, the most critical
>>>>>being trying to get two DagEdit windows open at the same time so two
>>>>>ontologies can be viewed side by side.  In terms of the ontologies
>>>>>themselves, we immediately found a number of terms that are not in common
>>>>>use, or are in odd hierarchical relationships; these should be easy enough
>>>>>to change.
>>>>> A more interesting and complex issue comes with species-specific terms.
>>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>>>>>"fruit" if one is working with multiple species.  A more difficult one is
>>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>>>>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>>>>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>>>>>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
>>>>>abscission zones do not form in the grass fruit so couldn't be a part of
>>>>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>>>>>that this is inevitable, since the descriptors aren't strictly
>>>>>hierarchical.   Obviously one can get around this somewhat by creating
>>>>>species-specific bits of the hierarchy, and by making creative use of
>>>>>"sensu"; this will probably work fine as long as the ontology only has to
>>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>>>>>apply to all flowering plants, though, there may be a limit to how
>>>>>species-specific we make the ontologies.   For example we could divide
>>>>>fruits into indehiscent and dehiscent and then have abscission zone as
>>>
>>>part
>>>
>>>>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>>>>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>>>>>and I explored a little would be to add another category of connection,
>>>>>such as "a process that can occur in"  - in addition to "is part of", "is
>>>>>an instance of" and "develops from".  I suspect that another category
>>>
>>>might
>>>
>>>>>create more problems than it solves, but it seemed worth considering.
>>>>> Any thoughts on this are welcome!
>>>>>Toby
>>>>>
>>>>>Elizabeth A. Kellogg
>>>>>Department of Biology
>>>>>University of Missouri-St. Louis
>>>>>8001 Natural Bridge Road
>>>>>St. Louis, MO 63121
>>>>>phone: 314-516-6217
>>>>>fax: 314-516-6233
>>>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>>>
>>>>
>>>--
>>>******************************************
>>>Pankaj Jaiswal, Ph.D.
>>>Research 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
>>>******************************************
>>>
>>>
>>>
>>
>>
>>
>> _____________
>> Felipe Zapata
>> University of Missouri-St.Louis
>> Department of Biology
>> 8001 Natural Bridge Rd.
>> St. Louis MO, 63121
>> Phone: (314) 516-6200
>> Fax: (314) 516-6233
>>
>
>--
>******************************************
>Pankaj Jaiswal, Ph.D.
>Research 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
>******************************************


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From lreiser at acoma.Stanford.EDU  Fri Oct  3 12:48:47 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Oct 2003 09:48:47 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <l03130304bba34cc71189@[134.124.70.41]>
Message-ID: <Pine.GSO.4.44.0310030942510.4221-100000@acoma.Stanford.EDU>


In a way- what seems to be a solution is stages of development of an organ
as being instances of an organ (e.g gynoecium primordia is an instance of
gynoecium), aborted/rudimentary as other instances- so you have a node for
gynoecium that includes all instances (stages)

gynoecium
-%gynoecium primordium
-%aborted
-%mature
--<ovary
--<stigma
--<style

not being comprehensive here but this is the general picture.
Leonore


On Fri, 3 Oct 2003, Toby Kellogg wrote:

> Just a simultaneous addition to Felipe's comment:
> Unisexual flowers are pretty common in Poaceae and in angiosperms in
> general.  Among model systems they occur in Populus, sugar beet, Silene,
> and the outer florets of some sunflower relatives, so if we can solve the
> problem for maize, we will have solved a number of similar problems.  The
> difficulty is that in maize, as in many angiosperms, all flowers start
> development as bisexual structures; in staminate florets, the pistil then
> aborts.  This means that the structure:
> >----%tassel
> >-------<staminate floret; synonym: male floret
> >----------<androecium
> >-------------<stamen
> >----------------<anther
> >----------------<stamen filament
> also should include gynoecium, pistil (and nucellus, ultimately), and
> ovary, but not style and stigma.   As long as style and stigma are
> daughters of pistil, there's a problem.  The gene tasselseed2 is expressed
> in the young ovary of the staminate florets in the tassel, and we can't
> describe its expression pattern accurately unless staminate flowers are
> allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
> gynoecium" certainly seems like a step in the right direction, as long as a
> search on gynoecium will find the rudimentary ones as well.
> toby
>
> >Lincoln Stein wrote:
> >
> >> The stigma issue is harder and I suspect it represents an incorrect
> >>structure
> >> in the tassel->floret->gynoecium->pistil path.
> >>
> >
> >The problem with maize is often the male and female florets occur in the
> >female
> >and male inflorescences respectively. Though this is not a normal
> >condition. I
> >agree with Sue, when we have the implementation of slots/properties linking
> >different anatomical terms at some point in future, we should be able to
> >build
> >the correct structures. Please let me know if the following structure works.
> >
> >inflorescence
> >----%tassel
> >-------<staminate floret; synonym: male floret
> >----------<androecium
> >-------------<stamen
> >----------------<anther
> >----------------<stamen filament
> >----%spike
> >------%spike  (sensu zea); synonym:cob
> >-------<pistillate floret; synonym: female floret
> >----------<gynoecium
> >-------------<pistil
> >---------------<style
> >---------------<stigma
> >---------------<ovary
> >----%panicle
> >--------<perfect floret
> >----------<gynoecium
> >------------<pistil
> >--------------<style
> >--------------<stigma
> >--------------<ovary
> >----------<androecium
> >------------<stamen
> >--------------<anther
> >--------------<stamen filament
> >----%capitulum (sensu compositae)
> >--------<ray floret
> >--------<disc floret
> >----<floret
> >------%floret
> >--------%ray floret
> >--------%disc floret
> >------%floret (sensu Poaceae)
> >--------%perfect floret
> >----------<gynoecium
> >------------<pistil
> >--------------<style
> >--------------<stigma
> >--------------<ovary
> >----------<androecium
> >------------<stamen
> >--------------<anther
> >--------------<stamen filament
> >--------%imperfect floret
> >----------%staminate floret; synonym: male floret
> >-------------<androecium
> >---------------<stamen
> >---------------<anther
> >----------%pistillate floret; synonym: female floret
> >-------------<gynoecium
> >----------------<pistil
> >------------------<style
> >------------------<stigma
> >------------------<ovary
> >
> >
> >
> >
> >> Lincoln
> >>
> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> >>
> >>>Hi all -
> >>>  Felipe has made great progress here downloading the various programs
> >>>necessary for viewing and manipulating the ontologies.  He's run into some
> >>>mechanical problems that he can sort out with Pankaj, the most critical
> >>>being trying to get two DagEdit windows open at the same time so two
> >>>ontologies can be viewed side by side.  In terms of the ontologies
> >>>themselves, we immediately found a number of terms that are not in common
> >>>use, or are in odd hierarchical relationships; these should be easy enough
> >>>to change.
> >>>  A more interesting and complex issue comes with species-specific terms.
> >>>An easy one is "silique" in Arabidopsis, which would be an instance of
> >>>"fruit" if one is working with multiple species.  A more difficult one is
> >>>"stigma", which is a part of "pistil", part of "gynoecium", part of
> >>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> >>>tassels, because the gynoecium stops developing.  Similarly, "abscission
> >>>zone" is part of "silique" in Arabidopsis, and would end up being part of
> >>>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
> >>>abscission zones do not form in the grass fruit so couldn't be a part of
> >>>fruit.  in both cases we end up violating the True Path Rule.  It may be
> >>>that this is inevitable, since the descriptors aren't strictly
> >>>hierarchical.   Obviously one can get around this somewhat by creating
> >>>species-specific bits of the hierarchy, and by making creative use of
> >>>"sensu"; this will probably work fine as long as the ontology only has to
> >>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> >>>apply to all flowering plants, though, there may be a limit to how
> >>>species-specific we make the ontologies.   For example we could divide
> >>>fruits into indehiscent and dehiscent and then have abscission zone as part
> >>>of dehiscent fruits, which would be OK until we get to a fruit that forms
> >>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
> >>>and I explored a little would be to add another category of connection,
> >>>such as "a process that can occur in"  - in addition to "is part of", "is
> >>>an instance of" and "develops from".  I suspect that another category might
> >>>create more problems than it solves, but it seemed worth considering.
> >>>  Any thoughts on this are welcome!
> >>>Toby
> >>>
> >>>Elizabeth A. Kellogg
> >>>Department of Biology
> >>>University of Missouri-St. Louis
> >>>8001 Natural Bridge Road
> >>>St. Louis, MO 63121
> >>>phone: 314-516-6217
> >>>fax: 314-516-6233
> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >>
> >>
> >
> >--
> >******************************************
> >Pankaj Jaiswal, Ph.D.
> >Research 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
> >******************************************
>
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Fri Oct  3 12:50:45 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Oct 2003 12:50:45 -0400
Subject: POC observations so far
In-Reply-To: <Pine.GSO.4.44.0310030935520.4221-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310030935520.4221-100000@acoma.Stanford.EDU>
Message-ID: <3F7DA8E5.5040906@cornell.edu>

Hi Leonore,


Leonore Reiser wrote:

> My recollection with GO is that part if is CAN be a part of but not IS
> always a part of.
> Can the flower problem be resolved with perfect/imperfect/female/male??or
> more appropriate morphological terms?

pl. see my suggestion in one of the mails. there is somethink like that in the 
proposed str.
Pankaj






From pj37 at cornell.edu  Fri Oct  3 12:56:51 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Oct 2003 12:56:51 -0400
Subject: POC observations so far
In-Reply-To: <l03130305bba351d14074@[134.124.70.41]>
References: <1065195674.3f7d989a864c6@studentmail.umsl.edu> <l03130302bba2218f3e82@[134.124.70.41]> <200310030952.01419.lstein@cshl.edu> <3F7D8D1F.1050706@cornell.edu> <1065195674.3f7d989a864c6@studentmail.umsl.edu> <l03130305bba351d14074@[134.124.70.41]>
Message-ID: <3F7DAA53.4090202@cornell.edu>



Toby Kellogg wrote:

> Just a follow-up (messages crossing in the mail):
> Unfortunately, people do search for gynoecia in tassel florets, and even
> write papers about them.  (perhaps we have brain defects that make us do
> these sorts of things...)  let's try the "rudimentary" solution for a while
> and see how it plays out.  We'll want rudimentary stamens as well, although
> that term will overlap with staminodia.

no problem we can do that. Both the rudimentary terms will be instances of their 
parent terms, thus making it possible for the users to find what they are 
looking for. I will make changes in the cereal ontology next week.


>   On another subject, are we still planning a conference call on Monday?
> if so, I'll have to shift the time of my lab meeting.
> Toby
I guess Sue has some conflicts with the conf. call.

Pankaj



> 
> 
>>Felipe Zapata wrote:
>>
>>>The structure that Pankaj suggests could work, however what happens when
>>>you
>>>querry the ontology? Let's say for example you querry for gynoecium.
>>>You won't
>>>retrieve Tassel at all, even though there's a "gynoecium" (incomplet,
>>>imperfect)
>>>in tassels that simply stops developing.
>>
>>I think as of this time we should consider making very explicit
>>relationships. I
>>don't know if its true or not, please correct me here, will anybody search
>>for
>>gynoecium in Tassel floret. I presume not. Incase they do then alternative
>>would
>>be to have "rudimentary gynoecium", but i have no clues if it has developed
>>enough to have a proper pistil.
>>
>>-%gynoecium
>>---%rudimentary gynoecium
>>---<pistil
>>------<stigma
>>------<style
>>------<ovary
>>
>>
>>
>>----%tassel
>>-------<staminate floret; synonym: male floret
>>----------<androecium
>>-------------<stamen
>>----------------<anther
>>----------------<stamen filament
>>----------<rudimentary gynoecium
>>
>>
>>>Felipe
>>>
>>>
>>>Quoting Pankaj Jaiswal <pj37 at cornell.edu>:
>>>
>>>
>>>
>>>>Lincoln Stein wrote:
>>>>
>>>>
>>>>
>>>>>The stigma issue is harder and I suspect it represents an incorrect
>>>>
>>>>structure
>>>>
>>>>
>>>>>in the tassel->floret->gynoecium->pistil path.
>>>>>
>>>>
>>>>The problem with maize is often the male and female florets occur in the
>>>>female
>>>>and male inflorescences respectively. Though this is not a normal condition.
>>>>I
>>>>agree with Sue, when we have the implementation of slots/properties linking
>>>>different anatomical terms at some point in future, we should be able to
>>>>build
>>>>the correct structures. Please let me know if the following structure works.
>>>>
>>>>inflorescence
>>>>----%tassel
>>>>-------<staminate floret; synonym: male floret
>>>>----------<androecium
>>>>-------------<stamen
>>>>----------------<anther
>>>>----------------<stamen filament
>>>>----%spike
>>>>------%spike  (sensu zea); synonym:cob
>>>>-------<pistillate floret; synonym: female floret
>>>>----------<gynoecium
>>>>-------------<pistil
>>>>---------------<style
>>>>---------------<stigma
>>>>---------------<ovary
>>>>----%panicle
>>>>--------<perfect floret
>>>>----------<gynoecium
>>>>------------<pistil
>>>>--------------<style
>>>>--------------<stigma
>>>>--------------<ovary
>>>>----------<androecium
>>>>------------<stamen
>>>>--------------<anther
>>>>--------------<stamen filament
>>>>----%capitulum (sensu compositae)
>>>>--------<ray floret
>>>>--------<disc floret
>>>>----<floret
>>>>------%floret
>>>>--------%ray floret
>>>>--------%disc floret
>>>>------%floret (sensu Poaceae)
>>>>--------%perfect floret
>>>>----------<gynoecium
>>>>------------<pistil
>>>>--------------<style
>>>>--------------<stigma
>>>>--------------<ovary
>>>>----------<androecium
>>>>------------<stamen
>>>>--------------<anther
>>>>--------------<stamen filament
>>>>--------%imperfect floret
>>>>----------%staminate floret; synonym: male floret
>>>>-------------<androecium
>>>>---------------<stamen
>>>>---------------<anther
>>>>----------%pistillate floret; synonym: female floret
>>>>-------------<gynoecium
>>>>----------------<pistil
>>>>------------------<style
>>>>------------------<stigma
>>>>------------------<ovary
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Lincoln
>>>>>
>>>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>>>>>
>>>>>
>>>>>
>>>>>>Hi all -
>>>>>>Felipe has made great progress here downloading the various programs
>>>>>>necessary for viewing and manipulating the ontologies.  He's run into some
>>>>>>mechanical problems that he can sort out with Pankaj, the most critical
>>>>>>being trying to get two DagEdit windows open at the same time so two
>>>>>>ontologies can be viewed side by side.  In terms of the ontologies
>>>>>>themselves, we immediately found a number of terms that are not in common
>>>>>>use, or are in odd hierarchical relationships; these should be easy enough
>>>>>>to change.
>>>>>>A more interesting and complex issue comes with species-specific terms.
>>>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>>>>>>"fruit" if one is working with multiple species.  A more difficult one is
>>>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>>>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>>>>>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>>>>>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>>>>>>"fruit" if "silique" were interpreted as an instance of "fruit".  However,
>>>>>>abscission zones do not form in the grass fruit so couldn't be a part of
>>>>>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>>>>>>that this is inevitable, since the descriptors aren't strictly
>>>>>>hierarchical.   Obviously one can get around this somewhat by creating
>>>>>>species-specific bits of the hierarchy, and by making creative use of
>>>>>>"sensu"; this will probably work fine as long as the ontology only has to
>>>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>>>>>>apply to all flowering plants, though, there may be a limit to how
>>>>>>species-specific we make the ontologies.   For example we could divide
>>>>>>fruits into indehiscent and dehiscent and then have abscission zone as
>>>>
>>>>part
>>>>
>>>>
>>>>>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>>>>>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>>>>>>and I explored a little would be to add another category of connection,
>>>>>>such as "a process that can occur in"  - in addition to "is part of", "is
>>>>>>an instance of" and "develops from".  I suspect that another category
>>>>
>>>>might
>>>>
>>>>
>>>>>>create more problems than it solves, but it seemed worth considering.
>>>>>>Any thoughts on this are welcome!
>>>>>>Toby
>>>>>>
>>>>>>Elizabeth A. Kellogg
>>>>>>Department of Biology
>>>>>>University of Missouri-St. Louis
>>>>>>8001 Natural Bridge Road
>>>>>>St. Louis, MO 63121
>>>>>>phone: 314-516-6217
>>>>>>fax: 314-516-6233
>>>>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>>>>
>>>>>
>>>>--
>>>>******************************************
>>>>Pankaj Jaiswal, Ph.D.
>>>>Research 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
>>>>******************************************
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>_____________
>>>Felipe Zapata
>>>University of Missouri-St.Louis
>>>Department of Biology
>>>8001 Natural Bridge Rd.
>>>St. Louis MO, 63121
>>>Phone: (314) 516-6200
>>>Fax: (314) 516-6233
>>>
>>
>>--
>>******************************************
>>Pankaj Jaiswal, Ph.D.
>>Research 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
>>******************************************
> 
> 
> 
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> 
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 kellogge at msx.umsl.edu  Fri Oct  3 13:26:52 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Fri, 3 Oct 2003 12:26:52 -0500
Subject: POC observations so far
In-Reply-To: <Pine.GSO.4.44.0310030942510.4221-100000@acoma.Stanford.EDU>
References: <l03130304bba34cc71189@[134.124.70.41]>
Message-ID: <l0313030abba3613fe0a6@[134.124.70.41]>

That would also be a good possibility - it's sort of an expanded and
slightly more precise version of Pankaj's "rudimentary" category.   A
trivial question:  does the word "gynoecium" need to follow "aborted" and
"mature", or is it understood?
Toby

>In a way- what seems to be a solution is stages of development of an organ
>as being instances of an organ (e.g gynoecium primordia is an instance of
>gynoecium), aborted/rudimentary as other instances- so you have a node for
>gynoecium that includes all instances (stages)
>
>gynoecium
>-%gynoecium primordium
>-%aborted
>-%mature
>--<ovary
>--<stigma
>--<style
>
>not being comprehensive here but this is the general picture.
>Leonore
>
>
>On Fri, 3 Oct 2003, Toby Kellogg wrote:
>
>> Just a simultaneous addition to Felipe's comment:
>> Unisexual flowers are pretty common in Poaceae and in angiosperms in
>> general.  Among model systems they occur in Populus, sugar beet, Silene,
>> and the outer florets of some sunflower relatives, so if we can solve the
>> problem for maize, we will have solved a number of similar problems.  The
>> difficulty is that in maize, as in many angiosperms, all flowers start
>> development as bisexual structures; in staminate florets, the pistil then
>> aborts.  This means that the structure:
>> >----%tassel
>> >-------<staminate floret; synonym: male floret
>> >----------<androecium
>> >-------------<stamen
>> >----------------<anther
>> >----------------<stamen filament
>> also should include gynoecium, pistil (and nucellus, ultimately), and
>> ovary, but not style and stigma.   As long as style and stigma are
>> daughters of pistil, there's a problem.  The gene tasselseed2 is expressed
>> in the young ovary of the staminate florets in the tassel, and we can't
>> describe its expression pattern accurately unless staminate flowers are
>> allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
>> gynoecium" certainly seems like a step in the right direction, as long as a
>> search on gynoecium will find the rudimentary ones as well.
>> toby
>>
>> >Lincoln Stein wrote:
>> >
>> >> The stigma issue is harder and I suspect it represents an incorrect
>> >>structure
>> >> in the tassel->floret->gynoecium->pistil path.
>> >>
>> >
>> >The problem with maize is often the male and female florets occur in the
>> >female
>> >and male inflorescences respectively. Though this is not a normal
>> >condition. I
>> >agree with Sue, when we have the implementation of slots/properties linking
>> >different anatomical terms at some point in future, we should be able to
>> >build
>> >the correct structures. Please let me know if the following structure
>>works.
>> >
>> >inflorescence
>> >----%tassel
>> >-------<staminate floret; synonym: male floret
>> >----------<androecium
>> >-------------<stamen
>> >----------------<anther
>> >----------------<stamen filament
>> >----%spike
>> >------%spike  (sensu zea); synonym:cob
>> >-------<pistillate floret; synonym: female floret
>> >----------<gynoecium
>> >-------------<pistil
>> >---------------<style
>> >---------------<stigma
>> >---------------<ovary
>> >----%panicle
>> >--------<perfect floret
>> >----------<gynoecium
>> >------------<pistil
>> >--------------<style
>> >--------------<stigma
>> >--------------<ovary
>> >----------<androecium
>> >------------<stamen
>> >--------------<anther
>> >--------------<stamen filament
>> >----%capitulum (sensu compositae)
>> >--------<ray floret
>> >--------<disc floret
>> >----<floret
>> >------%floret
>> >--------%ray floret
>> >--------%disc floret
>> >------%floret (sensu Poaceae)
>> >--------%perfect floret
>> >----------<gynoecium
>> >------------<pistil
>> >--------------<style
>> >--------------<stigma
>> >--------------<ovary
>> >----------<androecium
>> >------------<stamen
>> >--------------<anther
>> >--------------<stamen filament
>> >--------%imperfect floret
>> >----------%staminate floret; synonym: male floret
>> >-------------<androecium
>> >---------------<stamen
>> >---------------<anther
>> >----------%pistillate floret; synonym: female floret
>> >-------------<gynoecium
>> >----------------<pistil
>> >------------------<style
>> >------------------<stigma
>> >------------------<ovary
>> >
>> >
>> >
>> >
>> >> Lincoln
>> >>
>> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>> >>
>> >>>Hi all -
>> >>>  Felipe has made great progress here downloading the various programs
>> >>>necessary for viewing and manipulating the ontologies.  He's run into
>>some
>> >>>mechanical problems that he can sort out with Pankaj, the most critical
>> >>>being trying to get two DagEdit windows open at the same time so two
>> >>>ontologies can be viewed side by side.  In terms of the ontologies
>> >>>themselves, we immediately found a number of terms that are not in common
>> >>>use, or are in odd hierarchical relationships; these should be easy
>>enough
>> >>>to change.
>> >>>  A more interesting and complex issue comes with species-specific terms.
>> >>>An easy one is "silique" in Arabidopsis, which would be an instance of
>> >>>"fruit" if one is working with multiple species.  A more difficult one is
>> >>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>> >>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>> >>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>> >>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>> >>>"fruit" if "silique" were interpreted as an instance of "fruit".
>>However,
>> >>>abscission zones do not form in the grass fruit so couldn't be a part of
>> >>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>> >>>that this is inevitable, since the descriptors aren't strictly
>> >>>hierarchical.   Obviously one can get around this somewhat by creating
>> >>>species-specific bits of the hierarchy, and by making creative use of
>> >>>"sensu"; this will probably work fine as long as the ontology only has to
>> >>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>> >>>apply to all flowering plants, though, there may be a limit to how
>> >>>species-specific we make the ontologies.   For example we could divide
>> >>>fruits into indehiscent and dehiscent and then have abscission zone
>>as part
>> >>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>> >>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>> >>>and I explored a little would be to add another category of connection,
>> >>>such as "a process that can occur in"  - in addition to "is part of", "is
>> >>>an instance of" and "develops from".  I suspect that another category
>>might
>> >>>create more problems than it solves, but it seemed worth considering.
>> >>>  Any thoughts on this are welcome!
>> >>>Toby
>> >>>
>> >>>Elizabeth A. Kellogg
>> >>>Department of Biology
>> >>>University of Missouri-St. Louis
>> >>>8001 Natural Bridge Road
>> >>>St. Louis, MO 63121
>> >>>phone: 314-516-6217
>> >>>fax: 314-516-6233
>> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>> >>
>> >>
>> >
>> >--
>> >******************************************
>> >Pankaj Jaiswal, Ph.D.
>> >Research 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
>> >******************************************
>>
>>
>> Elizabeth A. Kellogg
>> Department of Biology
>> University of Missouri-St. Louis
>> 8001 Natural Bridge Road
>> St. Louis, MO 63121
>> phone: 314-516-6217
>> fax: 314-516-6233
>> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>
>>
>>
>
>-------------------------------------------------------------------------------
>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>The Arabidopsis Information Resource	FAX: (650) 325-6857
>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>Department of Plant Biology		URL: http://arabidopsis.org/
>260 Panama St.
>Stanford, CA 94305
>-------------------------------------------------------------------------------


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From lreiser at acoma.Stanford.EDU  Fri Oct  3 13:37:39 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Oct 2003 10:37:39 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <3F7DA8E5.5040906@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310031034440.6934-100000@acoma.Stanford.EDU>


Yes- I responded to one before I saw your reponse which looks
great-.I think combined with some temporal component (instances of body
parts) either as some development X anatomy cross product or as instances
w/in the anatomy ontology would solve some of the problems that Toby
pointed out.


On Fri, 3 Oct 2003, Pankaj Jaiswal wrote:

> Hi Leonore,
>
>
> Leonore Reiser wrote:
>
> > My recollection with GO is that part if is CAN be a part of but not IS
> > always a part of.
> > Can the flower problem be resolved with perfect/imperfect/female/male??or
> > more appropriate morphological terms?
>
> pl. see my suggestion in one of the mails. there is somethink like that in the
> proposed str.
> Pankaj
>
>
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From lreiser at acoma.Stanford.EDU  Fri Oct  3 13:42:02 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Oct 2003 10:42:02 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <l0313030abba3613fe0a6@[134.124.70.41]>
Message-ID: <Pine.GSO.4.44.0310031040420.6934-100000@acoma.Stanford.EDU>


I'd be in favor of including the body part- although it may be implicit in
the structure- I think its confusing to leave it off.And would look weird
to someone searching with the term gynoecium to see 'aborted' vs. aborted
gynoecium.


On Fri, 3 Oct 2003, Toby Kellogg wrote:

> That would also be a good possibility - it's sort of an expanded and
> slightly more precise version of Pankaj's "rudimentary" category.   A
> trivial question:  does the word "gynoecium" need to follow "aborted" and
> "mature", or is it understood?
> Toby
>
> >In a way- what seems to be a solution is stages of development of an organ
> >as being instances of an organ (e.g gynoecium primordia is an instance of
> >gynoecium), aborted/rudimentary as other instances- so you have a node for
> >gynoecium that includes all instances (stages)
> >
> >gynoecium
> >-%gynoecium primordium
> >-%aborted
> >-%mature
> >--<ovary
> >--<stigma
> >--<style
> >
> >not being comprehensive here but this is the general picture.
> >Leonore
> >
> >
> >On Fri, 3 Oct 2003, Toby Kellogg wrote:
> >
> >> Just a simultaneous addition to Felipe's comment:
> >> Unisexual flowers are pretty common in Poaceae and in angiosperms in
> >> general.  Among model systems they occur in Populus, sugar beet, Silene,
> >> and the outer florets of some sunflower relatives, so if we can solve the
> >> problem for maize, we will have solved a number of similar problems.  The
> >> difficulty is that in maize, as in many angiosperms, all flowers start
> >> development as bisexual structures; in staminate florets, the pistil then
> >> aborts.  This means that the structure:
> >> >----%tassel
> >> >-------<staminate floret; synonym: male floret
> >> >----------<androecium
> >> >-------------<stamen
> >> >----------------<anther
> >> >----------------<stamen filament
> >> also should include gynoecium, pistil (and nucellus, ultimately), and
> >> ovary, but not style and stigma.   As long as style and stigma are
> >> daughters of pistil, there's a problem.  The gene tasselseed2 is expressed
> >> in the young ovary of the staminate florets in the tassel, and we can't
> >> describe its expression pattern accurately unless staminate flowers are
> >> allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
> >> gynoecium" certainly seems like a step in the right direction, as long as a
> >> search on gynoecium will find the rudimentary ones as well.
> >> toby
> >>
> >> >Lincoln Stein wrote:
> >> >
> >> >> The stigma issue is harder and I suspect it represents an incorrect
> >> >>structure
> >> >> in the tassel->floret->gynoecium->pistil path.
> >> >>
> >> >
> >> >The problem with maize is often the male and female florets occur in the
> >> >female
> >> >and male inflorescences respectively. Though this is not a normal
> >> >condition. I
> >> >agree with Sue, when we have the implementation of slots/properties linking
> >> >different anatomical terms at some point in future, we should be able to
> >> >build
> >> >the correct structures. Please let me know if the following structure
> >>works.
> >> >
> >> >inflorescence
> >> >----%tassel
> >> >-------<staminate floret; synonym: male floret
> >> >----------<androecium
> >> >-------------<stamen
> >> >----------------<anther
> >> >----------------<stamen filament
> >> >----%spike
> >> >------%spike  (sensu zea); synonym:cob
> >> >-------<pistillate floret; synonym: female floret
> >> >----------<gynoecium
> >> >-------------<pistil
> >> >---------------<style
> >> >---------------<stigma
> >> >---------------<ovary
> >> >----%panicle
> >> >--------<perfect floret
> >> >----------<gynoecium
> >> >------------<pistil
> >> >--------------<style
> >> >--------------<stigma
> >> >--------------<ovary
> >> >----------<androecium
> >> >------------<stamen
> >> >--------------<anther
> >> >--------------<stamen filament
> >> >----%capitulum (sensu compositae)
> >> >--------<ray floret
> >> >--------<disc floret
> >> >----<floret
> >> >------%floret
> >> >--------%ray floret
> >> >--------%disc floret
> >> >------%floret (sensu Poaceae)
> >> >--------%perfect floret
> >> >----------<gynoecium
> >> >------------<pistil
> >> >--------------<style
> >> >--------------<stigma
> >> >--------------<ovary
> >> >----------<androecium
> >> >------------<stamen
> >> >--------------<anther
> >> >--------------<stamen filament
> >> >--------%imperfect floret
> >> >----------%staminate floret; synonym: male floret
> >> >-------------<androecium
> >> >---------------<stamen
> >> >---------------<anther
> >> >----------%pistillate floret; synonym: female floret
> >> >-------------<gynoecium
> >> >----------------<pistil
> >> >------------------<style
> >> >------------------<stigma
> >> >------------------<ovary
> >> >
> >> >
> >> >
> >> >
> >> >> Lincoln
> >> >>
> >> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> >> >>
> >> >>>Hi all -
> >> >>>  Felipe has made great progress here downloading the various programs
> >> >>>necessary for viewing and manipulating the ontologies.  He's run into
> >>some
> >> >>>mechanical problems that he can sort out with Pankaj, the most critical
> >> >>>being trying to get two DagEdit windows open at the same time so two
> >> >>>ontologies can be viewed side by side.  In terms of the ontologies
> >> >>>themselves, we immediately found a number of terms that are not in common
> >> >>>use, or are in odd hierarchical relationships; these should be easy
> >>enough
> >> >>>to change.
> >> >>>  A more interesting and complex issue comes with species-specific terms.
> >> >>>An easy one is "silique" in Arabidopsis, which would be an instance of
> >> >>>"fruit" if one is working with multiple species.  A more difficult one is
> >> >>>"stigma", which is a part of "pistil", part of "gynoecium", part of
> >> >>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> >> >>>tassels, because the gynoecium stops developing.  Similarly, "abscission
> >> >>>zone" is part of "silique" in Arabidopsis, and would end up being part of
> >> >>>"fruit" if "silique" were interpreted as an instance of "fruit".
> >>However,
> >> >>>abscission zones do not form in the grass fruit so couldn't be a part of
> >> >>>fruit.  in both cases we end up violating the True Path Rule.  It may be
> >> >>>that this is inevitable, since the descriptors aren't strictly
> >> >>>hierarchical.   Obviously one can get around this somewhat by creating
> >> >>>species-specific bits of the hierarchy, and by making creative use of
> >> >>>"sensu"; this will probably work fine as long as the ontology only has to
> >> >>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> >> >>>apply to all flowering plants, though, there may be a limit to how
> >> >>>species-specific we make the ontologies.   For example we could divide
> >> >>>fruits into indehiscent and dehiscent and then have abscission zone
> >>as part
> >> >>>of dehiscent fruits, which would be OK until we get to a fruit that forms
> >> >>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
> >> >>>and I explored a little would be to add another category of connection,
> >> >>>such as "a process that can occur in"  - in addition to "is part of", "is
> >> >>>an instance of" and "develops from".  I suspect that another category
> >>might
> >> >>>create more problems than it solves, but it seemed worth considering.
> >> >>>  Any thoughts on this are welcome!
> >> >>>Toby
> >> >>>
> >> >>>Elizabeth A. Kellogg
> >> >>>Department of Biology
> >> >>>University of Missouri-St. Louis
> >> >>>8001 Natural Bridge Road
> >> >>>St. Louis, MO 63121
> >> >>>phone: 314-516-6217
> >> >>>fax: 314-516-6233
> >> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >> >>
> >> >>
> >> >
> >> >--
> >> >******************************************
> >> >Pankaj Jaiswal, Ph.D.
> >> >Research 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
> >> >******************************************
> >>
> >>
> >> Elizabeth A. Kellogg
> >> Department of Biology
> >> University of Missouri-St. Louis
> >> 8001 Natural Bridge Road
> >> St. Louis, MO 63121
> >> phone: 314-516-6217
> >> fax: 314-516-6233
> >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >>
> >>
> >>
> >
> >-------------------------------------------------------------------------------
> >Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> >The Arabidopsis Information Resource	FAX: (650) 325-6857
> >Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >Department of Plant Biology		URL: http://arabidopsis.org/
> >260 Panama St.
> >Stanford, CA 94305
> >-------------------------------------------------------------------------------
>
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Fri Oct  3 14:52:01 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Oct 2003 14:52:01 -0400
Subject: POC observations so far
In-Reply-To: <l0313030abba3613fe0a6@[134.124.70.41]>
References: <l03130304bba34cc71189@[134.124.70.41]> <l0313030abba3613fe0a6@[134.124.70.41]>
Message-ID: <3F7DC551.9080409@cornell.edu>

 >>gynoecium
 >>-%gynoecium primordium
 >>-%aborted
 >>-%mature
 >>--<ovary
 >>--<stigma
 >>--<style

Are you suggesting that ovary /style/stigma are PARTOF mature primordium?

I think the annotations of any gene product with an expression in this 
imperfect gynoecium should be annotated for
Anatomy Location: rudimentary gynoecium
dev. stage: aborted gynoecium development.

This stage can be child of Gynoecium development in dev. stage ontology. and a 
part of any species specific growth stage ontology.

Pankaj

Toby Kellogg wrote:

> That would also be a good possibility - it's sort of an expanded and
> slightly more precise version of Pankaj's "rudimentary" category.   A
> trivial question:  does the word "gynoecium" need to follow "aborted" and
> "mature", or is it understood?
> Toby
> 
> 
>>In a way- what seems to be a solution is stages of development of an organ
>>as being instances of an organ (e.g gynoecium primordia is an instance of
>>gynoecium), aborted/rudimentary as other instances- so you have a node for
>>gynoecium that includes all instances (stages)
>>
>>gynoecium
>>-%gynoecium primordium
>>-%aborted
>>-%mature
>>--<ovary
>>--<stigma
>>--<style
>>
>>not being comprehensive here but this is the general picture.
>>Leonore
>>
>>
>>On Fri, 3 Oct 2003, Toby Kellogg wrote:
>>
>>
>>>Just a simultaneous addition to Felipe's comment:
>>>Unisexual flowers are pretty common in Poaceae and in angiosperms in
>>>general.  Among model systems they occur in Populus, sugar beet, Silene,
>>>and the outer florets of some sunflower relatives, so if we can solve the
>>>problem for maize, we will have solved a number of similar problems.  The
>>>difficulty is that in maize, as in many angiosperms, all flowers start
>>>development as bisexual structures; in staminate florets, the pistil then
>>>aborts.  This means that the structure:
>>>
>>>>----%tassel
>>>>-------<staminate floret; synonym: male floret
>>>>----------<androecium
>>>>-------------<stamen
>>>>----------------<anther
>>>>----------------<stamen filament
>>>
>>>also should include gynoecium, pistil (and nucellus, ultimately), and
>>>ovary, but not style and stigma.   As long as style and stigma are
>>>daughters of pistil, there's a problem.  The gene tasselseed2 is expressed
>>>in the young ovary of the staminate florets in the tassel, and we can't
>>>describe its expression pattern accurately unless staminate flowers are
>>>allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
>>>gynoecium" certainly seems like a step in the right direction, as long as a
>>>search on gynoecium will find the rudimentary ones as well.
>>>toby
>>>
>>>
>>>>Lincoln Stein wrote:
>>>>
>>>>
>>>>>The stigma issue is harder and I suspect it represents an incorrect
>>>>>structure
>>>>>in the tassel->floret->gynoecium->pistil path.
>>>>>
>>>>
>>>>The problem with maize is often the male and female florets occur in the
>>>>female
>>>>and male inflorescences respectively. Though this is not a normal
>>>>condition. I
>>>>agree with Sue, when we have the implementation of slots/properties linking
>>>>different anatomical terms at some point in future, we should be able to
>>>>build
>>>>the correct structures. Please let me know if the following structure
>>>
>>>works.
>>>
>>>>inflorescence
>>>>----%tassel
>>>>-------<staminate floret; synonym: male floret
>>>>----------<androecium
>>>>-------------<stamen
>>>>----------------<anther
>>>>----------------<stamen filament
>>>>----%spike
>>>>------%spike  (sensu zea); synonym:cob
>>>>-------<pistillate floret; synonym: female floret
>>>>----------<gynoecium
>>>>-------------<pistil
>>>>---------------<style
>>>>---------------<stigma
>>>>---------------<ovary
>>>>----%panicle
>>>>--------<perfect floret
>>>>----------<gynoecium
>>>>------------<pistil
>>>>--------------<style
>>>>--------------<stigma
>>>>--------------<ovary
>>>>----------<androecium
>>>>------------<stamen
>>>>--------------<anther
>>>>--------------<stamen filament
>>>>----%capitulum (sensu compositae)
>>>>--------<ray floret
>>>>--------<disc floret
>>>>----<floret
>>>>------%floret
>>>>--------%ray floret
>>>>--------%disc floret
>>>>------%floret (sensu Poaceae)
>>>>--------%perfect floret
>>>>----------<gynoecium
>>>>------------<pistil
>>>>--------------<style
>>>>--------------<stigma
>>>>--------------<ovary
>>>>----------<androecium
>>>>------------<stamen
>>>>--------------<anther
>>>>--------------<stamen filament
>>>>--------%imperfect floret
>>>>----------%staminate floret; synonym: male floret
>>>>-------------<androecium
>>>>---------------<stamen
>>>>---------------<anther
>>>>----------%pistillate floret; synonym: female floret
>>>>-------------<gynoecium
>>>>----------------<pistil
>>>>------------------<style
>>>>------------------<stigma
>>>>------------------<ovary
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Lincoln
>>>>>
>>>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>>>>>
>>>>>
>>>>>>Hi all -
>>>>>> Felipe has made great progress here downloading the various programs
>>>>>>necessary for viewing and manipulating the ontologies.  He's run into
>>>
>>>some
>>>
>>>>>>mechanical problems that he can sort out with Pankaj, the most critical
>>>>>>being trying to get two DagEdit windows open at the same time so two
>>>>>>ontologies can be viewed side by side.  In terms of the ontologies
>>>>>>themselves, we immediately found a number of terms that are not in common
>>>>>>use, or are in odd hierarchical relationships; these should be easy
>>>
>>>enough
>>>
>>>>>>to change.
>>>>>> A more interesting and complex issue comes with species-specific terms.
>>>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>>>>>>"fruit" if one is working with multiple species.  A more difficult one is
>>>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>>>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>>>>>>tassels, because the gynoecium stops developing.  Similarly, "abscission
>>>>>>zone" is part of "silique" in Arabidopsis, and would end up being part of
>>>>>>"fruit" if "silique" were interpreted as an instance of "fruit".
>>>
>>>However,
>>>
>>>>>>abscission zones do not form in the grass fruit so couldn't be a part of
>>>>>>fruit.  in both cases we end up violating the True Path Rule.  It may be
>>>>>>that this is inevitable, since the descriptors aren't strictly
>>>>>>hierarchical.   Obviously one can get around this somewhat by creating
>>>>>>species-specific bits of the hierarchy, and by making creative use of
>>>>>>"sensu"; this will probably work fine as long as the ontology only has to
>>>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
>>>>>>apply to all flowering plants, though, there may be a limit to how
>>>>>>species-specific we make the ontologies.   For example we could divide
>>>>>>fruits into indehiscent and dehiscent and then have abscission zone
>>>
>>>as part
>>>
>>>>>>of dehiscent fruits, which would be OK until we get to a fruit that forms
>>>>>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
>>>>>>and I explored a little would be to add another category of connection,
>>>>>>such as "a process that can occur in"  - in addition to "is part of", "is
>>>>>>an instance of" and "develops from".  I suspect that another category
>>>
>>>might
>>>
>>>>>>create more problems than it solves, but it seemed worth considering.
>>>>>> Any thoughts on this are welcome!
>>>>>>Toby
>>>>>>
>>>>>>Elizabeth A. Kellogg
>>>>>>Department of Biology
>>>>>>University of Missouri-St. Louis
>>>>>>8001 Natural Bridge Road
>>>>>>St. Louis, MO 63121
>>>>>>phone: 314-516-6217
>>>>>>fax: 314-516-6233
>>>>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>>>>
>>>>>
>>>>--
>>>>******************************************
>>>>Pankaj Jaiswal, Ph.D.
>>>>Research 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
>>>>******************************************
>>>
>>>
>>>Elizabeth A. Kellogg
>>>Department of Biology
>>>University of Missouri-St. Louis
>>>8001 Natural Bridge Road
>>>St. Louis, MO 63121
>>>phone: 314-516-6217
>>>fax: 314-516-6233
>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>>>
>>>
>>>
>>
>>-------------------------------------------------------------------------------
>>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>>The Arabidopsis Information Resource	FAX: (650) 325-6857
>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>>Department of Plant Biology		URL: http://arabidopsis.org/
>>260 Panama St.
>>Stanford, CA 94305
>>-------------------------------------------------------------------------------
> 
> 
> 
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> 
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 lreiser at acoma.Stanford.EDU  Fri Oct  3 14:58:26 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Oct 2003 11:58:26 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <3F7DC551.9080409@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310031155180.6934-100000@acoma.Stanford.EDU>

No- it was bad shorthand (and I think what Toby was referring to with
respect to aborted gynoecium vs. aborted).
There were 3 instances of gynoecium: gynoecium primordium,
aborted(rudimentary) gynoecium and mature gynoecium. These were all
sibling terms right?
Leonore

On Fri, 3 Oct 2003, Pankaj Jaiswal wrote:

>  >>gynoecium
>  >>-%gynoecium primordium
>  >>-%aborted
>  >>-%mature
>  >>--<ovary
>  >>--<stigma
>  >>--<style
>
> Are you suggesting that ovary /style/stigma are PARTOF mature primordium?
>
> I think the annotations of any gene product with an expression in this
> imperfect gynoecium should be annotated for
> Anatomy Location: rudimentary gynoecium
> dev. stage: aborted gynoecium development.
>
> This stage can be child of Gynoecium development in dev. stage ontology. and a
> part of any species specific growth stage ontology.
>
> Pankaj
>
> Toby Kellogg wrote:
>
> > That would also be a good possibility - it's sort of an expanded and
> > slightly more precise version of Pankaj's "rudimentary" category.   A
> > trivial question:  does the word "gynoecium" need to follow "aborted" and
> > "mature", or is it understood?
> > Toby
> >
> >
> >>In a way- what seems to be a solution is stages of development of an organ
> >>as being instances of an organ (e.g gynoecium primordia is an instance of
> >>gynoecium), aborted/rudimentary as other instances- so you have a node for
> >>gynoecium that includes all instances (stages)
> >>
> >>gynoecium
> >>-%gynoecium primordium
> >>-%aborted
> >>-%mature
> >>--<ovary
> >>--<stigma
> >>--<style
> >>
> >>not being comprehensive here but this is the general picture.
> >>Leonore
> >>
> >>
> >>On Fri, 3 Oct 2003, Toby Kellogg wrote:
> >>
> >>
> >>>Just a simultaneous addition to Felipe's comment:
> >>>Unisexual flowers are pretty common in Poaceae and in angiosperms in
> >>>general.  Among model systems they occur in Populus, sugar beet, Silene,
> >>>and the outer florets of some sunflower relatives, so if we can solve the
> >>>problem for maize, we will have solved a number of similar problems.  The
> >>>difficulty is that in maize, as in many angiosperms, all flowers start
> >>>development as bisexual structures; in staminate florets, the pistil then
> >>>aborts.  This means that the structure:
> >>>
> >>>>----%tassel
> >>>>-------<staminate floret; synonym: male floret
> >>>>----------<androecium
> >>>>-------------<stamen
> >>>>----------------<anther
> >>>>----------------<stamen filament
> >>>
> >>>also should include gynoecium, pistil (and nucellus, ultimately), and
> >>>ovary, but not style and stigma.   As long as style and stigma are
> >>>daughters of pistil, there's a problem.  The gene tasselseed2 is expressed
> >>>in the young ovary of the staminate florets in the tassel, and we can't
> >>>describe its expression pattern accurately unless staminate flowers are
> >>>allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
> >>>gynoecium" certainly seems like a step in the right direction, as long as a
> >>>search on gynoecium will find the rudimentary ones as well.
> >>>toby
> >>>
> >>>
> >>>>Lincoln Stein wrote:
> >>>>
> >>>>
> >>>>>The stigma issue is harder and I suspect it represents an incorrect
> >>>>>structure
> >>>>>in the tassel->floret->gynoecium->pistil path.
> >>>>>
> >>>>
> >>>>The problem with maize is often the male and female florets occur in the
> >>>>female
> >>>>and male inflorescences respectively. Though this is not a normal
> >>>>condition. I
> >>>>agree with Sue, when we have the implementation of slots/properties linking
> >>>>different anatomical terms at some point in future, we should be able to
> >>>>build
> >>>>the correct structures. Please let me know if the following structure
> >>>
> >>>works.
> >>>
> >>>>inflorescence
> >>>>----%tassel
> >>>>-------<staminate floret; synonym: male floret
> >>>>----------<androecium
> >>>>-------------<stamen
> >>>>----------------<anther
> >>>>----------------<stamen filament
> >>>>----%spike
> >>>>------%spike  (sensu zea); synonym:cob
> >>>>-------<pistillate floret; synonym: female floret
> >>>>----------<gynoecium
> >>>>-------------<pistil
> >>>>---------------<style
> >>>>---------------<stigma
> >>>>---------------<ovary
> >>>>----%panicle
> >>>>--------<perfect floret
> >>>>----------<gynoecium
> >>>>------------<pistil
> >>>>--------------<style
> >>>>--------------<stigma
> >>>>--------------<ovary
> >>>>----------<androecium
> >>>>------------<stamen
> >>>>--------------<anther
> >>>>--------------<stamen filament
> >>>>----%capitulum (sensu compositae)
> >>>>--------<ray floret
> >>>>--------<disc floret
> >>>>----<floret
> >>>>------%floret
> >>>>--------%ray floret
> >>>>--------%disc floret
> >>>>------%floret (sensu Poaceae)
> >>>>--------%perfect floret
> >>>>----------<gynoecium
> >>>>------------<pistil
> >>>>--------------<style
> >>>>--------------<stigma
> >>>>--------------<ovary
> >>>>----------<androecium
> >>>>------------<stamen
> >>>>--------------<anther
> >>>>--------------<stamen filament
> >>>>--------%imperfect floret
> >>>>----------%staminate floret; synonym: male floret
> >>>>-------------<androecium
> >>>>---------------<stamen
> >>>>---------------<anther
> >>>>----------%pistillate floret; synonym: female floret
> >>>>-------------<gynoecium
> >>>>----------------<pistil
> >>>>------------------<style
> >>>>------------------<stigma
> >>>>------------------<ovary
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>Lincoln
> >>>>>
> >>>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> >>>>>
> >>>>>
> >>>>>>Hi all -
> >>>>>> Felipe has made great progress here downloading the various programs
> >>>>>>necessary for viewing and manipulating the ontologies.  He's run into
> >>>
> >>>some
> >>>
> >>>>>>mechanical problems that he can sort out with Pankaj, the most critical
> >>>>>>being trying to get two DagEdit windows open at the same time so two
> >>>>>>ontologies can be viewed side by side.  In terms of the ontologies
> >>>>>>themselves, we immediately found a number of terms that are not in common
> >>>>>>use, or are in odd hierarchical relationships; these should be easy
> >>>
> >>>enough
> >>>
> >>>>>>to change.
> >>>>>> A more interesting and complex issue comes with species-specific terms.
> >>>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
> >>>>>>"fruit" if one is working with multiple species.  A more difficult one is
> >>>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
> >>>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
> >>>>>>tassels, because the gynoecium stops developing.  Similarly, "abscission
> >>>>>>zone" is part of "silique" in Arabidopsis, and would end up being part of
> >>>>>>"fruit" if "silique" were interpreted as an instance of "fruit".
> >>>
> >>>However,
> >>>
> >>>>>>abscission zones do not form in the grass fruit so couldn't be a part of
> >>>>>>fruit.  in both cases we end up violating the True Path Rule.  It may be
> >>>>>>that this is inevitable, since the descriptors aren't strictly
> >>>>>>hierarchical.   Obviously one can get around this somewhat by creating
> >>>>>>species-specific bits of the hierarchy, and by making creative use of
> >>>>>>"sensu"; this will probably work fine as long as the ontology only has to
> >>>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to make it
> >>>>>>apply to all flowering plants, though, there may be a limit to how
> >>>>>>species-specific we make the ontologies.   For example we could divide
> >>>>>>fruits into indehiscent and dehiscent and then have abscission zone
> >>>
> >>>as part
> >>>
> >>>>>>of dehiscent fruits, which would be OK until we get to a fruit that forms
> >>>>>>an abscission zone but doesn't dehisce.  Another possibility that Felipe
> >>>>>>and I explored a little would be to add another category of connection,
> >>>>>>such as "a process that can occur in"  - in addition to "is part of", "is
> >>>>>>an instance of" and "develops from".  I suspect that another category
> >>>
> >>>might
> >>>
> >>>>>>create more problems than it solves, but it seemed worth considering.
> >>>>>> Any thoughts on this are welcome!
> >>>>>>Toby
> >>>>>>
> >>>>>>Elizabeth A. Kellogg
> >>>>>>Department of Biology
> >>>>>>University of Missouri-St. Louis
> >>>>>>8001 Natural Bridge Road
> >>>>>>St. Louis, MO 63121
> >>>>>>phone: 314-516-6217
> >>>>>>fax: 314-516-6233
> >>>>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >>>>>
> >>>>>
> >>>>--
> >>>>******************************************
> >>>>Pankaj Jaiswal, Ph.D.
> >>>>Research 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
> >>>>******************************************
> >>>
> >>>
> >>>Elizabeth A. Kellogg
> >>>Department of Biology
> >>>University of Missouri-St. Louis
> >>>8001 Natural Bridge Road
> >>>St. Louis, MO 63121
> >>>phone: 314-516-6217
> >>>fax: 314-516-6233
> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >>>
> >>>
> >>>
> >>
> >>-------------------------------------------------------------------------------
> >>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> >>The Arabidopsis Information Resource	FAX: (650) 325-6857
> >>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >>Department of Plant Biology		URL: http://arabidopsis.org/
> >>260 Panama St.
> >>Stanford, CA 94305
> >>-------------------------------------------------------------------------------
> >
> >
> >
> > Elizabeth A. Kellogg
> > Department of Biology
> > University of Missouri-St. Louis
> > 8001 Natural Bridge Road
> > St. Louis, MO 63121
> > phone: 314-516-6217
> > fax: 314-516-6233
> > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >
> >
> >
>
> --
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Research 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
> ******************************************
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From kellogge at msx.umsl.edu  Fri Oct  3 19:05:45 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Fri, 3 Oct 2003 18:05:45 -0500
Subject: POC observations so far
In-Reply-To: <Pine.GSO.4.44.0310031155180.6934-100000@acoma.Stanford.EDU>
References: <3F7DC551.9080409@cornell.edu>
Message-ID: <l03130306bba3b06077fd@[134.124.70.41]>

I think we're all converging on a similar solution, and perhaps we could do
with two sibling terms:
gynoecium primordium
gynoecium mature
Then ovary/style/stigma would be part of gynoecium mature.
For the expression domain of tasselseed2, it would be Anatomy location:
gynoecium primordium, dev. stage: aborted gynoecium development.
to be continued...
Toby

>No- it was bad shorthand (and I think what Toby was referring to with
>respect to aborted gynoecium vs. aborted).
>There were 3 instances of gynoecium: gynoecium primordium,
>aborted(rudimentary) gynoecium and mature gynoecium. These were all
>sibling terms right?
>Leonore
>
>On Fri, 3 Oct 2003, Pankaj Jaiswal wrote:
>
>>  >>gynoecium
>>  >>-%gynoecium primordium
>>  >>-%aborted
>>  >>-%mature
>>  >>--<ovary
>>  >>--<stigma
>>  >>--<style
>>
>> Are you suggesting that ovary /style/stigma are PARTOF mature primordium?
>>
>> I think the annotations of any gene product with an expression in this
>> imperfect gynoecium should be annotated for
>> Anatomy Location: rudimentary gynoecium
>> dev. stage: aborted gynoecium development.
>>
>> This stage can be child of Gynoecium development in dev. stage ontology.
>>and a
>> part of any species specific growth stage ontology.
>>
>> Pankaj
>>
>> Toby Kellogg wrote:
>>
>> > That would also be a good possibility - it's sort of an expanded and
>> > slightly more precise version of Pankaj's "rudimentary" category.   A
>> > trivial question:  does the word "gynoecium" need to follow "aborted" and
>> > "mature", or is it understood?
>> > Toby
>> >
>> >
>> >>In a way- what seems to be a solution is stages of development of an organ
>> >>as being instances of an organ (e.g gynoecium primordia is an instance of
>> >>gynoecium), aborted/rudimentary as other instances- so you have a node for
>> >>gynoecium that includes all instances (stages)
>> >>
>> >>gynoecium
>> >>-%gynoecium primordium
>> >>-%aborted
>> >>-%mature
>> >>--<ovary
>> >>--<stigma
>> >>--<style
>> >>
>> >>not being comprehensive here but this is the general picture.
>> >>Leonore
>> >>
>> >>
>> >>On Fri, 3 Oct 2003, Toby Kellogg wrote:
>> >>
>> >>
>> >>>Just a simultaneous addition to Felipe's comment:
>> >>>Unisexual flowers are pretty common in Poaceae and in angiosperms in
>> >>>general.  Among model systems they occur in Populus, sugar beet, Silene,
>> >>>and the outer florets of some sunflower relatives, so if we can solve the
>> >>>problem for maize, we will have solved a number of similar problems.  The
>> >>>difficulty is that in maize, as in many angiosperms, all flowers start
>> >>>development as bisexual structures; in staminate florets, the pistil then
>> >>>aborts.  This means that the structure:
>> >>>
>> >>>>----%tassel
>> >>>>-------<staminate floret; synonym: male floret
>> >>>>----------<androecium
>> >>>>-------------<stamen
>> >>>>----------------<anther
>> >>>>----------------<stamen filament
>> >>>
>> >>>also should include gynoecium, pistil (and nucellus, ultimately), and
>> >>>ovary, but not style and stigma.   As long as style and stigma are
>> >>>daughters of pistil, there's a problem.  The gene tasselseed2 is
>>expressed
>> >>>in the young ovary of the staminate florets in the tassel, and we can't
>> >>>describe its expression pattern accurately unless staminate flowers are
>> >>>allowed to have pistils somehow.  Pankaj's idea of including "rudimentary
>> >>>gynoecium" certainly seems like a step in the right direction, as
>>long as a
>> >>>search on gynoecium will find the rudimentary ones as well.
>> >>>toby
>> >>>
>> >>>
>> >>>>Lincoln Stein wrote:
>> >>>>
>> >>>>
>> >>>>>The stigma issue is harder and I suspect it represents an incorrect
>> >>>>>structure
>> >>>>>in the tassel->floret->gynoecium->pistil path.
>> >>>>>
>> >>>>
>> >>>>The problem with maize is often the male and female florets occur in the
>> >>>>female
>> >>>>and male inflorescences respectively. Though this is not a normal
>> >>>>condition. I
>> >>>>agree with Sue, when we have the implementation of slots/properties
>>linking
>> >>>>different anatomical terms at some point in future, we should be able to
>> >>>>build
>> >>>>the correct structures. Please let me know if the following structure
>> >>>
>> >>>works.
>> >>>
>> >>>>inflorescence
>> >>>>----%tassel
>> >>>>-------<staminate floret; synonym: male floret
>> >>>>----------<androecium
>> >>>>-------------<stamen
>> >>>>----------------<anther
>> >>>>----------------<stamen filament
>> >>>>----%spike
>> >>>>------%spike  (sensu zea); synonym:cob
>> >>>>-------<pistillate floret; synonym: female floret
>> >>>>----------<gynoecium
>> >>>>-------------<pistil
>> >>>>---------------<style
>> >>>>---------------<stigma
>> >>>>---------------<ovary
>> >>>>----%panicle
>> >>>>--------<perfect floret
>> >>>>----------<gynoecium
>> >>>>------------<pistil
>> >>>>--------------<style
>> >>>>--------------<stigma
>> >>>>--------------<ovary
>> >>>>----------<androecium
>> >>>>------------<stamen
>> >>>>--------------<anther
>> >>>>--------------<stamen filament
>> >>>>----%capitulum (sensu compositae)
>> >>>>--------<ray floret
>> >>>>--------<disc floret
>> >>>>----<floret
>> >>>>------%floret
>> >>>>--------%ray floret
>> >>>>--------%disc floret
>> >>>>------%floret (sensu Poaceae)
>> >>>>--------%perfect floret
>> >>>>----------<gynoecium
>> >>>>------------<pistil
>> >>>>--------------<style
>> >>>>--------------<stigma
>> >>>>--------------<ovary
>> >>>>----------<androecium
>> >>>>------------<stamen
>> >>>>--------------<anther
>> >>>>--------------<stamen filament
>> >>>>--------%imperfect floret
>> >>>>----------%staminate floret; synonym: male floret
>> >>>>-------------<androecium
>> >>>>---------------<stamen
>> >>>>---------------<anther
>> >>>>----------%pistillate floret; synonym: female floret
>> >>>>-------------<gynoecium
>> >>>>----------------<pistil
>> >>>>------------------<style
>> >>>>------------------<stigma
>> >>>>------------------<ovary
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>
>> >>>>>Lincoln
>> >>>>>
>> >>>>>On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
>> >>>>>
>> >>>>>
>> >>>>>>Hi all -
>> >>>>>> Felipe has made great progress here downloading the various programs
>> >>>>>>necessary for viewing and manipulating the ontologies.  He's run into
>> >>>
>> >>>some
>> >>>
>> >>>>>>mechanical problems that he can sort out with Pankaj, the most
>>critical
>> >>>>>>being trying to get two DagEdit windows open at the same time so two
>> >>>>>>ontologies can be viewed side by side.  In terms of the ontologies
>> >>>>>>themselves, we immediately found a number of terms that are not in
>>common
>> >>>>>>use, or are in odd hierarchical relationships; these should be easy
>> >>>
>> >>>enough
>> >>>
>> >>>>>>to change.
>> >>>>>> A more interesting and complex issue comes with species-specific
>>terms.
>> >>>>>>An easy one is "silique" in Arabidopsis, which would be an instance of
>> >>>>>>"fruit" if one is working with multiple species.  A more difficult
>>one is
>> >>>>>>"stigma", which is a part of "pistil", part of "gynoecium", part of
>> >>>>>>"floret", etc. up to tassel.  Unfortunately, stigmas do not form in
>> >>>>>>tassels, because the gynoecium stops developing.  Similarly,
>>"abscission
>> >>>>>>zone" is part of "silique" in Arabidopsis, and would end up being
>>part of
>> >>>>>>"fruit" if "silique" were interpreted as an instance of "fruit".
>> >>>
>> >>>However,
>> >>>
>> >>>>>>abscission zones do not form in the grass fruit so couldn't be a
>>part of
>> >>>>>>fruit.  in both cases we end up violating the True Path Rule.  It
>>may be
>> >>>>>>that this is inevitable, since the descriptors aren't strictly
>> >>>>>>hierarchical.   Obviously one can get around this somewhat by creating
>> >>>>>>species-specific bits of the hierarchy, and by making creative use of
>> >>>>>>"sensu"; this will probably work fine as long as the ontology only
>>has to
>> >>>>>>apply to Brassicaceae and Gramineae.  If the long-term goal is to
>>make it
>> >>>>>>apply to all flowering plants, though, there may be a limit to how
>> >>>>>>species-specific we make the ontologies.   For example we could divide
>> >>>>>>fruits into indehiscent and dehiscent and then have abscission zone
>> >>>
>> >>>as part
>> >>>
>> >>>>>>of dehiscent fruits, which would be OK until we get to a fruit
>>that forms
>> >>>>>>an abscission zone but doesn't dehisce.  Another possibility that
>>Felipe
>> >>>>>>and I explored a little would be to add another category of
>>connection,
>> >>>>>>such as "a process that can occur in"  - in addition to "is part
>>of", "is
>> >>>>>>an instance of" and "develops from".  I suspect that another category
>> >>>
>> >>>might
>> >>>
>> >>>>>>create more problems than it solves, but it seemed worth considering.
>> >>>>>> Any thoughts on this are welcome!
>> >>>>>>Toby
>> >>>>>>
>> >>>>>>Elizabeth A. Kellogg
>> >>>>>>Department of Biology
>> >>>>>>University of Missouri-St. Louis
>> >>>>>>8001 Natural Bridge Road
>> >>>>>>St. Louis, MO 63121
>> >>>>>>phone: 314-516-6217
>> >>>>>>fax: 314-516-6233
>> >>>>>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>> >>>>>
>> >>>>>
>> >>>>--
>> >>>>******************************************
>> >>>>Pankaj Jaiswal, Ph.D.
>> >>>>Research 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
>> >>>>******************************************
>> >>>
>> >>>
>> >>>Elizabeth A. Kellogg
>> >>>Department of Biology
>> >>>University of Missouri-St. Louis
>> >>>8001 Natural Bridge Road
>> >>>St. Louis, MO 63121
>> >>>phone: 314-516-6217
>> >>>fax: 314-516-6233
>> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>> >>>
>> >>>
>> >>>
>> >>
>>
>>>>------------------------------------------------------------------------------
>>-
>> >>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>> >>The Arabidopsis Information Resource	FAX: (650) 325-6857
>> >>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>> >>Department of Plant Biology		URL: http://arabidopsis.org/
>> >>260 Panama St.
>> >>Stanford, CA 94305
>>
>>>>------------------------------------------------------------------------------
>>-
>> >
>> >
>> >
>> > Elizabeth A. Kellogg
>> > Department of Biology
>> > University of Missouri-St. Louis
>> > 8001 Natural Bridge Road
>> > St. Louis, MO 63121
>> > phone: 314-516-6217
>> > fax: 314-516-6233
>> > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>> >
>> >
>> >
>>
>> --
>> ******************************************
>> Pankaj Jaiswal, Ph.D.
>> Research 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
>> ******************************************
>>
>>
>>
>
>-------------------------------------------------------------------------------
>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>The Arabidopsis Information Resource	FAX: (650) 325-6857
>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>Department of Plant Biology		URL: http://arabidopsis.org/
>260 Panama St.
>Stanford, CA 94305
>-------------------------------------------------------------------------------


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From lstein at cshl.edu  Sat Oct  4 13:46:30 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat, 04 Oct 2003 13:46:30 -0400
Subject: POC observations so far
In-Reply-To: <l0313030abba3613fe0a6@[134.124.70.41]>
References: <l03130304bba34cc71189@[134.124.70.41]>
 <l0313030abba3613fe0a6@[134.124.70.41]>
Message-ID: <200310041346.30798.lstein@cshl.edu>

We should also consider whether it will help to add more relationship types, 
such as "derived from".  It does not seem to me to be appropriate to describe 
a temporal development relationship between two organs as either "isa" or 
"partof"

Lincoln

On Friday 03 October 2003 01:26 pm, Toby Kellogg wrote:
> That would also be a good possibility - it's sort of an expanded and
> slightly more precise version of Pankaj's "rudimentary" category.   A
> trivial question:  does the word "gynoecium" need to follow "aborted" and
> "mature", or is it understood?
> Toby
>
> >In a way- what seems to be a solution is stages of development of an organ
> >as being instances of an organ (e.g gynoecium primordia is an instance of
> >gynoecium), aborted/rudimentary as other instances- so you have a node for
> >gynoecium that includes all instances (stages)
> >
> >gynoecium
> >-%gynoecium primordium
> >-%aborted
> >-%mature
> >--<ovary
> >--<stigma
> >--<style
> >
> >not being comprehensive here but this is the general picture.
> >Leonore
> >
> >On Fri, 3 Oct 2003, Toby Kellogg wrote:
> >> Just a simultaneous addition to Felipe's comment:
> >> Unisexual flowers are pretty common in Poaceae and in angiosperms in
> >> general.  Among model systems they occur in Populus, sugar beet, Silene,
> >> and the outer florets of some sunflower relatives, so if we can solve
> >> the problem for maize, we will have solved a number of similar problems.
> >>  The difficulty is that in maize, as in many angiosperms, all flowers
> >> start development as bisexual structures; in staminate florets, the
> >> pistil then
> >>
> >> aborts.  This means that the structure:
> >> >----%tassel
> >> >-------<staminate floret; synonym: male floret
> >> >----------<androecium
> >> >-------------<stamen
> >> >----------------<anther
> >> >----------------<stamen filament
> >>
> >> also should include gynoecium, pistil (and nucellus, ultimately), and
> >> ovary, but not style and stigma.   As long as style and stigma are
> >> daughters of pistil, there's a problem.  The gene tasselseed2 is
> >> expressed in the young ovary of the staminate florets in the tassel, and
> >> we can't describe its expression pattern accurately unless staminate
> >> flowers are allowed to have pistils somehow.  Pankaj's idea of including
> >> "rudimentary gynoecium" certainly seems like a step in the right
> >> direction, as long as a search on gynoecium will find the rudimentary
> >> ones as well.
> >> toby
> >>
> >> >Lincoln Stein wrote:
> >> >> The stigma issue is harder and I suspect it represents an incorrect
> >> >>structure
> >> >> in the tassel->floret->gynoecium->pistil path.
> >> >
> >> >The problem with maize is often the male and female florets occur in
> >> > the female
> >> >and male inflorescences respectively. Though this is not a normal
> >> >condition. I
> >> >agree with Sue, when we have the implementation of slots/properties
> >> > linking different anatomical terms at some point in future, we should
> >> > be able to build
> >> >the correct structures. Please let me know if the following structure
> >>
> >>works.
> >>
> >> >inflorescence
> >> >----%tassel
> >> >-------<staminate floret; synonym: male floret
> >> >----------<androecium
> >> >-------------<stamen
> >> >----------------<anther
> >> >----------------<stamen filament
> >> >----%spike
> >> >------%spike  (sensu zea); synonym:cob
> >> >-------<pistillate floret; synonym: female floret
> >> >----------<gynoecium
> >> >-------------<pistil
> >> >---------------<style
> >> >---------------<stigma
> >> >---------------<ovary
> >> >----%panicle
> >> >--------<perfect floret
> >> >----------<gynoecium
> >> >------------<pistil
> >> >--------------<style
> >> >--------------<stigma
> >> >--------------<ovary
> >> >----------<androecium
> >> >------------<stamen
> >> >--------------<anther
> >> >--------------<stamen filament
> >> >----%capitulum (sensu compositae)
> >> >--------<ray floret
> >> >--------<disc floret
> >> >----<floret
> >> >------%floret
> >> >--------%ray floret
> >> >--------%disc floret
> >> >------%floret (sensu Poaceae)
> >> >--------%perfect floret
> >> >----------<gynoecium
> >> >------------<pistil
> >> >--------------<style
> >> >--------------<stigma
> >> >--------------<ovary
> >> >----------<androecium
> >> >------------<stamen
> >> >--------------<anther
> >> >--------------<stamen filament
> >> >--------%imperfect floret
> >> >----------%staminate floret; synonym: male floret
> >> >-------------<androecium
> >> >---------------<stamen
> >> >---------------<anther
> >> >----------%pistillate floret; synonym: female floret
> >> >-------------<gynoecium
> >> >----------------<pistil
> >> >------------------<style
> >> >------------------<stigma
> >> >------------------<ovary
> >> >
> >> >> Lincoln
> >> >>
> >> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> >> >>>Hi all -
> >> >>>  Felipe has made great progress here downloading the various
> >> >>> programs necessary for viewing and manipulating the ontologies. 
> >> >>> He's run into
> >>
> >>some
> >>
> >> >>>mechanical problems that he can sort out with Pankaj, the most
> >> >>> critical being trying to get two DagEdit windows open at the same
> >> >>> time so two ontologies can be viewed side by side.  In terms of the
> >> >>> ontologies themselves, we immediately found a number of terms that
> >> >>> are not in common use, or are in odd hierarchical relationships;
> >> >>> these should be easy
> >>
> >>enough
> >>
> >> >>>to change.
> >> >>>  A more interesting and complex issue comes with species-specific
> >> >>> terms. An easy one is "silique" in Arabidopsis, which would be an
> >> >>> instance of "fruit" if one is working with multiple species.  A more
> >> >>> difficult one is "stigma", which is a part of "pistil", part of
> >> >>> "gynoecium", part of "floret", etc. up to tassel.  Unfortunately,
> >> >>> stigmas do not form in tassels, because the gynoecium stops
> >> >>> developing.  Similarly, "abscission zone" is part of "silique" in
> >> >>> Arabidopsis, and would end up being part of "fruit" if "silique"
> >> >>> were interpreted as an instance of "fruit".
> >>
> >>However,
> >>
> >> >>>abscission zones do not form in the grass fruit so couldn't be a part
> >> >>> of fruit.  in both cases we end up violating the True Path Rule.  It
> >> >>> may be that this is inevitable, since the descriptors aren't
> >> >>> strictly hierarchical.   Obviously one can get around this somewhat
> >> >>> by creating species-specific bits of the hierarchy, and by making
> >> >>> creative use of "sensu"; this will probably work fine as long as the
> >> >>> ontology only has to apply to Brassicaceae and Gramineae.  If the
> >> >>> long-term goal is to make it apply to all flowering plants, though,
> >> >>> there may be a limit to how species-specific we make the ontologies.
> >> >>>   For example we could divide fruits into indehiscent and dehiscent
> >> >>> and then have abscission zone
> >>
> >>as part
> >>
> >> >>>of dehiscent fruits, which would be OK until we get to a fruit that
> >> >>> forms an abscission zone but doesn't dehisce.  Another possibility
> >> >>> that Felipe and I explored a little would be to add another category
> >> >>> of connection, such as "a process that can occur in"  - in addition
> >> >>> to "is part of", "is an instance of" and "develops from".  I suspect
> >> >>> that another category
> >>
> >>might
> >>
> >> >>>create more problems than it solves, but it seemed worth considering.
> >> >>>  Any thoughts on this are welcome!
> >> >>>Toby
> >> >>>
> >> >>>Elizabeth A. Kellogg
> >> >>>Department of Biology
> >> >>>University of Missouri-St. Louis
> >> >>>8001 Natural Bridge Road
> >> >>>St. Louis, MO 63121
> >> >>>phone: 314-516-6217
> >> >>>fax: 314-516-6233
> >> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >> >
> >> >--
> >> >******************************************
> >> >Pankaj Jaiswal, Ph.D.
> >> >Research 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
> >> >******************************************
> >>
> >> Elizabeth A. Kellogg
> >> Department of Biology
> >> University of Missouri-St. Louis
> >> 8001 Natural Bridge Road
> >> St. Louis, MO 63121
> >> phone: 314-516-6217
> >> fax: 314-516-6233
> >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >
> >--------------------------------------------------------------------------
> >----- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource	FAX: (650) 325-6857
> >Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >Department of Plant Biology		URL: http://arabidopsis.org/
> >260 Panama St.
> >Stanford, CA 94305
> >--------------------------------------------------------------------------
> >-----
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)


From fzqhd at studentmail.umsl.edu  Sat Oct  4 15:58:33 2003
From: fzqhd at studentmail.umsl.edu (Felipe Zapata)
Date: Sat,  4 Oct 2003 14:58:33 -0500
Subject: POC observations so far
In-Reply-To: <200310041346.30798.lstein@cshl.edu>
References: <l03130304bba34cc71189@[134.124.70.41]> <l0313030abba3613fe0a6@[134.124.70.41]> <200310041346.30798.lstein@cshl.edu>
Message-ID: <1065297513.3f7f266970547@studentmail.umsl.edu>

Actually that relationship already exists. At least TAIR uses:

!version: $Revision: 1.13 $
!type: % ISA Is a
!type: < PARTOF Part of
!type: ~ DEVELOPSFROM develops from
!editors: Leonore Reiser, Jonathan Clarke
$Arabidopsis ontology ; TAIR:0000001
.....
..
..

What we probably need to do, is to go through the current ontologies and look for 
nodes where this relationship would have more biological meaning.

Felipe


Quoting Lincoln Stein <lstein at cshl.edu>:

> We should also consider whether it will help to add more relationship types,
> 
> such as "derived from".  It does not seem to me to be appropriate to describe
> 
> a temporal development relationship between two organs as either "isa" or 
> "partof"
> 
> Lincoln
> 
> On Friday 03 October 2003 01:26 pm, Toby Kellogg wrote:
> > That would also be a good possibility - it's sort of an expanded and
> > slightly more precise version of Pankaj's "rudimentary" category.   A
> > trivial question:  does the word "gynoecium" need to follow "aborted" and
> > "mature", or is it understood?
> > Toby
> >
> > >In a way- what seems to be a solution is stages of development of an
> organ
> > >as being instances of an organ (e.g gynoecium primordia is an instance of
> > >gynoecium), aborted/rudimentary as other instances- so you have a node
> for
> > >gynoecium that includes all instances (stages)
> > >
> > >gynoecium
> > >-%gynoecium primordium
> > >-%aborted
> > >-%mature
> > >--<ovary
> > >--<stigma
> > >--<style
> > >
> > >not being comprehensive here but this is the general picture.
> > >Leonore
> > >
> > >On Fri, 3 Oct 2003, Toby Kellogg wrote:
> > >> Just a simultaneous addition to Felipe's comment:
> > >> Unisexual flowers are pretty common in Poaceae and in angiosperms in
> > >> general.  Among model systems they occur in Populus, sugar beet,
> Silene,
> > >> and the outer florets of some sunflower relatives, so if we can solve
> > >> the problem for maize, we will have solved a number of similar
> problems.
> > >>  The difficulty is that in maize, as in many angiosperms, all flowers
> > >> start development as bisexual structures; in staminate florets, the
> > >> pistil then
> > >>
> > >> aborts.  This means that the structure:
> > >> >----%tassel
> > >> >-------<staminate floret; synonym: male floret
> > >> >----------<androecium
> > >> >-------------<stamen
> > >> >----------------<anther
> > >> >----------------<stamen filament
> > >>
> > >> also should include gynoecium, pistil (and nucellus, ultimately), and
> > >> ovary, but not style and stigma.   As long as style and stigma are
> > >> daughters of pistil, there's a problem.  The gene tasselseed2 is
> > >> expressed in the young ovary of the staminate florets in the tassel,
> and
> > >> we can't describe its expression pattern accurately unless staminate
> > >> flowers are allowed to have pistils somehow.  Pankaj's idea of
> including
> > >> "rudimentary gynoecium" certainly seems like a step in the right
> > >> direction, as long as a search on gynoecium will find the rudimentary
> > >> ones as well.
> > >> toby
> > >>
> > >> >Lincoln Stein wrote:
> > >> >> The stigma issue is harder and I suspect it represents an incorrect
> > >> >>structure
> > >> >> in the tassel->floret->gynoecium->pistil path.
> > >> >
> > >> >The problem with maize is often the male and female florets occur in
> > >> > the female
> > >> >and male inflorescences respectively. Though this is not a normal
> > >> >condition. I
> > >> >agree with Sue, when we have the implementation of slots/properties
> > >> > linking different anatomical terms at some point in future, we should
> > >> > be able to build
> > >> >the correct structures. Please let me know if the following structure
> > >>
> > >>works.
> > >>
> > >> >inflorescence
> > >> >----%tassel
> > >> >-------<staminate floret; synonym: male floret
> > >> >----------<androecium
> > >> >-------------<stamen
> > >> >----------------<anther
> > >> >----------------<stamen filament
> > >> >----%spike
> > >> >------%spike  (sensu zea); synonym:cob
> > >> >-------<pistillate floret; synonym: female floret
> > >> >----------<gynoecium
> > >> >-------------<pistil
> > >> >---------------<style
> > >> >---------------<stigma
> > >> >---------------<ovary
> > >> >----%panicle
> > >> >--------<perfect floret
> > >> >----------<gynoecium
> > >> >------------<pistil
> > >> >--------------<style
> > >> >--------------<stigma
> > >> >--------------<ovary
> > >> >----------<androecium
> > >> >------------<stamen
> > >> >--------------<anther
> > >> >--------------<stamen filament
> > >> >----%capitulum (sensu compositae)
> > >> >--------<ray floret
> > >> >--------<disc floret
> > >> >----<floret
> > >> >------%floret
> > >> >--------%ray floret
> > >> >--------%disc floret
> > >> >------%floret (sensu Poaceae)
> > >> >--------%perfect floret
> > >> >----------<gynoecium
> > >> >------------<pistil
> > >> >--------------<style
> > >> >--------------<stigma
> > >> >--------------<ovary
> > >> >----------<androecium
> > >> >------------<stamen
> > >> >--------------<anther
> > >> >--------------<stamen filament
> > >> >--------%imperfect floret
> > >> >----------%staminate floret; synonym: male floret
> > >> >-------------<androecium
> > >> >---------------<stamen
> > >> >---------------<anther
> > >> >----------%pistillate floret; synonym: female floret
> > >> >-------------<gynoecium
> > >> >----------------<pistil
> > >> >------------------<style
> > >> >------------------<stigma
> > >> >------------------<ovary
> > >> >
> > >> >> Lincoln
> > >> >>
> > >> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> > >> >>>Hi all -
> > >> >>>  Felipe has made great progress here downloading the various
> > >> >>> programs necessary for viewing and manipulating the ontologies. 
> > >> >>> He's run into
> > >>
> > >>some
> > >>
> > >> >>>mechanical problems that he can sort out with Pankaj, the most
> > >> >>> critical being trying to get two DagEdit windows open at the same
> > >> >>> time so two ontologies can be viewed side by side.  In terms of the
> > >> >>> ontologies themselves, we immediately found a number of terms that
> > >> >>> are not in common use, or are in odd hierarchical relationships;
> > >> >>> these should be easy
> > >>
> > >>enough
> > >>
> > >> >>>to change.
> > >> >>>  A more interesting and complex issue comes with species-specific
> > >> >>> terms. An easy one is "silique" in Arabidopsis, which would be an
> > >> >>> instance of "fruit" if one is working with multiple species.  A
> more
> > >> >>> difficult one is "stigma", which is a part of "pistil", part of
> > >> >>> "gynoecium", part of "floret", etc. up to tassel.  Unfortunately,
> > >> >>> stigmas do not form in tassels, because the gynoecium stops
> > >> >>> developing.  Similarly, "abscission zone" is part of "silique" in
> > >> >>> Arabidopsis, and would end up being part of "fruit" if "silique"
> > >> >>> were interpreted as an instance of "fruit".
> > >>
> > >>However,
> > >>
> > >> >>>abscission zones do not form in the grass fruit so couldn't be a
> part
> > >> >>> of fruit.  in both cases we end up violating the True Path Rule. 
> It
> > >> >>> may be that this is inevitable, since the descriptors aren't
> > >> >>> strictly hierarchical.   Obviously one can get around this somewhat
> > >> >>> by creating species-specific bits of the hierarchy, and by making
> > >> >>> creative use of "sensu"; this will probably work fine as long as
> the
> > >> >>> ontology only has to apply to Brassicaceae and Gramineae.  If the
> > >> >>> long-term goal is to make it apply to all flowering plants, though,
> > >> >>> there may be a limit to how species-specific we make the
> ontologies.
> > >> >>>   For example we could divide fruits into indehiscent and dehiscent
> > >> >>> and then have abscission zone
> > >>
> > >>as part
> > >>
> > >> >>>of dehiscent fruits, which would be OK until we get to a fruit that
> > >> >>> forms an abscission zone but doesn't dehisce.  Another possibility
> > >> >>> that Felipe and I explored a little would be to add another
> category
> > >> >>> of connection, such as "a process that can occur in"  - in addition
> > >> >>> to "is part of", "is an instance of" and "develops from".  I
> suspect
> > >> >>> that another category
> > >>
> > >>might
> > >>
> > >> >>>create more problems than it solves, but it seemed worth
> considering.
> > >> >>>  Any thoughts on this are welcome!
> > >> >>>Toby
> > >> >>>
> > >> >>>Elizabeth A. Kellogg
> > >> >>>Department of Biology
> > >> >>>University of Missouri-St. Louis
> > >> >>>8001 Natural Bridge Road
> > >> >>>St. Louis, MO 63121
> > >> >>>phone: 314-516-6217
> > >> >>>fax: 314-516-6233
> > >> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > >> >
> > >> >--
> > >> >******************************************
> > >> >Pankaj Jaiswal, Ph.D.
> > >> >Research 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
> > >> >******************************************
> > >>
> > >> Elizabeth A. Kellogg
> > >> Department of Biology
> > >> University of Missouri-St. Louis
> > >> 8001 Natural Bridge Road
> > >> St. Louis, MO 63121
> > >> phone: 314-516-6217
> > >> fax: 314-516-6233
> > >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > >
> >
> >--------------------------------------------------------------------------
> > >----- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > > The Arabidopsis Information Resource	FAX: (650) 325-6857
> > >Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > >Department of Plant Biology		URL: http://arabidopsis.org/
> > >260 Panama St.
> > >Stanford, CA 94305
> >
> >--------------------------------------------------------------------------
> > >-----
> >
> > Elizabeth A. Kellogg
> > Department of Biology
> > University of Missouri-St. Louis
> > 8001 Natural Bridge Road
> > St. Louis, MO 63121
> > phone: 314-516-6217
> > fax: 314-516-6233
> > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> 
> -- 
> Lincoln Stein
> lstein at cshl.edu
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> 


_____________
Felipe Zapata
University of Missouri-St.Louis
Department of Biology
8001 Natural Bridge Rd.
St. Louis MO, 63121
Phone: (314) 516-6200
Fax: (314) 516-6233


From rhee at acoma.Stanford.EDU  Sat Oct  4 17:44:33 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Sat, 4 Oct 2003 14:44:33 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <1065297513.3f7f266970547@studentmail.umsl.edu>
Message-ID: <Pine.GSO.4.44.0310041442170.15615-100000@acoma.Stanford.EDU>

Sounds good. There are currently four nodes where this relationship
resides in the Arabidopsis anatomy ontologies.

parent nodes:
+-------------+
| name        |
+-------------+
| trichoblast |
| silique     |
| ovary wall  |
| L1          |
+-------------+

Sue


On Sat, 4 Oct 2003, Felipe Zapata wrote:

> Actually that relationship already exists. At least TAIR uses:
>
> !version: $Revision: 1.13 $
> !type: % ISA Is a
> !type: < PARTOF Part of
> !type: ~ DEVELOPSFROM develops from
> !editors: Leonore Reiser, Jonathan Clarke
> $Arabidopsis ontology ; TAIR:0000001
> .....
> ..
> ..
>
> What we probably need to do, is to go through the current ontologies and look for
> nodes where this relationship would have more biological meaning.
>
> Felipe
>
>
> Quoting Lincoln Stein <lstein at cshl.edu>:
>
> > We should also consider whether it will help to add more relationship types,
> >
> > such as "derived from".  It does not seem to me to be appropriate to describe
> >
> > a temporal development relationship between two organs as either "isa" or
> > "partof"
> >
> > Lincoln
> >
> > On Friday 03 October 2003 01:26 pm, Toby Kellogg wrote:
> > > That would also be a good possibility - it's sort of an expanded and
> > > slightly more precise version of Pankaj's "rudimentary" category.   A
> > > trivial question:  does the word "gynoecium" need to follow "aborted" and
> > > "mature", or is it understood?
> > > Toby
> > >
> > > >In a way- what seems to be a solution is stages of development of an
> > organ
> > > >as being instances of an organ (e.g gynoecium primordia is an instance of
> > > >gynoecium), aborted/rudimentary as other instances- so you have a node
> > for
> > > >gynoecium that includes all instances (stages)
> > > >
> > > >gynoecium
> > > >-%gynoecium primordium
> > > >-%aborted
> > > >-%mature
> > > >--<ovary
> > > >--<stigma
> > > >--<style
> > > >
> > > >not being comprehensive here but this is the general picture.
> > > >Leonore
> > > >
> > > >On Fri, 3 Oct 2003, Toby Kellogg wrote:
> > > >> Just a simultaneous addition to Felipe's comment:
> > > >> Unisexual flowers are pretty common in Poaceae and in angiosperms in
> > > >> general.  Among model systems they occur in Populus, sugar beet,
> > Silene,
> > > >> and the outer florets of some sunflower relatives, so if we can solve
> > > >> the problem for maize, we will have solved a number of similar
> > problems.
> > > >>  The difficulty is that in maize, as in many angiosperms, all flowers
> > > >> start development as bisexual structures; in staminate florets, the
> > > >> pistil then
> > > >>
> > > >> aborts.  This means that the structure:
> > > >> >----%tassel
> > > >> >-------<staminate floret; synonym: male floret
> > > >> >----------<androecium
> > > >> >-------------<stamen
> > > >> >----------------<anther
> > > >> >----------------<stamen filament
> > > >>
> > > >> also should include gynoecium, pistil (and nucellus, ultimately), and
> > > >> ovary, but not style and stigma.   As long as style and stigma are
> > > >> daughters of pistil, there's a problem.  The gene tasselseed2 is
> > > >> expressed in the young ovary of the staminate florets in the tassel,
> > and
> > > >> we can't describe its expression pattern accurately unless staminate
> > > >> flowers are allowed to have pistils somehow.  Pankaj's idea of
> > including
> > > >> "rudimentary gynoecium" certainly seems like a step in the right
> > > >> direction, as long as a search on gynoecium will find the rudimentary
> > > >> ones as well.
> > > >> toby
> > > >>
> > > >> >Lincoln Stein wrote:
> > > >> >> The stigma issue is harder and I suspect it represents an incorrect
> > > >> >>structure
> > > >> >> in the tassel->floret->gynoecium->pistil path.
> > > >> >
> > > >> >The problem with maize is often the male and female florets occur in
> > > >> > the female
> > > >> >and male inflorescences respectively. Though this is not a normal
> > > >> >condition. I
> > > >> >agree with Sue, when we have the implementation of slots/properties
> > > >> > linking different anatomical terms at some point in future, we should
> > > >> > be able to build
> > > >> >the correct structures. Please let me know if the following structure
> > > >>
> > > >>works.
> > > >>
> > > >> >inflorescence
> > > >> >----%tassel
> > > >> >-------<staminate floret; synonym: male floret
> > > >> >----------<androecium
> > > >> >-------------<stamen
> > > >> >----------------<anther
> > > >> >----------------<stamen filament
> > > >> >----%spike
> > > >> >------%spike  (sensu zea); synonym:cob
> > > >> >-------<pistillate floret; synonym: female floret
> > > >> >----------<gynoecium
> > > >> >-------------<pistil
> > > >> >---------------<style
> > > >> >---------------<stigma
> > > >> >---------------<ovary
> > > >> >----%panicle
> > > >> >--------<perfect floret
> > > >> >----------<gynoecium
> > > >> >------------<pistil
> > > >> >--------------<style
> > > >> >--------------<stigma
> > > >> >--------------<ovary
> > > >> >----------<androecium
> > > >> >------------<stamen
> > > >> >--------------<anther
> > > >> >--------------<stamen filament
> > > >> >----%capitulum (sensu compositae)
> > > >> >--------<ray floret
> > > >> >--------<disc floret
> > > >> >----<floret
> > > >> >------%floret
> > > >> >--------%ray floret
> > > >> >--------%disc floret
> > > >> >------%floret (sensu Poaceae)
> > > >> >--------%perfect floret
> > > >> >----------<gynoecium
> > > >> >------------<pistil
> > > >> >--------------<style
> > > >> >--------------<stigma
> > > >> >--------------<ovary
> > > >> >----------<androecium
> > > >> >------------<stamen
> > > >> >--------------<anther
> > > >> >--------------<stamen filament
> > > >> >--------%imperfect floret
> > > >> >----------%staminate floret; synonym: male floret
> > > >> >-------------<androecium
> > > >> >---------------<stamen
> > > >> >---------------<anther
> > > >> >----------%pistillate floret; synonym: female floret
> > > >> >-------------<gynoecium
> > > >> >----------------<pistil
> > > >> >------------------<style
> > > >> >------------------<stigma
> > > >> >------------------<ovary
> > > >> >
> > > >> >> Lincoln
> > > >> >>
> > > >> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> > > >> >>>Hi all -
> > > >> >>>  Felipe has made great progress here downloading the various
> > > >> >>> programs necessary for viewing and manipulating the ontologies.
> > > >> >>> He's run into
> > > >>
> > > >>some
> > > >>
> > > >> >>>mechanical problems that he can sort out with Pankaj, the most
> > > >> >>> critical being trying to get two DagEdit windows open at the same
> > > >> >>> time so two ontologies can be viewed side by side.  In terms of the
> > > >> >>> ontologies themselves, we immediately found a number of terms that
> > > >> >>> are not in common use, or are in odd hierarchical relationships;
> > > >> >>> these should be easy
> > > >>
> > > >>enough
> > > >>
> > > >> >>>to change.
> > > >> >>>  A more interesting and complex issue comes with species-specific
> > > >> >>> terms. An easy one is "silique" in Arabidopsis, which would be an
> > > >> >>> instance of "fruit" if one is working with multiple species.  A
> > more
> > > >> >>> difficult one is "stigma", which is a part of "pistil", part of
> > > >> >>> "gynoecium", part of "floret", etc. up to tassel.  Unfortunately,
> > > >> >>> stigmas do not form in tassels, because the gynoecium stops
> > > >> >>> developing.  Similarly, "abscission zone" is part of "silique" in
> > > >> >>> Arabidopsis, and would end up being part of "fruit" if "silique"
> > > >> >>> were interpreted as an instance of "fruit".
> > > >>
> > > >>However,
> > > >>
> > > >> >>>abscission zones do not form in the grass fruit so couldn't be a
> > part
> > > >> >>> of fruit.  in both cases we end up violating the True Path Rule.
> > It
> > > >> >>> may be that this is inevitable, since the descriptors aren't
> > > >> >>> strictly hierarchical.   Obviously one can get around this somewhat
> > > >> >>> by creating species-specific bits of the hierarchy, and by making
> > > >> >>> creative use of "sensu"; this will probably work fine as long as
> > the
> > > >> >>> ontology only has to apply to Brassicaceae and Gramineae.  If the
> > > >> >>> long-term goal is to make it apply to all flowering plants, though,
> > > >> >>> there may be a limit to how species-specific we make the
> > ontologies.
> > > >> >>>   For example we could divide fruits into indehiscent and dehiscent
> > > >> >>> and then have abscission zone
> > > >>
> > > >>as part
> > > >>
> > > >> >>>of dehiscent fruits, which would be OK until we get to a fruit that
> > > >> >>> forms an abscission zone but doesn't dehisce.  Another possibility
> > > >> >>> that Felipe and I explored a little would be to add another
> > category
> > > >> >>> of connection, such as "a process that can occur in"  - in addition
> > > >> >>> to "is part of", "is an instance of" and "develops from".  I
> > suspect
> > > >> >>> that another category
> > > >>
> > > >>might
> > > >>
> > > >> >>>create more problems than it solves, but it seemed worth
> > considering.
> > > >> >>>  Any thoughts on this are welcome!
> > > >> >>>Toby
> > > >> >>>
> > > >> >>>Elizabeth A. Kellogg
> > > >> >>>Department of Biology
> > > >> >>>University of Missouri-St. Louis
> > > >> >>>8001 Natural Bridge Road
> > > >> >>>St. Louis, MO 63121
> > > >> >>>phone: 314-516-6217
> > > >> >>>fax: 314-516-6233
> > > >> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > > >> >
> > > >> >--
> > > >> >******************************************
> > > >> >Pankaj Jaiswal, Ph.D.
> > > >> >Research 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
> > > >> >******************************************
> > > >>
> > > >> Elizabeth A. Kellogg
> > > >> Department of Biology
> > > >> University of Missouri-St. Louis
> > > >> 8001 Natural Bridge Road
> > > >> St. Louis, MO 63121
> > > >> phone: 314-516-6217
> > > >> fax: 314-516-6233
> > > >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > > >
> > >
> > >--------------------------------------------------------------------------
> > > >----- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > > > The Arabidopsis Information Resource	FAX: (650) 325-6857
> > > >Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > > >Department of Plant Biology		URL: http://arabidopsis.org/
> > > >260 Panama St.
> > > >Stanford, CA 94305
> > >
> > >--------------------------------------------------------------------------
> > > >-----
> > >
> > > Elizabeth A. Kellogg
> > > Department of Biology
> > > University of Missouri-St. Louis
> > > 8001 Natural Bridge Road
> > > St. Louis, MO 63121
> > > phone: 314-516-6217
> > > fax: 314-516-6233
> > > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> >
> > --
> > Lincoln Stein
> > lstein at cshl.edu
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > (516) 367-8380 (voice)
> > (516) 367-8389 (fax)
> >
>
>
> _____________
> Felipe Zapata
> University of Missouri-St.Louis
> Department of Biology
> 8001 Natural Bridge Rd.
> St. Louis MO, 63121
> Phone: (314) 516-6200
> Fax: (314) 516-6233
>

-----------------------------------------------------------------------------
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 lreiser at acoma.Stanford.EDU  Sun Oct  5 20:47:12 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Sun, 5 Oct 2003 17:47:12 -0700 (PDT)
Subject: POC observations so far
In-Reply-To: <200310041346.30798.lstein@cshl.edu>
Message-ID: <Pine.GSO.4.44.0310051745400.22605-100000@acoma.Stanford.EDU>


Yes- TAIR has made some use of derived from though not as comprehensively
as we could (e.g. trichome is derived from meristemoid, root hair derived
from trichoblast).But not say- leaf derived from leaf primordia.
Leonore

On Sat, 4 Oct 2003, Lincoln Stein wrote:

> We should also consider whether it will help to add more relationship types,
> such as "derived from".  It does not seem to me to be appropriate to describe
> a temporal development relationship between two organs as either "isa" or
> "partof"
>
> Lincoln
>
> On Friday 03 October 2003 01:26 pm, Toby Kellogg wrote:
> > That would also be a good possibility - it's sort of an expanded and
> > slightly more precise version of Pankaj's "rudimentary" category.   A
> > trivial question:  does the word "gynoecium" need to follow "aborted" and
> > "mature", or is it understood?
> > Toby
> >
> > >In a way- what seems to be a solution is stages of development of an organ
> > >as being instances of an organ (e.g gynoecium primordia is an instance of
> > >gynoecium), aborted/rudimentary as other instances- so you have a node for
> > >gynoecium that includes all instances (stages)
> > >
> > >gynoecium
> > >-%gynoecium primordium
> > >-%aborted
> > >-%mature
> > >--<ovary
> > >--<stigma
> > >--<style
> > >
> > >not being comprehensive here but this is the general picture.
> > >Leonore
> > >
> > >On Fri, 3 Oct 2003, Toby Kellogg wrote:
> > >> Just a simultaneous addition to Felipe's comment:
> > >> Unisexual flowers are pretty common in Poaceae and in angiosperms in
> > >> general.  Among model systems they occur in Populus, sugar beet, Silene,
> > >> and the outer florets of some sunflower relatives, so if we can solve
> > >> the problem for maize, we will have solved a number of similar problems.
> > >>  The difficulty is that in maize, as in many angiosperms, all flowers
> > >> start development as bisexual structures; in staminate florets, the
> > >> pistil then
> > >>
> > >> aborts.  This means that the structure:
> > >> >----%tassel
> > >> >-------<staminate floret; synonym: male floret
> > >> >----------<androecium
> > >> >-------------<stamen
> > >> >----------------<anther
> > >> >----------------<stamen filament
> > >>
> > >> also should include gynoecium, pistil (and nucellus, ultimately), and
> > >> ovary, but not style and stigma.   As long as style and stigma are
> > >> daughters of pistil, there's a problem.  The gene tasselseed2 is
> > >> expressed in the young ovary of the staminate florets in the tassel, and
> > >> we can't describe its expression pattern accurately unless staminate
> > >> flowers are allowed to have pistils somehow.  Pankaj's idea of including
> > >> "rudimentary gynoecium" certainly seems like a step in the right
> > >> direction, as long as a search on gynoecium will find the rudimentary
> > >> ones as well.
> > >> toby
> > >>
> > >> >Lincoln Stein wrote:
> > >> >> The stigma issue is harder and I suspect it represents an incorrect
> > >> >>structure
> > >> >> in the tassel->floret->gynoecium->pistil path.
> > >> >
> > >> >The problem with maize is often the male and female florets occur in
> > >> > the female
> > >> >and male inflorescences respectively. Though this is not a normal
> > >> >condition. I
> > >> >agree with Sue, when we have the implementation of slots/properties
> > >> > linking different anatomical terms at some point in future, we should
> > >> > be able to build
> > >> >the correct structures. Please let me know if the following structure
> > >>
> > >>works.
> > >>
> > >> >inflorescence
> > >> >----%tassel
> > >> >-------<staminate floret; synonym: male floret
> > >> >----------<androecium
> > >> >-------------<stamen
> > >> >----------------<anther
> > >> >----------------<stamen filament
> > >> >----%spike
> > >> >------%spike  (sensu zea); synonym:cob
> > >> >-------<pistillate floret; synonym: female floret
> > >> >----------<gynoecium
> > >> >-------------<pistil
> > >> >---------------<style
> > >> >---------------<stigma
> > >> >---------------<ovary
> > >> >----%panicle
> > >> >--------<perfect floret
> > >> >----------<gynoecium
> > >> >------------<pistil
> > >> >--------------<style
> > >> >--------------<stigma
> > >> >--------------<ovary
> > >> >----------<androecium
> > >> >------------<stamen
> > >> >--------------<anther
> > >> >--------------<stamen filament
> > >> >----%capitulum (sensu compositae)
> > >> >--------<ray floret
> > >> >--------<disc floret
> > >> >----<floret
> > >> >------%floret
> > >> >--------%ray floret
> > >> >--------%disc floret
> > >> >------%floret (sensu Poaceae)
> > >> >--------%perfect floret
> > >> >----------<gynoecium
> > >> >------------<pistil
> > >> >--------------<style
> > >> >--------------<stigma
> > >> >--------------<ovary
> > >> >----------<androecium
> > >> >------------<stamen
> > >> >--------------<anther
> > >> >--------------<stamen filament
> > >> >--------%imperfect floret
> > >> >----------%staminate floret; synonym: male floret
> > >> >-------------<androecium
> > >> >---------------<stamen
> > >> >---------------<anther
> > >> >----------%pistillate floret; synonym: female floret
> > >> >-------------<gynoecium
> > >> >----------------<pistil
> > >> >------------------<style
> > >> >------------------<stigma
> > >> >------------------<ovary
> > >> >
> > >> >> Lincoln
> > >> >>
> > >> >> On Thursday 02 October 2003 02:45 pm, Toby Kellogg wrote:
> > >> >>>Hi all -
> > >> >>>  Felipe has made great progress here downloading the various
> > >> >>> programs necessary for viewing and manipulating the ontologies.
> > >> >>> He's run into
> > >>
> > >>some
> > >>
> > >> >>>mechanical problems that he can sort out with Pankaj, the most
> > >> >>> critical being trying to get two DagEdit windows open at the same
> > >> >>> time so two ontologies can be viewed side by side.  In terms of the
> > >> >>> ontologies themselves, we immediately found a number of terms that
> > >> >>> are not in common use, or are in odd hierarchical relationships;
> > >> >>> these should be easy
> > >>
> > >>enough
> > >>
> > >> >>>to change.
> > >> >>>  A more interesting and complex issue comes with species-specific
> > >> >>> terms. An easy one is "silique" in Arabidopsis, which would be an
> > >> >>> instance of "fruit" if one is working with multiple species.  A more
> > >> >>> difficult one is "stigma", which is a part of "pistil", part of
> > >> >>> "gynoecium", part of "floret", etc. up to tassel.  Unfortunately,
> > >> >>> stigmas do not form in tassels, because the gynoecium stops
> > >> >>> developing.  Similarly, "abscission zone" is part of "silique" in
> > >> >>> Arabidopsis, and would end up being part of "fruit" if "silique"
> > >> >>> were interpreted as an instance of "fruit".
> > >>
> > >>However,
> > >>
> > >> >>>abscission zones do not form in the grass fruit so couldn't be a part
> > >> >>> of fruit.  in both cases we end up violating the True Path Rule.  It
> > >> >>> may be that this is inevitable, since the descriptors aren't
> > >> >>> strictly hierarchical.   Obviously one can get around this somewhat
> > >> >>> by creating species-specific bits of the hierarchy, and by making
> > >> >>> creative use of "sensu"; this will probably work fine as long as the
> > >> >>> ontology only has to apply to Brassicaceae and Gramineae.  If the
> > >> >>> long-term goal is to make it apply to all flowering plants, though,
> > >> >>> there may be a limit to how species-specific we make the ontologies.
> > >> >>>   For example we could divide fruits into indehiscent and dehiscent
> > >> >>> and then have abscission zone
> > >>
> > >>as part
> > >>
> > >> >>>of dehiscent fruits, which would be OK until we get to a fruit that
> > >> >>> forms an abscission zone but doesn't dehisce.  Another possibility
> > >> >>> that Felipe and I explored a little would be to add another category
> > >> >>> of connection, such as "a process that can occur in"  - in addition
> > >> >>> to "is part of", "is an instance of" and "develops from".  I suspect
> > >> >>> that another category
> > >>
> > >>might
> > >>
> > >> >>>create more problems than it solves, but it seemed worth considering.
> > >> >>>  Any thoughts on this are welcome!
> > >> >>>Toby
> > >> >>>
> > >> >>>Elizabeth A. Kellogg
> > >> >>>Department of Biology
> > >> >>>University of Missouri-St. Louis
> > >> >>>8001 Natural Bridge Road
> > >> >>>St. Louis, MO 63121
> > >> >>>phone: 314-516-6217
> > >> >>>fax: 314-516-6233
> > >> >>>http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > >> >
> > >> >--
> > >> >******************************************
> > >> >Pankaj Jaiswal, Ph.D.
> > >> >Research 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
> > >> >******************************************
> > >>
> > >> Elizabeth A. Kellogg
> > >> Department of Biology
> > >> University of Missouri-St. Louis
> > >> 8001 Natural Bridge Road
> > >> St. Louis, MO 63121
> > >> phone: 314-516-6217
> > >> fax: 314-516-6233
> > >> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> > >
> > >--------------------------------------------------------------------------
> > >----- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > > The Arabidopsis Information Resource	FAX: (650) 325-6857
> > >Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > >Department of Plant Biology		URL: http://arabidopsis.org/
> > >260 Panama St.
> > >Stanford, CA 94305
> > >--------------------------------------------------------------------------
> > >-----
> >
> > Elizabeth A. Kellogg
> > Department of Biology
> > University of Missouri-St. Louis
> > 8001 Natural Bridge Road
> > St. Louis, MO 63121
> > phone: 314-516-6217
> > fax: 314-516-6233
> > http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
> --
> Lincoln Stein
> lstein at cshl.edu
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Mon Oct  6 11:21:14 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 06 Oct 2003 11:21:14 -0400
Subject: POC observations so far
In-Reply-To: <Pine.GSO.4.44.0310041442170.15615-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310041442170.15615-100000@acoma.Stanford.EDU>
Message-ID: <3F81886A.6040601@cornell.edu>

In one of our earlier version, which did not go to the CVS, we had relationship 
type, develops_from for parent terms. We dropped this relationship type because 
we were not displaying it in our browser.

seed coat
nucellar cells
pericarp
megaspore
periderm
meristem
cork cambium
pistil

I agree with Felipe, we need to bring this relation_type back and use it 
extensively, wherever applicable.

Pankaj

Sue Rhee wrote:

> Sounds good. There are currently four nodes where this relationship
> resides in the Arabidopsis anatomy ontologies.
> 
> parent nodes:
> +-------------+
> | name        |
> +-------------+
> | trichoblast |
> | silique     |
> | ovary wall  |
> | L1          |
> +-------------+
> 
> Sue
> 
> 
> On Sat, 4 Oct 2003, Felipe Zapata wrote:
> 
> 
>>Actually that relationship already exists. At least TAIR uses:
>>
>>!version: $Revision: 1.13 $
>>!type: % ISA Is a
>>!type: < PARTOF Part of
>>!type: ~ DEVELOPSFROM develops from
>>!editors: Leonore Reiser, Jonathan Clarke
>>$Arabidopsis ontology ; TAIR:0000001
>>.....
>>..
>>..
>>
>>What we probably need to do, is to go through the current ontologies and look for
>>nodes where this relationship would have more biological meaning.
>>
>>Felipe
>>




From Leszek at missouri.edu  Wed Oct  8 17:23:41 2003
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Wed, 8 Oct 2003 16:23:41 -0500
Subject: A delayed response on "POC observations so far"
Message-ID: <3D4AD7F06881FD42A720D33D8E399DF3010ECC69@COL-EMAIL4.col.missouri.edu>

Hi POC colleagues,

Here's some 'bedtime reading'.

Recently there was discussion about the representation of unisexual
florets in a taxon which bears both functionally male & female florets
in separate flowering structures e.g. adequate representation of monoecy
in taxa such as Zea mays. Furthermore concern was raised about querying
an ontology, involving a monoecious taxon, for the term gynoecium - that
such a search should be able to retrieve gynoecium-related info.
associated with the tassel as well as the ear as in Zea mays.

Pankaj & possibly some others may recall that some of us visited this
area sometime last year & the synthesis of that dialogue was recorded in
the current ontology for Zea mays (freely available from
plantontology.org). But to show you an example of the tentative solution
to the challenge I've reproduced a portion of the representation below:

organ
  %tassel (functionally male inflorescence)
    <pedicellate spikelet of tassel
      <lower floret of pedicellate spikelet of tassel
        <gynoecial tissue (abortive) of lower floret of pedicellate
spikelet of tassel
        <lodicules of lower floret of ....
        <palea of lower floret of .....
        <stamens of lower floret of ....
      <lower glume of pedicellate spikelet of tassel
      <upper glume of .....
    <sessile spikelet of tassel
      etc.
  %lateral branch
    <ear (functionally female inflorescence)
      <pedicellate spikelet of ear
etc....

Yes, it is a little complex (view it via DAG-Edit for a clearer
representation than that provided here) but it is my/our best attempt
yet at capturing the biological complexity such that the true path rule
is met for this biological reality in Zea mays. Furthermore, it should
satisfy the query needs referred to above. Of course there may be other
considerations that have since transpired...

For me, as a botanist & plant systematist, I think it is a good solution
because it captures the ontogenetic detail for these structures and it
is also consistent with phylogenetic argument concerning these
structures - and consequently should be applicable to taxa, other than
Zea, where monoecy & dioecy is found.

It is true that some folk may not (at first) appreciate the biological
relevance of including both the androecium & gynoecium in both the
tassel & ear. My attempt to cover that 'base' is provided in the
definition for "floret". In this definition I spell out the ontogenetic
reality of both the androecium & gynoecium being initially present in
both the tassel & ear florets - hence their need to be included in both
the tassel & lateral branch/ear nodes. It also draws attention to the
putative phylogenetic necessity for such a representation. Implicitly
what I'm practicing is that ontogenetic & phylogenetic information are
both extremely important for inclusion in the application of the 'true
path rule'.

Here's the definition for floret (yes, it is detailed): 
"The floret is the individual flower of the Zea mays plant. In the grass
family (Poaceae, alt. Gramineae) each floret is typically bisexual
(perfect), possessing both an androecium and a gynoecium. Each floret
typically has a pair of bracts, the lemma and palea, which subtend the
floret. It is important to note that In Zea mays the florets of the
'tassel' are functionally male (the female component (gynoecium) having
aborted early on in development). The florets of the 'ear' are
functionally female (the male components (androecium) having aborted
early on in development). The possession of functionally male and
functionally female florets (or flowers) on the same plant is a
condition called monoecy. While Zea mays is functionally monoecious, the
presence of both androecial and gynoecial tissue in the early stages of
floret ontogeny is phylogenetically significant. Consequently, the
androecium is represented in the florets of the ear and the gynoecium is
represented in the florets of the tassel, even though either of these
whorls is absent in the functional florets. The inclusion of both whorls
in the floret ontology for the florets of ears and spikelets is based on
this phylogenetically significant ontogeny. East and Hayes (1911, p.
134-135) provided the following: "Perhaps it should be mentioned in
passing that the immature sex organs, so called, of maize seem endowed
with the power of becoming either stamens or carpels. One often finds a
normal ear ending in stamens, and nearly every plant produces lateral
branches which have carpels and stamens mixed together
indiscriminantly." Studies of mutants have explored these occurrences
and similar occurrences in tassels, corroborating the inherent bisexual
nature of the floret meristem prior to the subsequent development of the
monoecious condition." (the length of this defn. possibly provides
argument for the inclusion of some sort of comment field closely
associated with the definition?).

I've also been using the Derived/Develops_from relationship in the Zea
ontology. This relationship accommodates the temporal & spatial needs
associated with ontogeny e.g. the development of primordia.

You'll note, when browsing the ontology via DAG-Edit, that I still need
to provide definitions for some terms - an ever pressing need.

Let me have your candid comments/thoughts.

Leszek
 
===========================
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
Yahoo! Messenger: leszekvincent
Plant Systematist on the Plant Ontology Consortium
Associate Curator, Dunn-Palmer Herbarium (UMO)
Research Associate, Missouri Botanical Garden, USA
CEO - PhytoSynergy, LLC
=======================



From rhee at acoma.Stanford.EDU  Wed Oct  8 17:54:12 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Wed, 8 Oct 2003 14:54:12 -0700 (PDT)
Subject: A delayed response on "POC observations so far"
In-Reply-To: <3D4AD7F06881FD42A720D33D8E399DF3010ECC69@COL-EMAIL4.col.missouri.edu>
Message-ID: <Pine.GSO.4.44.0310081454010.9792-100000@acoma.Stanford.EDU>

give me the bottom line in three sentences or less.

thanks,
sue

On Wed, 8 Oct 2003, Vincent, Leszek wrote:

> Hi POC colleagues,
>
> Here's some 'bedtime reading'.
>
> Recently there was discussion about the representation of unisexual
> florets in a taxon which bears both functionally male & female florets
> in separate flowering structures e.g. adequate representation of monoecy
> in taxa such as Zea mays. Furthermore concern was raised about querying
> an ontology, involving a monoecious taxon, for the term gynoecium - that
> such a search should be able to retrieve gynoecium-related info.
> associated with the tassel as well as the ear as in Zea mays.
>
> Pankaj & possibly some others may recall that some of us visited this
> area sometime last year & the synthesis of that dialogue was recorded in
> the current ontology for Zea mays (freely available from
> plantontology.org). But to show you an example of the tentative solution
> to the challenge I've reproduced a portion of the representation below:
>
> organ
>   %tassel (functionally male inflorescence)
>     <pedicellate spikelet of tassel
>       <lower floret of pedicellate spikelet of tassel
>         <gynoecial tissue (abortive) of lower floret of pedicellate
> spikelet of tassel
>         <lodicules of lower floret of ....
>         <palea of lower floret of .....
>         <stamens of lower floret of ....
>       <lower glume of pedicellate spikelet of tassel
>       <upper glume of .....
>     <sessile spikelet of tassel
>       etc.
>   %lateral branch
>     <ear (functionally female inflorescence)
>       <pedicellate spikelet of ear
> etc....
>
> Yes, it is a little complex (view it via DAG-Edit for a clearer
> representation than that provided here) but it is my/our best attempt
> yet at capturing the biological complexity such that the true path rule
> is met for this biological reality in Zea mays. Furthermore, it should
> satisfy the query needs referred to above. Of course there may be other
> considerations that have since transpired...
>
> For me, as a botanist & plant systematist, I think it is a good solution
> because it captures the ontogenetic detail for these structures and it
> is also consistent with phylogenetic argument concerning these
> structures - and consequently should be applicable to taxa, other than
> Zea, where monoecy & dioecy is found.
>
> It is true that some folk may not (at first) appreciate the biological
> relevance of including both the androecium & gynoecium in both the
> tassel & ear. My attempt to cover that 'base' is provided in the
> definition for "floret". In this definition I spell out the ontogenetic
> reality of both the androecium & gynoecium being initially present in
> both the tassel & ear florets - hence their need to be included in both
> the tassel & lateral branch/ear nodes. It also draws attention to the
> putative phylogenetic necessity for such a representation. Implicitly
> what I'm practicing is that ontogenetic & phylogenetic information are
> both extremely important for inclusion in the application of the 'true
> path rule'.
>
> Here's the definition for floret (yes, it is detailed):
> "The floret is the individual flower of the Zea mays plant. In the grass
> family (Poaceae, alt. Gramineae) each floret is typically bisexual
> (perfect), possessing both an androecium and a gynoecium. Each floret
> typically has a pair of bracts, the lemma and palea, which subtend the
> floret. It is important to note that In Zea mays the florets of the
> 'tassel' are functionally male (the female component (gynoecium) having
> aborted early on in development). The florets of the 'ear' are
> functionally female (the male components (androecium) having aborted
> early on in development). The possession of functionally male and
> functionally female florets (or flowers) on the same plant is a
> condition called monoecy. While Zea mays is functionally monoecious, the
> presence of both androecial and gynoecial tissue in the early stages of
> floret ontogeny is phylogenetically significant. Consequently, the
> androecium is represented in the florets of the ear and the gynoecium is
> represented in the florets of the tassel, even though either of these
> whorls is absent in the functional florets. The inclusion of both whorls
> in the floret ontology for the florets of ears and spikelets is based on
> this phylogenetically significant ontogeny. East and Hayes (1911, p.
> 134-135) provided the following: "Perhaps it should be mentioned in
> passing that the immature sex organs, so called, of maize seem endowed
> with the power of becoming either stamens or carpels. One often finds a
> normal ear ending in stamens, and nearly every plant produces lateral
> branches which have carpels and stamens mixed together
> indiscriminantly." Studies of mutants have explored these occurrences
> and similar occurrences in tassels, corroborating the inherent bisexual
> nature of the floret meristem prior to the subsequent development of the
> monoecious condition." (the length of this defn. possibly provides
> argument for the inclusion of some sort of comment field closely
> associated with the definition?).
>
> I've also been using the Derived/Develops_from relationship in the Zea
> ontology. This relationship accommodates the temporal & spatial needs
> associated with ontogeny e.g. the development of primordia.
>
> You'll note, when browsing the ontology via DAG-Edit, that I still need
> to provide definitions for some terms - an ever pressing need.
>
> Let me have your candid comments/thoughts.
>
> Leszek
>
> ===========================
> 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
> Yahoo! Messenger: leszekvincent
> Plant Systematist on the Plant Ontology Consortium
> Associate Curator, Dunn-Palmer Herbarium (UMO)
> Research Associate, Missouri Botanical Garden, USA
> CEO - PhytoSynergy, LLC
> =======================
>
>

-----------------------------------------------------------------------------
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 Leszek at missouri.edu  Thu Oct  9 10:45:11 2003
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Thu, 9 Oct 2003 09:45:11 -0500
Subject: A delayed response on "POC observations so far"
Message-ID: <3D4AD7F06881FD42A720D33D8E399DF3010ECC6A@COL-EMAIL4.col.missouri.edu>

Sue (& possibly others),

The "bottom line" (elevator pitch) is that the Zea mays Plant Structure
ontology has attempted to represent the biological reality of monoecy
via incorporating ontogenetic data & reflecting phylogenetic theory &
satisfies the 'true path rule'- check it out.

- Leszek

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Sue Rhee
> Sent: Wednesday, October 08, 2003 4:54 PM
> To: po-dev at plantontology.org
> Subject: Re: A delayed response on "POC observations so far"
> 
> 
> give me the bottom line in three sentences or less.
> 
> thanks,
> sue
> 
> On Wed, 8 Oct 2003, Vincent, Leszek wrote:
> 
> > Hi POC colleagues,
> >
> > Here's some 'bedtime reading'.
> >
> > Recently there was discussion about the representation of unisexual 
> > florets in a taxon which bears both functionally male & 
> female florets 
> > in separate flowering structures e.g. adequate representation of 
> > monoecy in taxa such as Zea mays. Furthermore concern was 
> raised about 
> > querying an ontology, involving a monoecious taxon, for the term 
> > gynoecium - that such a search should be able to retrieve 
> > gynoecium-related info. associated with the tassel as well 
> as the ear 
> > as in Zea mays.
> >
> > Pankaj & possibly some others may recall that some of us 
> visited this 
> > area sometime last year & the synthesis of that dialogue 
> was recorded 
> > in the current ontology for Zea mays (freely available from 
> > plantontology.org). But to show you an example of the tentative 
> > solution to the challenge I've reproduced a portion of the 
> > representation below:
> >
> > organ
> >   %tassel (functionally male inflorescence)
> >     <pedicellate spikelet of tassel
> >       <lower floret of pedicellate spikelet of tassel
> >         <gynoecial tissue (abortive) of lower floret of pedicellate 
> > spikelet of tassel
> >         <lodicules of lower floret of ....
> >         <palea of lower floret of .....
> >         <stamens of lower floret of ....
> >       <lower glume of pedicellate spikelet of tassel
> >       <upper glume of .....
> >     <sessile spikelet of tassel
> >       etc.
> >   %lateral branch
> >     <ear (functionally female inflorescence)
> >       <pedicellate spikelet of ear
> > etc....
> >
> > Yes, it is a little complex (view it via DAG-Edit for a clearer 
> > representation than that provided here) but it is my/our 
> best attempt 
> > yet at capturing the biological complexity such that the true path 
> > rule is met for this biological reality in Zea mays. 
> Furthermore, it 
> > should satisfy the query needs referred to above. Of course 
> there may 
> > be other considerations that have since transpired...
> >
> > For me, as a botanist & plant systematist, I think it is a good 
> > solution because it captures the ontogenetic detail for these 
> > structures and it is also consistent with phylogenetic argument 
> > concerning these structures - and consequently should be 
> applicable to 
> > taxa, other than Zea, where monoecy & dioecy is found.
> >
> > It is true that some folk may not (at first) appreciate the 
> biological 
> > relevance of including both the androecium & gynoecium in both the 
> > tassel & ear. My attempt to cover that 'base' is provided in the 
> > definition for "floret". In this definition I spell out the 
> > ontogenetic reality of both the androecium & gynoecium 
> being initially 
> > present in both the tassel & ear florets - hence their need to be 
> > included in both the tassel & lateral branch/ear nodes. It 
> also draws 
> > attention to the putative phylogenetic necessity for such a 
> > representation. Implicitly what I'm practicing is that 
> ontogenetic & 
> > phylogenetic information are both extremely important for 
> inclusion in 
> > the application of the 'true path rule'.
> >
> > Here's the definition for floret (yes, it is detailed):
> > "The floret is the individual flower of the Zea mays plant. In the 
> > grass family (Poaceae, alt. Gramineae) each floret is typically 
> > bisexual (perfect), possessing both an androecium and a gynoecium. 
> > Each floret typically has a pair of bracts, the lemma and 
> palea, which 
> > subtend the floret. It is important to note that In Zea mays the 
> > florets of the 'tassel' are functionally male (the female component 
> > (gynoecium) having aborted early on in development). The florets of 
> > the 'ear' are functionally female (the male components (androecium) 
> > having aborted early on in development). The possession of 
> > functionally male and functionally female florets (or 
> flowers) on the 
> > same plant is a condition called monoecy. While Zea mays is 
> > functionally monoecious, the presence of both androecial 
> and gynoecial 
> > tissue in the early stages of floret ontogeny is phylogenetically 
> > significant. Consequently, the androecium is represented in the 
> > florets of the ear and the gynoecium is represented in the 
> florets of 
> > the tassel, even though either of these whorls is absent in the 
> > functional florets. The inclusion of both whorls in the floret 
> > ontology for the florets of ears and spikelets is based on this 
> > phylogenetically significant ontogeny. East and Hayes (1911, p.
> > 134-135) provided the following: "Perhaps it should be mentioned in
> > passing that the immature sex organs, so called, of maize 
> seem endowed
> > with the power of becoming either stamens or carpels. One 
> often finds a
> > normal ear ending in stamens, and nearly every plant 
> produces lateral
> > branches which have carpels and stamens mixed together
> > indiscriminantly." Studies of mutants have explored these 
> occurrences
> > and similar occurrences in tassels, corroborating the 
> inherent bisexual
> > nature of the floret meristem prior to the subsequent 
> development of the
> > monoecious condition." (the length of this defn. possibly provides
> > argument for the inclusion of some sort of comment field closely
> > associated with the definition?).
> >
> > I've also been using the Derived/Develops_from relationship 
> in the Zea 
> > ontology. This relationship accommodates the temporal & 
> spatial needs 
> > associated with ontogeny e.g. the development of primordia.
> >
> > You'll note, when browsing the ontology via DAG-Edit, that I still 
> > need to provide definitions for some terms - an ever pressing need.
> >
> > Let me have your candid comments/thoughts.
> >
> > Leszek
> >
> > ===========================
> > 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
> > Yahoo! Messenger: leszekvincent
> > Plant Systematist on the Plant Ontology Consortium
> > Associate Curator, Dunn-Palmer Herbarium (UMO)
> > Research Associate, Missouri Botanical Garden, USA
> > CEO - PhytoSynergy, LLC
> > =======================
> >
> >
> 
> --------------------------------------------------------------
> ---------------
> 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 pj37 at cornell.edu  Mon Oct 13 10:16:34 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 13 Oct 2003 10:16:34 -0400
Subject: POC-dev resolution required !
Message-ID: <3F8AB3C2.8050704@cornell.edu>


Hi Everyone,

Do you think that we should invite some experts other than the core participants 
on our POC-development mailing list. I think if we do so, the POC development 
will benefit a lot and giving us an opportunity to establish a plant_interest_group.

I have the names of Jerry Davis, Dom Paolillo Jr. and Jeff Doyle from Cornell, 
who are willing to join our dev-mailing list. Also we need to set up the 
priorities on what goes on which mailing list. There are three right now..

po at plantontology.org
po-dev at plantontolgy.org
po-announce at plantontology.org

Based on your responses I will list more people depending on their interest.

Thanks
Pankaj





From pj37 at cornell.edu  Mon Oct 13 11:27:59 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 13 Oct 2003 11:27:59 -0400
Subject: First meeting of POC core members 
Message-ID: <3F8AC47F.6010402@cornell.edu>


Hi Everyone,

Can we finalize the first consortium meeting scheduled for PAG. Sue suggested 
for holding it on either 10th or 11th January.

Thanks
Pankaj



From lstein at cshl.edu  Mon Oct 13 12:41:38 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon, 13 Oct 2003 12:41:38 -0400
Subject: First meeting of POC core members
In-Reply-To: <3F8AC47F.6010402@cornell.edu>
References: <3F8AC47F.6010402@cornell.edu>
Message-ID: <200310131241.38055.lstein@cshl.edu>

The 11th January is better for me.

Lincoln

On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
> Hi Everyone,
>
> Can we finalize the first consortium meeting scheduled for PAG. Sue
> suggested for holding it on either 10th or 11th January.
>
> Thanks
> Pankaj

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From lreiser at acoma.Stanford.EDU  Mon Oct 13 13:26:12 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Mon, 13 Oct 2003 10:26:12 -0700 (PDT)
Subject: POC-dev resolution required !
In-Reply-To: <3F8AB3C2.8050704@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310131021410.22498-100000@acoma.Stanford.EDU>

Pankaj
I think that is a great idea. I was also thinking that it might be a good
idea to send letters to the recipients of PGRP grants for this year (and
continuing projects from last year) -and contact groups outside US (like
the Populus people Sue mentioned). We did specify that initial outreach
would be to researchers with functiional genomics projects... e.g. the
apple functional genomics group (also involves people from cornell, right)
What do y'all think of sending a letter asking to see if they want to
join this 'plant interest group'.
Leonore


>
> Hi Everyone,
>
> Do you think that we should invite some experts other than the core participants
> on our POC-development mailing list. I think if we do so, the POC development
> will benefit a lot and giving us an opportunity to establish a plant_interest_group.
>
> I have the names of Jerry Davis, Dom Paolillo Jr. and Jeff Doyle from Cornell,
> who are willing to join our dev-mailing list. Also we need to set up the
> priorities on what goes on which mailing list. There are three right now..
>
> po at plantontology.org
> po-dev at plantontolgy.org
> po-announce at plantontology.org
>
> Based on your responses I will list more people depending on their interest.
>
> Thanks
> Pankaj
>
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From srm4 at cornell.edu  Mon Oct 13 13:45:37 2003
From: srm4 at cornell.edu (Susan McCouch)
Date: Mon, 13 Oct 2003 13:45:37 -0400
Subject: First meeting of POC core members
In-Reply-To: <200310131241.38055.lstein@cshl.edu>
References: <3F8AC47F.6010402@cornell.edu>
 <200310131241.38055.lstein@cshl.edu>
Message-ID: <p0510030dbbb0941fcadd@[128.253.41.150]>

I can do it on the 10th between 10:40 - noon or on the 11th anytime 
except during the rice workshop (noon - 2:40 PM).

Susan



>The 11th January is better for me.
>
>Lincoln
>
>On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
>>  Hi Everyone,
>>
>>  Can we finalize the first consortium meeting scheduled for PAG. Sue
>>  suggested for holding it on either 10th or 11th January.
>>
>>  Thanks
>>  Pankaj
>
>--
>========================================================================
>Lincoln D. Stein                           Cold Spring Harbor Laboratory
>lstein at cshl.org			                  Cold Spring 
>Harbor, NY
>========================================================================


-- 
******************************************
Susan McCouch
Dept of Plant Breeding
162 Emerson Hall
Cornell University
Ithaca, NY  14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu

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


From kellogge at msx.umsl.edu  Tue Oct 14 14:21:22 2003
From: kellogge at msx.umsl.edu (Toby Kellogg)
Date: Tue, 14 Oct 2003 13:21:22 -0500
Subject: A delayed response on "POC observations so far"
In-Reply-To:  <3D4AD7F06881FD42A720D33D8E399DF3010ECC6A@COL-EMAIL4.col.missouri.edu>
Message-ID: <l03130309bbb1ee506bec@[134.124.70.41]>

Hi all -
  this correspondence raises a question - are we trying to get all the
various databases to conform to a single ontology, or are we just trying to
establish some sort of synonymy so that one can move easily among them?
The ontology that Leszek proposes seems quite maize-specific, which is of
course not a problem until the maize database needs to connect with the
rice or Arabidopsis ones.
Toby

>Sue (& possibly others),
>
>The "bottom line" (elevator pitch) is that the Zea mays Plant Structure
>ontology has attempted to represent the biological reality of monoecy
>via incorporating ontogenetic data & reflecting phylogenetic theory &
>satisfies the 'true path rule'- check it out.
>
>- Leszek
>
>> -----Original Message-----
>> From: owner-po-dev at brie4.cshl.org
>> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Sue Rhee
>> Sent: Wednesday, October 08, 2003 4:54 PM
>> To: po-dev at plantontology.org
>> Subject: Re: A delayed response on "POC observations so far"
>>
>>
>> give me the bottom line in three sentences or less.
>>
>> thanks,
>> sue
>>
>> On Wed, 8 Oct 2003, Vincent, Leszek wrote:
>>
>> > Hi POC colleagues,
>> >
>> > Here's some 'bedtime reading'.
>> >
>> > Recently there was discussion about the representation of unisexual
>> > florets in a taxon which bears both functionally male &
>> female florets
>> > in separate flowering structures e.g. adequate representation of
>> > monoecy in taxa such as Zea mays. Furthermore concern was
>> raised about
>> > querying an ontology, involving a monoecious taxon, for the term
>> > gynoecium - that such a search should be able to retrieve
>> > gynoecium-related info. associated with the tassel as well
>> as the ear
>> > as in Zea mays.
>> >
>> > Pankaj & possibly some others may recall that some of us
>> visited this
>> > area sometime last year & the synthesis of that dialogue
>> was recorded
>> > in the current ontology for Zea mays (freely available from
>> > plantontology.org). But to show you an example of the tentative
>> > solution to the challenge I've reproduced a portion of the
>> > representation below:
>> >
>> > organ
>> >   %tassel (functionally male inflorescence)
>> >     <pedicellate spikelet of tassel
>> >       <lower floret of pedicellate spikelet of tassel
>> >         <gynoecial tissue (abortive) of lower floret of pedicellate
>> > spikelet of tassel
>> >         <lodicules of lower floret of ....
>> >         <palea of lower floret of .....
>> >         <stamens of lower floret of ....
>> >       <lower glume of pedicellate spikelet of tassel
>> >       <upper glume of .....
>> >     <sessile spikelet of tassel
>> >       etc.
>> >   %lateral branch
>> >     <ear (functionally female inflorescence)
>> >       <pedicellate spikelet of ear
>> > etc....
>> >
>> > Yes, it is a little complex (view it via DAG-Edit for a clearer
>> > representation than that provided here) but it is my/our
>> best attempt
>> > yet at capturing the biological complexity such that the true path
>> > rule is met for this biological reality in Zea mays.
>> Furthermore, it
>> > should satisfy the query needs referred to above. Of course
>> there may
>> > be other considerations that have since transpired...
>> >
>> > For me, as a botanist & plant systematist, I think it is a good
>> > solution because it captures the ontogenetic detail for these
>> > structures and it is also consistent with phylogenetic argument
>> > concerning these structures - and consequently should be
>> applicable to
>> > taxa, other than Zea, where monoecy & dioecy is found.
>> >
>> > It is true that some folk may not (at first) appreciate the
>> biological
>> > relevance of including both the androecium & gynoecium in both the
>> > tassel & ear. My attempt to cover that 'base' is provided in the
>> > definition for "floret". In this definition I spell out the
>> > ontogenetic reality of both the androecium & gynoecium
>> being initially
>> > present in both the tassel & ear florets - hence their need to be
>> > included in both the tassel & lateral branch/ear nodes. It
>> also draws
>> > attention to the putative phylogenetic necessity for such a
>> > representation. Implicitly what I'm practicing is that
>> ontogenetic &
>> > phylogenetic information are both extremely important for
>> inclusion in
>> > the application of the 'true path rule'.
>> >
>> > Here's the definition for floret (yes, it is detailed):
>> > "The floret is the individual flower of the Zea mays plant. In the
>> > grass family (Poaceae, alt. Gramineae) each floret is typically
>> > bisexual (perfect), possessing both an androecium and a gynoecium.
>> > Each floret typically has a pair of bracts, the lemma and
>> palea, which
>> > subtend the floret. It is important to note that In Zea mays the
>> > florets of the 'tassel' are functionally male (the female component
>> > (gynoecium) having aborted early on in development). The florets of
>> > the 'ear' are functionally female (the male components (androecium)
>> > having aborted early on in development). The possession of
>> > functionally male and functionally female florets (or
>> flowers) on the
>> > same plant is a condition called monoecy. While Zea mays is
>> > functionally monoecious, the presence of both androecial
>> and gynoecial
>> > tissue in the early stages of floret ontogeny is phylogenetically
>> > significant. Consequently, the androecium is represented in the
>> > florets of the ear and the gynoecium is represented in the
>> florets of
>> > the tassel, even though either of these whorls is absent in the
>> > functional florets. The inclusion of both whorls in the floret
>> > ontology for the florets of ears and spikelets is based on this
>> > phylogenetically significant ontogeny. East and Hayes (1911, p.
>> > 134-135) provided the following: "Perhaps it should be mentioned in
>> > passing that the immature sex organs, so called, of maize
>> seem endowed
>> > with the power of becoming either stamens or carpels. One
>> often finds a
>> > normal ear ending in stamens, and nearly every plant
>> produces lateral
>> > branches which have carpels and stamens mixed together
>> > indiscriminantly." Studies of mutants have explored these
>> occurrences
>> > and similar occurrences in tassels, corroborating the
>> inherent bisexual
>> > nature of the floret meristem prior to the subsequent
>> development of the
>> > monoecious condition." (the length of this defn. possibly provides
>> > argument for the inclusion of some sort of comment field closely
>> > associated with the definition?).
>> >
>> > I've also been using the Derived/Develops_from relationship
>> in the Zea
>> > ontology. This relationship accommodates the temporal &
>> spatial needs
>> > associated with ontogeny e.g. the development of primordia.
>> >
>> > You'll note, when browsing the ontology via DAG-Edit, that I still
>> > need to provide definitions for some terms - an ever pressing need.
>> >
>> > Let me have your candid comments/thoughts.
>> >
>> > Leszek
>> >
>> > ===========================
>> > 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
>> > Yahoo! Messenger: leszekvincent
>> > Plant Systematist on the Plant Ontology Consortium
>> > Associate Curator, Dunn-Palmer Herbarium (UMO)
>> > Research Associate, Missouri Botanical Garden, USA
>> > CEO - PhytoSynergy, LLC
>> > =======================
>> >
>> >
>>
>> --------------------------------------------------------------
>> ---------------
>> 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.
>> --------------------------------------------------------------
>> ---------------
>>
>>


Elizabeth A. Kellogg
Department of Biology
University of Missouri-St. Louis
8001 Natural Bridge Road
St. Louis, MO 63121
phone: 314-516-6217
fax: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/




From pj37 at cornell.edu  Tue Oct 14 14:51:16 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 14 Oct 2003 14:51:16 -0400
Subject: A delayed response on "POC observations so far"
In-Reply-To: <l03130309bbb1ee506bec@[134.124.70.41]>
References: <l03130309bbb1ee506bec@[134.124.70.41]>
Message-ID: <3F8C45A4.10404@cornell.edu>

Hi,

Our goal is to be as generic as possible and have a single ontology. No synonymy 
in different ontology sets. If a particular node requires a species specific 
string, then it can be created within the same Ontology tree by effectively 
using the "sensu" rule. Atleast that is what we are going to have in POC and 
encourage others to use it.

Best
Pankaj

Toby Kellogg wrote:

> Hi all -
>   this correspondence raises a question - are we trying to get all the
> various databases to conform to a single ontology, or are we just trying to
> establish some sort of synonymy so that one can move easily among them?
> The ontology that Leszek proposes seems quite maize-specific, which is of
> course not a problem until the maize database needs to connect with the
> rice or Arabidopsis ones.
> Toby
> 
> 
>>Sue (& possibly others),
>>
>>The "bottom line" (elevator pitch) is that the Zea mays Plant Structure
>>ontology has attempted to represent the biological reality of monoecy
>>via incorporating ontogenetic data & reflecting phylogenetic theory &
>>satisfies the 'true path rule'- check it out.
>>
>>- Leszek
>>
>>
>>>-----Original Message-----
>>>From: owner-po-dev at brie4.cshl.org
>>>[mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Sue Rhee
>>>Sent: Wednesday, October 08, 2003 4:54 PM
>>>To: po-dev at plantontology.org
>>>Subject: Re: A delayed response on "POC observations so far"
>>>
>>>
>>>give me the bottom line in three sentences or less.
>>>
>>>thanks,
>>>sue
>>>
>>>On Wed, 8 Oct 2003, Vincent, Leszek wrote:
>>>
>>>
>>>>Hi POC colleagues,
>>>>
>>>>Here's some 'bedtime reading'.
>>>>
>>>>Recently there was discussion about the representation of unisexual
>>>>florets in a taxon which bears both functionally male &
>>>
>>>female florets
>>>
>>>>in separate flowering structures e.g. adequate representation of
>>>>monoecy in taxa such as Zea mays. Furthermore concern was
>>>
>>>raised about
>>>
>>>>querying an ontology, involving a monoecious taxon, for the term
>>>>gynoecium - that such a search should be able to retrieve
>>>>gynoecium-related info. associated with the tassel as well
>>>
>>>as the ear
>>>
>>>>as in Zea mays.
>>>>
>>>>Pankaj & possibly some others may recall that some of us
>>>
>>>visited this
>>>
>>>>area sometime last year & the synthesis of that dialogue
>>>
>>>was recorded
>>>
>>>>in the current ontology for Zea mays (freely available from
>>>>plantontology.org). But to show you an example of the tentative
>>>>solution to the challenge I've reproduced a portion of the
>>>>representation below:
>>>>
>>>>organ
>>>>  %tassel (functionally male inflorescence)
>>>>    <pedicellate spikelet of tassel
>>>>      <lower floret of pedicellate spikelet of tassel
>>>>        <gynoecial tissue (abortive) of lower floret of pedicellate
>>>>spikelet of tassel
>>>>        <lodicules of lower floret of ....
>>>>        <palea of lower floret of .....
>>>>        <stamens of lower floret of ....
>>>>      <lower glume of pedicellate spikelet of tassel
>>>>      <upper glume of .....
>>>>    <sessile spikelet of tassel
>>>>      etc.
>>>>  %lateral branch
>>>>    <ear (functionally female inflorescence)
>>>>      <pedicellate spikelet of ear
>>>>etc....
>>>>
>>>>Yes, it is a little complex (view it via DAG-Edit for a clearer
>>>>representation than that provided here) but it is my/our
>>>
>>>best attempt
>>>
>>>>yet at capturing the biological complexity such that the true path
>>>>rule is met for this biological reality in Zea mays.
>>>
>>>Furthermore, it
>>>
>>>>should satisfy the query needs referred to above. Of course
>>>
>>>there may
>>>
>>>>be other considerations that have since transpired...
>>>>
>>>>For me, as a botanist & plant systematist, I think it is a good
>>>>solution because it captures the ontogenetic detail for these
>>>>structures and it is also consistent with phylogenetic argument
>>>>concerning these structures - and consequently should be
>>>
>>>applicable to
>>>
>>>>taxa, other than Zea, where monoecy & dioecy is found.
>>>>
>>>>It is true that some folk may not (at first) appreciate the
>>>
>>>biological
>>>
>>>>relevance of including both the androecium & gynoecium in both the
>>>>tassel & ear. My attempt to cover that 'base' is provided in the
>>>>definition for "floret". In this definition I spell out the
>>>>ontogenetic reality of both the androecium & gynoecium
>>>
>>>being initially
>>>
>>>>present in both the tassel & ear florets - hence their need to be
>>>>included in both the tassel & lateral branch/ear nodes. It
>>>
>>>also draws
>>>
>>>>attention to the putative phylogenetic necessity for such a
>>>>representation. Implicitly what I'm practicing is that
>>>
>>>ontogenetic &
>>>
>>>>phylogenetic information are both extremely important for
>>>
>>>inclusion in
>>>
>>>>the application of the 'true path rule'.
>>>>
>>>>Here's the definition for floret (yes, it is detailed):
>>>>"The floret is the individual flower of the Zea mays plant. In the
>>>>grass family (Poaceae, alt. Gramineae) each floret is typically
>>>>bisexual (perfect), possessing both an androecium and a gynoecium.
>>>>Each floret typically has a pair of bracts, the lemma and
>>>
>>>palea, which
>>>
>>>>subtend the floret. It is important to note that In Zea mays the
>>>>florets of the 'tassel' are functionally male (the female component
>>>>(gynoecium) having aborted early on in development). The florets of
>>>>the 'ear' are functionally female (the male components (androecium)
>>>>having aborted early on in development). The possession of
>>>>functionally male and functionally female florets (or
>>>
>>>flowers) on the
>>>
>>>>same plant is a condition called monoecy. While Zea mays is
>>>>functionally monoecious, the presence of both androecial
>>>
>>>and gynoecial
>>>
>>>>tissue in the early stages of floret ontogeny is phylogenetically
>>>>significant. Consequently, the androecium is represented in the
>>>>florets of the ear and the gynoecium is represented in the
>>>
>>>florets of
>>>
>>>>the tassel, even though either of these whorls is absent in the
>>>>functional florets. The inclusion of both whorls in the floret
>>>>ontology for the florets of ears and spikelets is based on this
>>>>phylogenetically significant ontogeny. East and Hayes (1911, p.
>>>>134-135) provided the following: "Perhaps it should be mentioned in
>>>>passing that the immature sex organs, so called, of maize
>>>
>>>seem endowed
>>>
>>>>with the power of becoming either stamens or carpels. One
>>>
>>>often finds a
>>>
>>>>normal ear ending in stamens, and nearly every plant
>>>
>>>produces lateral
>>>
>>>>branches which have carpels and stamens mixed together
>>>>indiscriminantly." Studies of mutants have explored these
>>>
>>>occurrences
>>>
>>>>and similar occurrences in tassels, corroborating the
>>>
>>>inherent bisexual
>>>
>>>>nature of the floret meristem prior to the subsequent
>>>
>>>development of the
>>>
>>>>monoecious condition." (the length of this defn. possibly provides
>>>>argument for the inclusion of some sort of comment field closely
>>>>associated with the definition?).
>>>>
>>>>I've also been using the Derived/Develops_from relationship
>>>
>>>in the Zea
>>>
>>>>ontology. This relationship accommodates the temporal &
>>>
>>>spatial needs
>>>
>>>>associated with ontogeny e.g. the development of primordia.
>>>>
>>>>You'll note, when browsing the ontology via DAG-Edit, that I still
>>>>need to provide definitions for some terms - an ever pressing need.
>>>>
>>>>Let me have your candid comments/thoughts.
>>>>
>>>>Leszek
>>>>
>>>>===========================
>>>>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
>>>>Yahoo! Messenger: leszekvincent
>>>>Plant Systematist on the Plant Ontology Consortium
>>>>Associate Curator, Dunn-Palmer Herbarium (UMO)
>>>>Research Associate, Missouri Botanical Garden, USA
>>>>CEO - PhytoSynergy, LLC
>>>>=======================
>>>>
>>>>
>>>
>>>--------------------------------------------------------------
>>>---------------
>>>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.
>>>--------------------------------------------------------------
>>>---------------
>>>
>>>
> 
> 
> 
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
> 
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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  Tue Oct 14 15:21:06 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 14 Oct 2003 15:21:06 -0400
Subject: Question on part of seedling
Message-ID: <3F8C4CA2.6040603@cornell.edu>


Hi

Can somebody help me in identifying what is this term "crown" stands for in 
barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm

Thanks

Pankaj



From Leszek at missouri.edu  Tue Oct 14 16:25:07 2003
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Tue, 14 Oct 2003 15:25:07 -0500
Subject: Question on part of seedling
Message-ID: <3D4AD7F06881FD42A720D33D8E399DF3010ECC72@COL-EMAIL4.col.missouri.edu>

Hi Pankaj,

This is one of those terms with a very variable definition - the
definition being dependent upon the taxon & context in which it is used.
For example the term "crown" is described as "The persistent base of a
herbaceous perennial" or "the top part of a tree"; or A synonym for the
"corona" (crown) of some flower structures (fide/according to Harris &
Harris); or "of the root, the point where root and stem meet" (fide
Jackson). 

In my ontology for Zea the terms "crown roots" & "subterranean crown
roots" are used - the term "crown" being used for the basal portion of
the growing stem/culm.

Below I've provided copy of the defns. for the terms "subterranean crown
roots" & "crown roots" which further demo. the context-specific use of
"crown" - you can skip the detail in these defns. - although it's
provided for context/illustration of use:

"subterranean crown roots": The subterranean crown roots are a component
of the adventitious root system. They are termed crown roots because
they originate from the basal portion of the growing stem/culm known as
the crown. The first subterranean crown roots (4-5), arranged in a
whorl, appear at the base of the second internode about as soon as the
tip of the coleoptile reaches the soil surface. A few of the subsequent
higher internodes may have a similar number of crown roots (in whorls),
after which the successive internodes have more and larger crown roots
up to 2-3 internodes above the soil surface. Note that the crown roots
above the soil surface (aerial) are frequently called 'brace' or 'prop'
roots. The crown roots emerge from the extreme base of the internode.
The subterranean crown roots produce numerous lateral adventitious roots
(see 'root branches')  early in their development. The crown roots
arising from internodes 2 to approximately 5 tend to grow horizontally
for some distance before turning downward. The crown roots from the base
of the higher internodes (appearing later in the growing season) grow
downward immediately after initiation.

"crown roots": There are two spatial components of the adventitious root
system. 1. A subterranean (below-ground) origin; 2. An aerial
(above-ground) origin. The subterranean adventitious roots are
frequently called crown roots because they originate from the basal
portion of the growing stem known as the crown. The first crown roots
(4-5), arranged in a whorl, appear at the base of the second internode
about as soon as the tip of the coleoptile reaches the soil surface. A
few of the subsequent higher internodes may have a similar number of
crown roots (in whorls), after which the successive internodes have more
and larger crown roots up to 2-3 internodes above the soil surface. Note
that the crown roots of the adventitious root system may appear to arise
from the nodes of the culm but careful inspection will reveal their
origin from the very base of the internode, frequently disrupting the
leaf sheath tissue that arises from the node immediately below the whorl
of crown roots. Those crown roots which are initially aerial in position
relative to the soil surface are termed 'brace' or 'prop' roots. Until
each prop root reaches the soil, it remains unbranched and relatively
rigid, and is usually covered by a mucilaginous substance that protects
the aerial part of the root from drying (desiccation). Note that once
the brace / prop roots enter the soil they produce numerous lateral
adventitious roots (see 'root branches'). The subterranean crown roots
produce numerous lateral adventitious roots early in their development.
The crown roots arising from internodes 2 to approximately 5 tend to
grow horizontally for some distance before turning downward. The crown
roots from the base of the higher internodes (appearing later in the
growing season) grow downward immediately after initiation.

- Leszek
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 215 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
Yahoo! Messenger: leszekvincent
Plant Systematist on The Plant Ontology Consortium - NSF award 0321666
Associate Curator, Dunn-Palmer Herbarium (UMO)
Research Associate, Missouri Botanical Garden (MO), USA
CEO - PhytoSynergy, LLC
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Pankaj Jaiswal
> Sent: Tuesday, October 14, 2003 2:21 PM
> To: POC-dev
> Subject: Question on part of seedling
> 
> 
> 
> Hi
> 
> Can somebody help me in identifying what is this term "crown" 
> stands for in 
> barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm
> 
> Thanks
> 
> Pankaj
> 
> 



From pj37 at cornell.edu  Tue Oct 14 17:39:17 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 14 Oct 2003 17:39:17 -0400
Subject: Question on part of seedling
In-Reply-To: <Pine.GSO.4.44.0310141316230.17395-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310141316230.17395-100000@acoma.Stanford.EDU>
Message-ID: <3F8C6D05.2080805@cornell.edu>

Hi Everyone,

Thank you for your responses. Here are some of the definitions I found in the 
literature.


CROWN -

1
part of the wheat/barley plant located about 0.5 inches below the soil surface. 
The crown is where the nodes are tightly packed together, tiller buds develop, 
and coronal root buds develop.

2
Located between the coleoptile and the mesocotyl, the crown contains the growing 
point where the rest of the plant will begin to form and the nodes where the 
nodal or permanent roots will form.

I think we might have to create new term "germinating/juvenile seedling" as an 
instance of "vegetative shoot", in order to introduce "crown" as part of it.

Any suggestions ?

Pankaj


Leonore Reiser wrote:

> Hmm_ I did find:
> 
> 
> on this page:http://www.hcs.ohio-state.edu/hcs200/Stems.html
> 
> 
> Tillers?  are secondary stems that arise from nodes       at the base of
> the main stem, and are almost vertical in position.?        The crown of a
> plant is a group of modified stems with       very short internodes that
> occur very close to the soil surface.       It usually functions as a site
> for food storage and new growth       in perennial species. Most forage
> grasses, and some forage legumes       (alfalfa and clovers)?  have a
> crown.? 
> 
> 
> But doesnt quite sound like what is described in the url you sent.
> 
> Actually there are some interesting pages on this website (e.g. soybean
> growth stage information).
> Leonore
> 
> 
> On Tue, 14 Oct 2003, Pankaj Jaiswal wrote:
> 
> 
>>Hi
>>
>>Can somebody help me in identifying what is this term "crown" stands for in
>>barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm
>>
>>Thanks
>>
>>Pankaj
>>
>>
> 
> 
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 peter.stevens at mobot.org  Tue Oct 14 16:21:57 2003
From: peter.stevens at mobot.org (Peter Stevens)
Date: Tue, 14 Oct 2003 16:21:57 -0400
Subject: Question on part of seedling
In-Reply-To: <3F8C6D05.2080805@cornell.edu>
References: <Pine.GSO.4.44.0310141316230.17395-100000@acoma.Stanford.EDU>
 <3F8C6D05.2080805@cornell.edu>
Message-ID: <f0433010bbbb20ab826cb@[172.16.18.1]>

>There will be a number of other terms that refer to this part of the 
>plant - like mesocotyl itself (along with hypocotyl, etc.).  Or one 
>may have to include "embryo" as part of this new term, since the 
>mesocotyl (f.i.) is visible there.


P.



>Hi Everyone,
>
>Thank you for your responses. Here are some of the definitions I 
>found in the literature.
>
>
>CROWN -
>
>1
>part of the wheat/barley plant located about 0.5 inches below the 
>soil surface. The crown is where the nodes are tightly packed 
>together, tiller buds develop, and coronal root buds develop.
>
>2
>Located between the coleoptile and the mesocotyl, the crown contains 
>the growing point where the rest of the plant will begin to form and 
>the nodes where the nodal or permanent roots will form.
>
>I think we might have to create new term "germinating/juvenile 
>seedling" as an instance of "vegetative shoot", in order to 
>introduce "crown" as part of it.
>
>Any suggestions ?
>
>Pankaj
>
>
>Leonore Reiser wrote:
>
>>Hmm_ I did find:
>>
>>
>>on this page:http://www.hcs.ohio-state.edu/hcs200/Stems.html
>>
>>
>>Tillers?  are secondary stems that arise from nodes       at the base of
>>the main stem, and are almost vertical in position.?        The crown of a
>>plant is a group of modified stems with       very short internodes that
>>occur very close to the soil surface.       It usually functions as a site
>>for food storage and new growth       in perennial species. Most forage
>>grasses, and some forage legumes       (alfalfa and clovers)?  have a
>>crown.?
>>
>>But doesnt quite sound like what is described in the url you sent.
>>
>>Actually there are some interesting pages on this website (e.g. soybean
>>growth stage information).
>>Leonore
>>
>>
>>On Tue, 14 Oct 2003, Pankaj Jaiswal wrote:
>>
>>>Hi
>>>
>>>Can somebody help me in identifying what is this term "crown" stands for in
>>>barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm
>>>
>>>Thanks
>>>
>>>Pankaj
>>>
>>
>>
>>-------------------------------------------------------------------------------
>>Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>>The Arabidopsis Information Resource	FAX: (650) 325-6857
>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>>Department of Plant Biology		URL: http://arabidopsis.org/
>>260 Panama St.
>>Stanford, CA 94305
>>-------------------------------------------------------------------------------
>>
>
>--
>******************************************
>Pankaj Jaiswal, Ph.D.
>Research 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  Tue Oct 14 19:41:39 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 14 Oct 2003 19:41:39 -0400
Subject: Question on part of seedling
In-Reply-To: <f0433010bbbb20ab826cb@[172.16.18.1]>
References: <Pine.GSO.4.44.0310141316230.17395-100000@acoma.Stanford.EDU> <3F8C6D05.2080805@cornell.edu> <f0433010bbbb20ab826cb@[172.16.18.1]>
Message-ID: <3F8C89B3.8040609@cornell.edu>

Right ! Most of the other terms are there under seed/embryo. I will need to pull 
the appropriate ones and give them another parent  "germinating/juvenile  seedling".

Thanks
Pankaj


Peter Stevens wrote:
>> There will be a number of other terms that refer to this part of the 
>> plant - like mesocotyl itself (along with hypocotyl, etc.).  Or one 
>> may have to include "embryo" as part of this new term, since the 
>> mesocotyl (f.i.) is visible there.
> 
> 
> 
> P.
> 
> 
> 
>> Hi Everyone,
>>
>> Thank you for your responses. Here are some of the definitions I found 
>> in the literature.
>>
>>
>> CROWN -
>>
>> 1
>> part of the wheat/barley plant located about 0.5 inches below the soil 
>> surface. The crown is where the nodes are tightly packed together, 
>> tiller buds develop, and coronal root buds develop.
>>
>> 2
>> Located between the coleoptile and the mesocotyl, the crown contains 
>> the growing point where the rest of the plant will begin to form and 
>> the nodes where the nodal or permanent roots will form.
>>
>> I think we might have to create new term "germinating/juvenile 
>> seedling" as an instance of "vegetative shoot", in order to introduce 
>> "crown" as part of it.
>>
>> Any suggestions ?
>>
>> Pankaj
>>
>>
>> Leonore Reiser wrote:
>>
>>> Hmm_ I did find:
>>>
>>>
>>> on this page:http://www.hcs.ohio-state.edu/hcs200/Stems.html
>>>
>>>
>>> Tillers?  are secondary stems that arise from nodes       at the base of
>>> the main stem, and are almost vertical in position.?        The crown 
>>> of a
>>> plant is a group of modified stems with       very short internodes that
>>> occur very close to the soil surface.       It usually functions as a 
>>> site
>>> for food storage and new growth       in perennial species. Most forage
>>> grasses, and some forage legumes       (alfalfa and clovers)?  have a
>>> crown.?
>>>
>>> But doesnt quite sound like what is described in the url you sent.
>>>
>>> Actually there are some interesting pages on this website (e.g. soybean
>>> growth stage information).
>>> Leonore
>>>
>>>
>>> On Tue, 14 Oct 2003, Pankaj Jaiswal wrote:
>>>
>>>> Hi
>>>>
>>>> Can somebody help me in identifying what is this term "crown" stands 
>>>> for in
>>>> barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm
>>>>
>>>> Thanks
>>>>
>>>> Pankaj
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------- 
>>>
>>> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>>> The Arabidopsis Information Resource    FAX: (650) 325-6857
>>> Carnegie Institution of Washington    Tel: (650) 325-1521 ext. 311
>>> Department of Plant Biology        URL: http://arabidopsis.org/
>>> 260 Panama St.
>>> Stanford, CA 94305
>>> ------------------------------------------------------------------------------- 
>>>
>>>
>>
>> -- 
>> ******************************************
>> Pankaj Jaiswal, Ph.D.
>> Research 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.
Research 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 Oct 15 12:21:52 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 15 Oct 2003 12:21:52 -0400
Subject: Question on part of seedling
In-Reply-To: <p06002025bbb22f32a49e@[130.126.89.70]>
References: <Pine.GSO.4.44.0310141316230.17395-100000@acoma.Stanford.EDU> <3F8C6D05.2080805@cornell.edu> <p06002024bbb22af2a598@[130.126.89.70]> <p06002025bbb22f32a49e@[130.126.89.70]>
Message-ID: <3F8D7420.3050403@cornell.edu>

Dear Marty,

Thank you for looking into the maize perspective. By going through the 
references, it seems to be a pretty generic term atleast for the cereals. I will 
work with Felipe on introducing the possible ontology structures.

Pankaj

Marty Sachs wrote:

> OK, I guess the term is used in maize in same sense also:
> 
> http://www.ipm.iastate.edu/ipm/icm/1996/7-1-1996/corncrownrot.html
> 
> The general defination is: Several nodes whose internodes do not elongate
> 
> The crown is comprised of connective tissue which joins the root and 
> shoot. It develops at the base of the coleoptile during seedling 
> development. The crown produces buds that are the source of shoots 
> (tillers), adventitious roots, rhizomes, and stolons. Crowns also serve 
> as storage organs for carbohydrate reserves to support the growth of new 
> plant organs.
> 
> http://forages.orst.edu/projects/regrowth/print-section.cfm?title=Developmental%20Phases
> 
>         -Marty
> 
> At 5:43 PM -0500 10/14/03, Marty Sachs wrote:
> 
>> I've never seen 'crown' used in maize as you're describing its use in 
>> barley.
> 
>>
>> In maize, 'crown' has a very different meaning.  It most frequently 
>> refers to the top of the kernel.
> 
>>
>> E.g.,
> 
>>
>> From: http://www.hort.purdue.edu/newcrop/Crops/Corn.html
> 
>>
>> Dent corn, when fully ripe, has a pronounced depression or dent at the 
>> crown of the kernels. The kernels contain a hard form of starch at the 
>> sides and a soft type in the center. This latter starch shrinks as the 
>> kernel ripens resulting in the terminal depression. Dent varieties 
>> vary in kernel shape from long and narrow to wide and shallow. It is 
>> the type mainly grown in this country.
> 
>>
>> From: http://www.pcs-chromex.com/popcorn/aboutus.html
> 
>>
>> Pearls and Rice - 'Rice' are long kernels with a pointed crown and 
>> 'Pearls' have round crowns and are short and thick.
> 
>>
>>         -Marty Sachs
> 
>>
>> At 5:39 PM -0400 10/14/03, Pankaj Jaiswal wrote:
>>
>>> Hi Everyone,
>>>
>>> Thank you for your responses. Here are some of the definitions I 
>>> found in the literature.
>>>
>>>
>>> CROWN -
>>>
>>> 1
>>> part of the wheat/barley plant located about 0.5 inches below the 
>>> soil surface. The crown is where the nodes are tightly packed 
>>> together, tiller buds develop, and coronal root buds develop.
>>>
>>> 2
>>> Located between the coleoptile and the mesocotyl, the crown contains 
>>> the growing point where the rest of the plant will begin to form and 
>>> the nodes where the nodal or permanent roots will form.
>>>
>>> I think we might have to create new term "germinating/juvenile 
>>> seedling" as an instance of "vegetative shoot", in order to introduce 
>>> "crown" as part of it.
>>>
>>> Any suggestions ?
>>>
>>> Pankaj
>>>
>>>
>>> Leonore Reiser wrote:
>>>
>>>> Hmm_ I did find:
>>>
>>>> on this page:http://www.hcs.ohio-state.edu/hcs200/Stems.html
>>>>
>>>>
>>>> Tillers?  are secondary stems that arise from nodes       at the base of
>>>> the main stem, and are almost vertical in position.?        The 
>>>> crown of a
>>>> plant is a group of modified stems with       very short internodes that
>>>> occur very close to the soil surface.       It usually functions as 
>>>> a site
>>>> for food storage and new growth       in perennial species. Most forage
>>>> grasses, and some forage legumes       (alfalfa and clovers)?  have a
>>>> crown.?
>>>>
>>>> But doesnt quite sound like what is described in the url you sent.
>>>>
>>>> Actually there are some interesting pages on this website (e.g. soybean
>>>> growth stage information).
>>>> Leonore
>>>>
>>>>
>>>> On Tue, 14 Oct 2003, Pankaj Jaiswal wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> Can somebody help me in identifying what is this term "crown" 
>>>>> stands for in
>>>>
>>>>> barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm
>>>>>
>>>>> Thanks
>>>>>
>>>>> Pankaj




From pj37 at cornell.edu  Wed Oct 15 14:18:02 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 15 Oct 2003 14:18:02 -0400
Subject: [Fwd: Re: Question on part of seedling]
Message-ID: <3F8D8F5A.7060603@cornell.edu>

This is a forwarded message. It message was not sent to po-dev list.
Sorry about that.

Pankaj

-------- Original Message --------
From: Leonore Reiser <lreiser at acoma.Stanford.EDU>
Subject: Re: Question on part of seedling
To: Pankaj Jaiswal <pj37 at cornell.edu>


Hmm_ I did find:


on this page:http://www.hcs.ohio-state.edu/hcs200/Stems.html


Tillers?  are secondary stems that arise from nodes       at the base of
the main stem, and are almost vertical in position.?        The crown of a
plant is a group of modified stems with       very short internodes that
occur very close to the soil surface.       It usually functions as a site
for food storage and new growth       in perennial species. Most forage
grasses, and some forage legumes       (alfalfa and clovers)?  have a
crown.? 


But doesnt quite sound like what is described in the url you sent.

Actually there are some interesting pages on this website (e.g. soybean
growth stage information).
Leonore


On Tue, 14 Oct 2003, Pankaj Jaiswal wrote:

>
> Hi
>
> Can somebody help me in identifying what is this term "crown" stands for in
> barley, described at http://bioinf.scri.sari.ac.uk/affy/mx-crown.htm
>
> Thanks
>
> Pankaj
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------






From pj37 at cornell.edu  Wed Oct 15 14:34:29 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 15 Oct 2003 14:34:29 -0400
Subject: files on CVS
Message-ID: <3F8D9335.7070904@cornell.edu>


Hi Everyone,

I think we should try to be consistent in the file locations on CVS and flat 
file format. Therefore, Leszek, would you mind putting the maize ontology files 
under respective directories on CVS.

Poc/anatomy/ --->for anatomy ontology
Poc/definitions/--->for definitions

Right now they are under Poc/Zea_mays/.

Also try converting the flat file format similar to TAIR & Gramene.

This will help the developers and any potential users in the long run. Also can 
everyone point me to the most relevant files from their projects.  I will be 
cleaning up the CVS directories next week.

For the webview of CVS go to http://gorgonzola.cshl.org/viewcvs/Poc/

Thanks
Pankaj



From lreiser at acoma.Stanford.EDU  Wed Oct 15 15:05:13 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Wed, 15 Oct 2003 12:05:13 -0700 (PDT)
Subject: files on CVS
In-Reply-To: <3F8D9335.7070904@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310151202370.2122-100000@acoma.Stanford.EDU>


Pankaj
I think there are some remnant ontology files from TAIR that are in the
parent CVS repository- they can be removed:
anatomy_defs.tair
anatomy.tair
temporal_defs.tair

the ones in the subdirectories are the current versions.
-I'd maybe leave the poc2 files at least for a little while (they
represent some early attempt at intergration).Or at least they could be
archived some place.
Leonore

On Wed, 15 Oct 2003, Pankaj Jaiswal wrote:

>
> Hi Everyone,
>
> I think we should try to be consistent in the file locations on CVS and flat
> file format. Therefore, Leszek, would you mind putting the maize ontology files
> under respective directories on CVS.
>
> Poc/anatomy/ --->for anatomy ontology
> Poc/definitions/--->for definitions
>
> Right now they are under Poc/Zea_mays/.
>
> Also try converting the flat file format similar to TAIR & Gramene.
>
> This will help the developers and any potential users in the long run. Also can
> everyone point me to the most relevant files from their projects.  I will be
> cleaning up the CVS directories next week.
>
> For the webview of CVS go to http://gorgonzola.cshl.org/viewcvs/Poc/
>
> Thanks
> Pankaj
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From lreiser at acoma.Stanford.EDU  Thu Oct 16 09:54:44 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Thu, 16 Oct 2003 06:54:44 -0700 (PDT)
Subject: plant ontology, cooperation?
In-Reply-To: <D7D87C2E22166045999C9FB3DC656B290C7E76@scomp0017>
Message-ID: <Pine.GSO.4.44.0310160616520.24739-100000@acoma.Stanford.EDU>

Dear Paulien:

This is wonderful. TAIR is part of a recently funded project to develop
plant ontologies called the "Plant Ontology Consortium". The goals of this
project are exactly what you describe.

The project website is http://www.plantontology.org/. So far most of the
ontology development has been done by Gramene (rice), TAIR and Maize DB.
The website describes the project and how to access the ontologies. We are
using the DAGeditor and ontology representation developed by the GO
(directed, acyclic graphs). The plan is to make the ontologies as broadly
applicable as we can to accomodate as many organisms as possible. The
ontologies can be accessed without restriction and the GO has made the
DAGeditor freely available. We are using the CVS repository as a
shared development resource and communicating over email primarily for
development.

It would be fantastic to work with your group to develop the structure and
content of the ontologies.We were planning to have a users meeting in
January, following the PAG meeting in San Diego-will people from your
organization be attending?

I am ccing this email to the group.We have just hired a coordinator (your counterpart here)  who will
be starting soon. She will be based at TAIR but will coordinate the efforts
for the whole group-in the meantime, I am very happy to work with you.
Best Regards
Leonore Reiser



On Thu, 16 Oct 2003, Adamse, Paulien wrote:

> Dear Mrs. Reiser,
>
> I hope you are the right person to write to about this, but I will give it a try. If I should contact somebody else, please let me know.
>
> I am writing on behalf of seven partner labs in Europe, working together to establish a network of plant databases. The project is called PlaNet (at the moment the address is http://mips.gsf.de/proj/planet/). The 7 partners all have databases with information about Arabidopsis (and sometimes other plants). Some are working on prediction-tools, others have collections of mutantlines (or germplasm or accessions, etc.). The goal is to connect them all and build one general access to it, using BioMoby. People will be able to query through this site and do not have to worry about in which database they have to look for their information.
>
> To be able to query multiple databases with one type of question it is very important to standardize the available information as much as possible. One important aspect in this is the description of the mutants. We set up a working group to compare the different ontologies/vocabularies already used by the different partners. I am the coordinator of this group. In Wageningen I am in the process of building a database for our mutants (WAtDB, not online yet), but we already have a wealth of information about mutants, transgenics and natural variants. But no standard terminology (yet) for describing them.
>
> This is where my request to you is coming in. We have a lot of phenotype descriptions and already noticed that not everything has been covered by the TAIR vocabulary. One way to solve that is to send you numerous submissions/update requests. But we thought that it might be more useful to work together more structural. Are you interested in cooperation with our group? If so, what would be a good way to do this? In November our PO working group is meeting again here in Wageningen and I would like to discuss it with them during that meeting. But it would be very useful to know what you think about it and maybe already get some suggestions about how we could work together.
>
> I hope you are interested and have time to reply within a few weeks. That way I can use your information when I am preparing our coming EU PlaNet PO working group meeting.
>
> Thanks in advance!
>
> Best wishes,
> Paulien
>
>
> Dr Paulien Adamse
> BU Bioscience
> Plant Research International,
> P.O. Box 16,
> 6700 AA Wageningen,
> The Netherlands.
>
> Tel: +31 317 477001/476830
> FAX: +31 317 418094
> paulien.adamse at wur.nl
> www.plant.wageningen-ur.nl
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------






From lstein at cshl.edu  Thu Oct 16 10:23:23 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu, 16 Oct 2003 10:23:23 -0400
Subject: plant ontology, cooperation?
In-Reply-To: <Pine.GSO.4.44.0310160616520.24739-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310160616520.24739-100000@acoma.Stanford.EDU>
Message-ID: <200310161023.23621.lstein@cshl.edu>

Hello Paulien,

As PI of the POC project, I would like to personally express my enthusiasm for 
building a collaboration with your group to develop plant-wide ontologies to 
describe plant anatomy and developmental stages.  It would be very good for 
our groups to meet at the San Diego users' meeting.

Lincoln

On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> Dear Paulien:
>
> This is wonderful. TAIR is part of a recently funded project to develop
> plant ontologies called the "Plant Ontology Consortium". The goals of this
> project are exactly what you describe.
>
> The project website is http://www.plantontology.org/. So far most of the
> ontology development has been done by Gramene (rice), TAIR and Maize DB.
> The website describes the project and how to access the ontologies. We are
> using the DAGeditor and ontology representation developed by the GO
> (directed, acyclic graphs). The plan is to make the ontologies as broadly
> applicable as we can to accomodate as many organisms as possible. The
> ontologies can be accessed without restriction and the GO has made the
> DAGeditor freely available. We are using the CVS repository as a
> shared development resource and communicating over email primarily for
> development.
>
> It would be fantastic to work with your group to develop the structure and
> content of the ontologies.We were planning to have a users meeting in
> January, following the PAG meeting in San Diego-will people from your
> organization be attending?
>
> I am ccing this email to the group.We have just hired a coordinator (your
> counterpart here)  who will be starting soon. She will be based at TAIR but
> will coordinate the efforts for the whole group-in the meantime, I am very
> happy to work with you. Best Regards
> Leonore Reiser
>
> On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > Dear Mrs. Reiser,
> >
> > I hope you are the right person to write to about this, but I will give
> > it a try. If I should contact somebody else, please let me know.
> >
> > I am writing on behalf of seven partner labs in Europe, working together
> > to establish a network of plant databases. The project is called PlaNet
> > (at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > partners all have databases with information about Arabidopsis (and
> > sometimes other plants). Some are working on prediction-tools, others
> > have collections of mutantlines (or germplasm or accessions, etc.). The
> > goal is to connect them all and build one general access to it, using
> > BioMoby. People will be able to query through this site and do not have
> > to worry about in which database they have to look for their information.
> >
> > To be able to query multiple databases with one type of question it is
> > very important to standardize the available information as much as
> > possible. One important aspect in this is the description of the mutants.
> > We set up a working group to compare the different
> > ontologies/vocabularies already used by the different partners. I am the
> > coordinator of this group. In Wageningen I am in the process of building
> > a database for our mutants (WAtDB, not online yet), but we already have a
> > wealth of information about mutants, transgenics and natural variants.
> > But no standard terminology (yet) for describing them.
> >
> > This is where my request to you is coming in. We have a lot of phenotype
> > descriptions and already noticed that not everything has been covered by
> > the TAIR vocabulary. One way to solve that is to send you numerous
> > submissions/update requests. But we thought that it might be more useful
> > to work together more structural. Are you interested in cooperation with
> > our group? If so, what would be a good way to do this? In November our PO
> > working group is meeting again here in Wageningen and I would like to
> > discuss it with them during that meeting. But it would be very useful to
> > know what you think about it and maybe already get some suggestions about
> > how we could work together.
> >
> > I hope you are interested and have time to reply within a few weeks. That
> > way I can use your information when I am preparing our coming EU PlaNet
> > PO working group meeting.
> >
> > Thanks in advance!
> >
> > Best wishes,
> > Paulien
> >
> >
> > Dr Paulien Adamse
> > BU Bioscience
> > Plant Research International,
> > P.O. Box 16,
> > 6700 AA Wageningen,
> > The Netherlands.
> >
> > Tel: +31 317 477001/476830
> > FAX: +31 317 418094
> > paulien.adamse at wur.nl
> > www.plant.wageningen-ur.nl
>
> ---------------------------------------------------------------------------
>---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> ---------------------------------------------------------------------------
>----

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From lreiser at acoma.Stanford.EDU  Fri Oct 17 14:41:49 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 17 Oct 2003 11:41:49 -0700 (PDT)
Subject: About (RE: plant ontology, cooperation? (fwd))
Message-ID: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU>

Hi Everyone, I assume that ya'll have had a chance to read this email. I'd
like to send a response soon but want feedback as to how this should be
approached. I dont know anymore about what they are doing than what has
been written so obviously need to find out more about the project (Pankaj
do you know if this is the one Klaus is working with?).

Anyway- can I suggest this for an agenda item on the 22nd. In the
meanwhile what is the general feeling about how to proceed. If they have
some concrete suggestions/feedback it would be excellent to incorporate
this at the outset. It would be great to pick an area of an ontology to
work on with them and see how this goes.

Best
Leonore

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------

---------- Forwarded message ----------
Date: Fri, 17 Oct 2003 09:33:42 +0200
From: "Adamse, Paulien" <paulien.adamse at wur.nl>
To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
Cc: lstein at cshl.org, po-dev at plantontology.org
Subject: RE: plant ontology, cooperation?

Dear Leonore (and others),

Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?

Bye,
Paulien

-----Original Message-----
From: Lincoln Stein [mailto:lstein at cshl.edu]
Sent: Thursday, October 16, 2003 16:23
To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
Cc: po-dev at plantontology.org
Subject: Re: plant ontology, cooperation?


Hello Paulien,

As PI of the POC project, I would like to personally express my enthusiasm for
building a collaboration with your group to develop plant-wide ontologies to
describe plant anatomy and developmental stages.  It would be very good for
our groups to meet at the San Diego users' meeting.

Lincoln

On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> Dear Paulien:
>
> This is wonderful. TAIR is part of a recently funded project to develop
> plant ontologies called the "Plant Ontology Consortium". The goals of this
> project are exactly what you describe.
>
> The project website is http://www.plantontology.org/. So far most of the
> ontology development has been done by Gramene (rice), TAIR and Maize DB.
> The website describes the project and how to access the ontologies. We are
> using the DAGeditor and ontology representation developed by the GO
> (directed, acyclic graphs). The plan is to make the ontologies as broadly
> applicable as we can to accomodate as many organisms as possible. The
> ontologies can be accessed without restriction and the GO has made the
> DAGeditor freely available. We are using the CVS repository as a
> shared development resource and communicating over email primarily for
> development.
>
> It would be fantastic to work with your group to develop the structure and
> content of the ontologies.We were planning to have a users meeting in
> January, following the PAG meeting in San Diego-will people from your
> organization be attending?
>
> I am ccing this email to the group.We have just hired a coordinator (your
> counterpart here)  who will be starting soon. She will be based at TAIR but
> will coordinate the efforts for the whole group-in the meantime, I am very
> happy to work with you. Best Regards
> Leonore Reiser
>
> On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > Dear Mrs. Reiser,
> >
> > I hope you are the right person to write to about this, but I will give
> > it a try. If I should contact somebody else, please let me know.
> >
> > I am writing on behalf of seven partner labs in Europe, working together
> > to establish a network of plant databases. The project is called PlaNet
> > (at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > partners all have databases with information about Arabidopsis (and
> > sometimes other plants). Some are working on prediction-tools, others
> > have collections of mutantlines (or germplasm or accessions, etc.). The
> > goal is to connect them all and build one general access to it, using
> > BioMoby. People will be able to query through this site and do not have
> > to worry about in which database they have to look for their information.
> >
> > To be able to query multiple databases with one type of question it is
> > very important to standardize the available information as much as
> > possible. One important aspect in this is the description of the mutants.
> > We set up a working group to compare the different
> > ontologies/vocabularies already used by the different partners. I am the
> > coordinator of this group. In Wageningen I am in the process of building
> > a database for our mutants (WAtDB, not online yet), but we already have a
> > wealth of information about mutants, transgenics and natural variants.
> > But no standard terminology (yet) for describing them.
> >
> > This is where my request to you is coming in. We have a lot of phenotype
> > descriptions and already noticed that not everything has been covered by
> > the TAIR vocabulary. One way to solve that is to send you numerous
> > submissions/update requests. But we thought that it might be more useful
> > to work together more structural. Are you interested in cooperation with
> > our group? If so, what would be a good way to do this? In November our PO
> > working group is meeting again here in Wageningen and I would like to
> > discuss it with them during that meeting. But it would be very useful to
> > know what you think about it and maybe already get some suggestions about
> > how we could work together.
> >
> > I hope you are interested and have time to reply within a few weeks. That
> > way I can use your information when I am preparing our coming EU PlaNet
> > PO working group meeting.
> >
> > Thanks in advance!
> >
> > Best wishes,
> > Paulien
> >
> >
> > Dr Paulien Adamse
> > BU Bioscience
> > Plant Research International,
> > P.O. Box 16,
> > 6700 AA Wageningen,
> > The Netherlands.
> >
> > Tel: +31 317 477001/476830
> > FAX: +31 317 418094
> > paulien.adamse at wur.nl
> > www.plant.wageningen-ur.nl
>
> ---------------------------------------------------------------------------
>---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> ---------------------------------------------------------------------------
>----

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================





From rhee at acoma.Stanford.EDU  Fri Oct 17 15:03:49 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Fri, 17 Oct 2003 12:03:49 -0700 (PDT)
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0310171158320.12670-100000@acoma.Stanford.EDU>

Hi, Leonore,

Yes, it'd be a good agenda item. I like your suggestion of having them
pick an area of ontology. Since it looks like most of their mutant
phenotypes are for Arabidopsis, a good place to start may be for them to
start with one of the Arabidopsis ontologies? They could also start
learning (or perhaps they are already familiar?) DagEdit and get familiar
with the existing ontologies.

Sue



On Fri, 17 Oct 2003, Leonore Reiser wrote:

> Hi Everyone, I assume that ya'll have had a chance to read this email. I'd
> like to send a response soon but want feedback as to how this should be
> approached. I dont know anymore about what they are doing than what has
> been written so obviously need to find out more about the project (Pankaj
> do you know if this is the one Klaus is working with?).
>
> Anyway- can I suggest this for an agenda item on the 22nd. In the
> meanwhile what is the general feeling about how to proceed. If they have
> some concrete suggestions/feedback it would be excellent to incorporate
> this at the outset. It would be great to pick an area of an ontology to
> work on with them and see how this goes.
>
> Best
> Leonore
>
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------
>
> ---------- Forwarded message ----------
> Date: Fri, 17 Oct 2003 09:33:42 +0200
> From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> Cc: lstein at cshl.org, po-dev at plantontology.org
> Subject: RE: plant ontology, cooperation?
>
> Dear Leonore (and others),
>
> Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?
>
> Bye,
> Paulien
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.edu]
> Sent: Thursday, October 16, 2003 16:23
> To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> Cc: po-dev at plantontology.org
> Subject: Re: plant ontology, cooperation?
>
>
> Hello Paulien,
>
> As PI of the POC project, I would like to personally express my enthusiasm for
> building a collaboration with your group to develop plant-wide ontologies to
> describe plant anatomy and developmental stages.  It would be very good for
> our groups to meet at the San Diego users' meeting.
>
> Lincoln
>
> On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> > Dear Paulien:
> >
> > This is wonderful. TAIR is part of a recently funded project to develop
> > plant ontologies called the "Plant Ontology Consortium". The goals of this
> > project are exactly what you describe.
> >
> > The project website is http://www.plantontology.org/. So far most of the
> > ontology development has been done by Gramene (rice), TAIR and Maize DB.
> > The website describes the project and how to access the ontologies. We are
> > using the DAGeditor and ontology representation developed by the GO
> > (directed, acyclic graphs). The plan is to make the ontologies as broadly
> > applicable as we can to accomodate as many organisms as possible. The
> > ontologies can be accessed without restriction and the GO has made the
> > DAGeditor freely available. We are using the CVS repository as a
> > shared development resource and communicating over email primarily for
> > development.
> >
> > It would be fantastic to work with your group to develop the structure and
> > content of the ontologies.We were planning to have a users meeting in
> > January, following the PAG meeting in San Diego-will people from your
> > organization be attending?
> >
> > I am ccing this email to the group.We have just hired a coordinator (your
> > counterpart here)  who will be starting soon. She will be based at TAIR but
> > will coordinate the efforts for the whole group-in the meantime, I am very
> > happy to work with you. Best Regards
> > Leonore Reiser
> >
> > On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > > Dear Mrs. Reiser,
> > >
> > > I hope you are the right person to write to about this, but I will give
> > > it a try. If I should contact somebody else, please let me know.
> > >
> > > I am writing on behalf of seven partner labs in Europe, working together
> > > to establish a network of plant databases. The project is called PlaNet
> > > (at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > > partners all have databases with information about Arabidopsis (and
> > > sometimes other plants). Some are working on prediction-tools, others
> > > have collections of mutantlines (or germplasm or accessions, etc.). The
> > > goal is to connect them all and build one general access to it, using
> > > BioMoby. People will be able to query through this site and do not have
> > > to worry about in which database they have to look for their information.
> > >
> > > To be able to query multiple databases with one type of question it is
> > > very important to standardize the available information as much as
> > > possible. One important aspect in this is the description of the mutants.
> > > We set up a working group to compare the different
> > > ontologies/vocabularies already used by the different partners. I am the
> > > coordinator of this group. In Wageningen I am in the process of building
> > > a database for our mutants (WAtDB, not online yet), but we already have a
> > > wealth of information about mutants, transgenics and natural variants.
> > > But no standard terminology (yet) for describing them.
> > >
> > > This is where my request to you is coming in. We have a lot of phenotype
> > > descriptions and already noticed that not everything has been covered by
> > > the TAIR vocabulary. One way to solve that is to send you numerous
> > > submissions/update requests. But we thought that it might be more useful
> > > to work together more structural. Are you interested in cooperation with
> > > our group? If so, what would be a good way to do this? In November our PO
> > > working group is meeting again here in Wageningen and I would like to
> > > discuss it with them during that meeting. But it would be very useful to
> > > know what you think about it and maybe already get some suggestions about
> > > how we could work together.
> > >
> > > I hope you are interested and have time to reply within a few weeks. That
> > > way I can use your information when I am preparing our coming EU PlaNet
> > > PO working group meeting.
> > >
> > > Thanks in advance!
> > >
> > > Best wishes,
> > > Paulien
> > >
> > >
> > > Dr Paulien Adamse
> > > BU Bioscience
> > > Plant Research International,
> > > P.O. Box 16,
> > > 6700 AA Wageningen,
> > > The Netherlands.
> > >
> > > Tel: +31 317 477001/476830
> > > FAX: +31 317 418094
> > > paulien.adamse at wur.nl
> > > www.plant.wageningen-ur.nl
> >
> > ---------------------------------------------------------------------------
> >---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> > Arabidopsis Information Resource	FAX: (650) 325-6857
> > Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology		URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > ---------------------------------------------------------------------------
> >----
>
> --
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>
>
>
>

-----------------------------------------------------------------------------
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 paulien.adamse at wur.nl  Fri Oct 17 03:33:42 2003
From: paulien.adamse at wur.nl (Adamse, Paulien)
Date: Fri, 17 Oct 2003 09:33:42 +0200
Subject: plant ontology, cooperation?
Message-ID: <D7D87C2E22166045999C9FB3DC656B2906F30E@scomp0017>

Dear Leonore (and others),

Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?

Bye,
Paulien

-----Original Message-----
From: Lincoln Stein [mailto:lstein at cshl.edu]
Sent: Thursday, October 16, 2003 16:23
To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
Cc: po-dev at plantontology.org
Subject: Re: plant ontology, cooperation?


Hello Paulien,

As PI of the POC project, I would like to personally express my enthusiasm for 
building a collaboration with your group to develop plant-wide ontologies to 
describe plant anatomy and developmental stages.  It would be very good for 
our groups to meet at the San Diego users' meeting.

Lincoln

On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> Dear Paulien:
>
> This is wonderful. TAIR is part of a recently funded project to develop
> plant ontologies called the "Plant Ontology Consortium". The goals of this
> project are exactly what you describe.
>
> The project website is http://www.plantontology.org/. So far most of the
> ontology development has been done by Gramene (rice), TAIR and Maize DB.
> The website describes the project and how to access the ontologies. We are
> using the DAGeditor and ontology representation developed by the GO
> (directed, acyclic graphs). The plan is to make the ontologies as broadly
> applicable as we can to accomodate as many organisms as possible. The
> ontologies can be accessed without restriction and the GO has made the
> DAGeditor freely available. We are using the CVS repository as a
> shared development resource and communicating over email primarily for
> development.
>
> It would be fantastic to work with your group to develop the structure and
> content of the ontologies.We were planning to have a users meeting in
> January, following the PAG meeting in San Diego-will people from your
> organization be attending?
>
> I am ccing this email to the group.We have just hired a coordinator (your
> counterpart here)  who will be starting soon. She will be based at TAIR but
> will coordinate the efforts for the whole group-in the meantime, I am very
> happy to work with you. Best Regards
> Leonore Reiser
>
> On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > Dear Mrs. Reiser,
> >
> > I hope you are the right person to write to about this, but I will give
> > it a try. If I should contact somebody else, please let me know.
> >
> > I am writing on behalf of seven partner labs in Europe, working together
> > to establish a network of plant databases. The project is called PlaNet
> > (at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > partners all have databases with information about Arabidopsis (and
> > sometimes other plants). Some are working on prediction-tools, others
> > have collections of mutantlines (or germplasm or accessions, etc.). The
> > goal is to connect them all and build one general access to it, using
> > BioMoby. People will be able to query through this site and do not have
> > to worry about in which database they have to look for their information.
> >
> > To be able to query multiple databases with one type of question it is
> > very important to standardize the available information as much as
> > possible. One important aspect in this is the description of the mutants.
> > We set up a working group to compare the different
> > ontologies/vocabularies already used by the different partners. I am the
> > coordinator of this group. In Wageningen I am in the process of building
> > a database for our mutants (WAtDB, not online yet), but we already have a
> > wealth of information about mutants, transgenics and natural variants.
> > But no standard terminology (yet) for describing them.
> >
> > This is where my request to you is coming in. We have a lot of phenotype
> > descriptions and already noticed that not everything has been covered by
> > the TAIR vocabulary. One way to solve that is to send you numerous
> > submissions/update requests. But we thought that it might be more useful
> > to work together more structural. Are you interested in cooperation with
> > our group? If so, what would be a good way to do this? In November our PO
> > working group is meeting again here in Wageningen and I would like to
> > discuss it with them during that meeting. But it would be very useful to
> > know what you think about it and maybe already get some suggestions about
> > how we could work together.
> >
> > I hope you are interested and have time to reply within a few weeks. That
> > way I can use your information when I am preparing our coming EU PlaNet
> > PO working group meeting.
> >
> > Thanks in advance!
> >
> > Best wishes,
> > Paulien
> >
> >
> > Dr Paulien Adamse
> > BU Bioscience
> > Plant Research International,
> > P.O. Box 16,
> > 6700 AA Wageningen,
> > The Netherlands.
> >
> > Tel: +31 317 477001/476830
> > FAX: +31 317 418094
> > paulien.adamse at wur.nl
> > www.plant.wageningen-ur.nl
>
> ---------------------------------------------------------------------------
>---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> ---------------------------------------------------------------------------
>----

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From lreiser at acoma.Stanford.EDU  Fri Oct 17 15:31:50 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 17 Oct 2003 12:31:50 -0700 (PDT)
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <Pine.GSO.4.44.0310171158320.12670-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0310171227390.12875-100000@acoma.Stanford.EDU>

Yep- .I assume thats what they were looking for.I think they have been
looking at the ontologies and have some suggestions for improvement.
I'd suggest coming to TAIR to maybe hash out some things as well- but
probably later- see how things go via email.

Any other comments/suggestions before I respond?





On Fri, 17 Oct 2003, Sue Rhee wrote:

> Hi, Leonore,
>
> Yes, it'd be a good agenda item. I like your suggestion of having them
> pick an area of ontology. Since it looks like most of their mutant
> phenotypes are for Arabidopsis, a good place to start may be for them to
> start with one of the Arabidopsis ontologies? They could also start
> learning (or perhaps they are already familiar?) DagEdit and get familiar
> with the existing ontologies.
>
> Sue
>
>
>
> On Fri, 17 Oct 2003, Leonore Reiser wrote:
>
> > Hi Everyone, I assume that ya'll have had a chance to read this email. I'd
> > like to send a response soon but want feedback as to how this should be
> > approached. I dont know anymore about what they are doing than what has
> > been written so obviously need to find out more about the project (Pankaj
> > do you know if this is the one Klaus is working with?).
> >
> > Anyway- can I suggest this for an agenda item on the 22nd. In the
> > meanwhile what is the general feeling about how to proceed. If they have
> > some concrete suggestions/feedback it would be excellent to incorporate
> > this at the outset. It would be great to pick an area of an ontology to
> > work on with them and see how this goes.
> >
> > Best
> > Leonore
> >
> > -------------------------------------------------------------------------------
> > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource	FAX: (650) 325-6857
> > Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology		URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------------
> >
> > ---------- Forwarded message ----------
> > Date: Fri, 17 Oct 2003 09:33:42 +0200
> > From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> > To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> > Cc: lstein at cshl.org, po-dev at plantontology.org
> > Subject: RE: plant ontology, cooperation?
> >
> > Dear Leonore (and others),
> >
> > Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?
> >
> > Bye,
> > Paulien
> >
> > -----Original Message-----
> > From: Lincoln Stein [mailto:lstein at cshl.edu]
> > Sent: Thursday, October 16, 2003 16:23
> > To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> > Cc: po-dev at plantontology.org
> > Subject: Re: plant ontology, cooperation?
> >
> >
> > Hello Paulien,
> >
> > As PI of the POC project, I would like to personally express my enthusiasm for
> > building a collaboration with your group to develop plant-wide ontologies to
> > describe plant anatomy and developmental stages.  It would be very good for
> > our groups to meet at the San Diego users' meeting.
> >
> > Lincoln
> >
> > On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> > > Dear Paulien:
> > >
> > > This is wonderful. TAIR is part of a recently funded project to develop
> > > plant ontologies called the "Plant Ontology Consortium". The goals of this
> > > project are exactly what you describe.
> > >
> > > The project website is http://www.plantontology.org/. So far most of the
> > > ontology development has been done by Gramene (rice), TAIR and Maize DB.
> > > The website describes the project and how to access the ontologies. We are
> > > using the DAGeditor and ontology representation developed by the GO
> > > (directed, acyclic graphs). The plan is to make the ontologies as broadly
> > > applicable as we can to accomodate as many organisms as possible. The
> > > ontologies can be accessed without restriction and the GO has made the
> > > DAGeditor freely available. We are using the CVS repository as a
> > > shared development resource and communicating over email primarily for
> > > development.
> > >
> > > It would be fantastic to work with your group to develop the structure and
> > > content of the ontologies.We were planning to have a users meeting in
> > > January, following the PAG meeting in San Diego-will people from your
> > > organization be attending?
> > >
> > > I am ccing this email to the group.We have just hired a coordinator (your
> > > counterpart here)  who will be starting soon. She will be based at TAIR but
> > > will coordinate the efforts for the whole group-in the meantime, I am very
> > > happy to work with you. Best Regards
> > > Leonore Reiser
> > >
> > > On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > > > Dear Mrs. Reiser,
> > > >
> > > > I hope you are the right person to write to about this, but I will give
> > > > it a try. If I should contact somebody else, please let me know.
> > > >
> > > > I am writing on behalf of seven partner labs in Europe, working together
> > > > to establish a network of plant databases. The project is called PlaNet
> > > > (at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > > > partners all have databases with information about Arabidopsis (and
> > > > sometimes other plants). Some are working on prediction-tools, others
> > > > have collections of mutantlines (or germplasm or accessions, etc.). The
> > > > goal is to connect them all and build one general access to it, using
> > > > BioMoby. People will be able to query through this site and do not have
> > > > to worry about in which database they have to look for their information.
> > > >
> > > > To be able to query multiple databases with one type of question it is
> > > > very important to standardize the available information as much as
> > > > possible. One important aspect in this is the description of the mutants.
> > > > We set up a working group to compare the different
> > > > ontologies/vocabularies already used by the different partners. I am the
> > > > coordinator of this group. In Wageningen I am in the process of building
> > > > a database for our mutants (WAtDB, not online yet), but we already have a
> > > > wealth of information about mutants, transgenics and natural variants.
> > > > But no standard terminology (yet) for describing them.
> > > >
> > > > This is where my request to you is coming in. We have a lot of phenotype
> > > > descriptions and already noticed that not everything has been covered by
> > > > the TAIR vocabulary. One way to solve that is to send you numerous
> > > > submissions/update requests. But we thought that it might be more useful
> > > > to work together more structural. Are you interested in cooperation with
> > > > our group? If so, what would be a good way to do this? In November our PO
> > > > working group is meeting again here in Wageningen and I would like to
> > > > discuss it with them during that meeting. But it would be very useful to
> > > > know what you think about it and maybe already get some suggestions about
> > > > how we could work together.
> > > >
> > > > I hope you are interested and have time to reply within a few weeks. That
> > > > way I can use your information when I am preparing our coming EU PlaNet
> > > > PO working group meeting.
> > > >
> > > > Thanks in advance!
> > > >
> > > > Best wishes,
> > > > Paulien
> > > >
> > > >
> > > > Dr Paulien Adamse
> > > > BU Bioscience
> > > > Plant Research International,
> > > > P.O. Box 16,
> > > > 6700 AA Wageningen,
> > > > The Netherlands.
> > > >
> > > > Tel: +31 317 477001/476830
> > > > FAX: +31 317 418094
> > > > paulien.adamse at wur.nl
> > > > www.plant.wageningen-ur.nl
> > >
> > > ---------------------------------------------------------------------------
> > >---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> > > Arabidopsis Information Resource	FAX: (650) 325-6857
> > > Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > > Department of Plant Biology		URL: http://arabidopsis.org/
> > > 260 Panama St.
> > > Stanford, CA 94305
> > > ---------------------------------------------------------------------------
> > >----
> >
> > --
> > ========================================================================
> > Lincoln D. Stein                           Cold Spring Harbor Laboratory
> > lstein at cshl.org			                  Cold Spring Harbor, NY
> > ========================================================================
> >
> >
> >
> >
>
> -----------------------------------------------------------------------------
> 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.
> -----------------------------------------------------------------------------
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Fri Oct 17 15:39:13 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 17 Oct 2003 15:39:13 -0400
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU>
Message-ID: <3F904561.9040005@cornell.edu>

Hi Leonore,

Meeting Pauline at the PAG will be a great idea. We can have discussion with him 
and other potential target DBs and projects. However, POC's first user meeting 
is in July next year. In Jan at Stanford it will be a GO users meeting, where 
many of the plant people are trying to come, e.g. Deepgene group.

Leonore Reiser wrote:
> Hi Everyone, I assume that ya'll have had a chance to read this email. I'd
> like to send a response soon but want feedback as to how this should be
> approached. I dont know anymore about what they are doing than what has
> been written so obviously need to find out more about the project (Pankaj
> do you know if this is the one Klaus is working with?).
> 

Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
Project is at http://mips.gsf.de/proj/thal/phenotype/

> Anyway- can I suggest this for an agenda item on the 22nd. In the
> meanwhile what is the general feeling about how to proceed. If they have
> some concrete suggestions/feedback it would be excellent to incorporate
> this at the outset. It would be great to pick an area of an ontology to
> work on with them and see how this goes.

I agree with Sue, since their priority is on Arabidopsis.

> 
> Best
> Leonore
> 
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------
> 
> ---------- Forwarded message ----------
> Date: Fri, 17 Oct 2003 09:33:42 +0200
> From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> Cc: lstein at cshl.org, po-dev at plantontology.org
> Subject: RE: plant ontology, cooperation?
> 
> Dear Leonore (and others),
> 
> Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?
> 
> Bye,
> Paulien
> 
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.edu]
> Sent: Thursday, October 16, 2003 16:23
> To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> Cc: po-dev at plantontology.org
> Subject: Re: plant ontology, cooperation?
> 
> 
> Hello Paulien,
> 
> As PI of the POC project, I would like to personally express my enthusiasm for
> building a collaboration with your group to develop plant-wide ontologies to
> describe plant anatomy and developmental stages.  It would be very good for
> our groups to meet at the San Diego users' meeting.
> 
> Lincoln
> 
> On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> 
>>Dear Paulien:
>>
>>This is wonderful. TAIR is part of a recently funded project to develop
>>plant ontologies called the "Plant Ontology Consortium". The goals of this
>>project are exactly what you describe.
>>
>>The project website is http://www.plantontology.org/. So far most of the
>>ontology development has been done by Gramene (rice), TAIR and Maize DB.
>>The website describes the project and how to access the ontologies. We are
>>using the DAGeditor and ontology representation developed by the GO
>>(directed, acyclic graphs). The plan is to make the ontologies as broadly
>>applicable as we can to accomodate as many organisms as possible. The
>>ontologies can be accessed without restriction and the GO has made the
>>DAGeditor freely available. We are using the CVS repository as a
>>shared development resource and communicating over email primarily for
>>development.
>>
>>It would be fantastic to work with your group to develop the structure and
>>content of the ontologies.We were planning to have a users meeting in
>>January, following the PAG meeting in San Diego-will people from your
>>organization be attending?
>>
>>I am ccing this email to the group.We have just hired a coordinator (your
>>counterpart here)  who will be starting soon. She will be based at TAIR but
>>will coordinate the efforts for the whole group-in the meantime, I am very
>>happy to work with you. Best Regards
>>Leonore Reiser
>>
>>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
>>
>>>Dear Mrs. Reiser,
>>>
>>>I hope you are the right person to write to about this, but I will give
>>>it a try. If I should contact somebody else, please let me know.
>>>
>>>I am writing on behalf of seven partner labs in Europe, working together
>>>to establish a network of plant databases. The project is called PlaNet
>>>(at the moment the address is http://mips.gsf.de/proj/planet/). The 7
>>>partners all have databases with information about Arabidopsis (and
>>>sometimes other plants). Some are working on prediction-tools, others
>>>have collections of mutantlines (or germplasm or accessions, etc.). The
>>>goal is to connect them all and build one general access to it, using
>>>BioMoby. People will be able to query through this site and do not have
>>>to worry about in which database they have to look for their information.
>>>
>>>To be able to query multiple databases with one type of question it is
>>>very important to standardize the available information as much as
>>>possible. One important aspect in this is the description of the mutants.
>>>We set up a working group to compare the different
>>>ontologies/vocabularies already used by the different partners. I am the
>>>coordinator of this group. In Wageningen I am in the process of building
>>>a database for our mutants (WAtDB, not online yet), but we already have a
>>>wealth of information about mutants, transgenics and natural variants.
>>>But no standard terminology (yet) for describing them.
>>>
>>>This is where my request to you is coming in. We have a lot of phenotype
>>>descriptions and already noticed that not everything has been covered by
>>>the TAIR vocabulary. One way to solve that is to send you numerous
>>>submissions/update requests. But we thought that it might be more useful
>>>to work together more structural. Are you interested in cooperation with
>>>our group? If so, what would be a good way to do this? In November our PO
>>>working group is meeting again here in Wageningen and I would like to
>>>discuss it with them during that meeting. But it would be very useful to
>>>know what you think about it and maybe already get some suggestions about
>>>how we could work together.
>>>
>>>I hope you are interested and have time to reply within a few weeks. That
>>>way I can use your information when I am preparing our coming EU PlaNet
>>>PO working group meeting.
>>>
>>>Thanks in advance!
>>>
>>>Best wishes,
>>>Paulien
>>>
>>>
>>>Dr Paulien Adamse
>>>BU Bioscience
>>>Plant Research International,
>>>P.O. Box 16,
>>>6700 AA Wageningen,
>>>The Netherlands.
>>>
>>>Tel: +31 317 477001/476830
>>>FAX: +31 317 418094
>>>paulien.adamse at wur.nl
>>>www.plant.wageningen-ur.nl
>>
>>---------------------------------------------------------------------------
>>---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
>>Arabidopsis Information Resource	FAX: (650) 325-6857
>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>>Department of Plant Biology		URL: http://arabidopsis.org/
>>260 Panama St.
>>Stanford, CA 94305
>>---------------------------------------------------------------------------
>>----
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 lreiser at acoma.Stanford.EDU  Fri Oct 17 15:45:18 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 17 Oct 2003 12:45:18 -0700 (PDT)
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <3F904561.9040005@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310171243370.12875-100000@acoma.Stanford.EDU>


Thanks- great . But there is a POC development meeting then right- the
other alternative was to invite him to TAIR- but seems premature til we
have some concrete plan on what to work on.
So Ill still encourage coming to SD in January-
Leonore

On Fri, 17 Oct 2003, Pankaj Jaiswal wrote:

> Hi Leonore,
>
> Meeting Pauline at the PAG will be a great idea. We can have discussion with him
> and other potential target DBs and projects. However, POC's first user meeting
> is in July next year. In Jan at Stanford it will be a GO users meeting, where
> many of the plant people are trying to come, e.g. Deepgene group.
>
> Leonore Reiser wrote:
> > Hi Everyone, I assume that ya'll have had a chance to read this email. I'd
> > like to send a response soon but want feedback as to how this should be
> > approached. I dont know anymore about what they are doing than what has
> > been written so obviously need to find out more about the project (Pankaj
> > do you know if this is the one Klaus is working with?).
> >
>
> Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
> Project is at http://mips.gsf.de/proj/thal/phenotype/
>
> > Anyway- can I suggest this for an agenda item on the 22nd. In the
> > meanwhile what is the general feeling about how to proceed. If they have
> > some concrete suggestions/feedback it would be excellent to incorporate
> > this at the outset. It would be great to pick an area of an ontology to
> > work on with them and see how this goes.
>
> I agree with Sue, since their priority is on Arabidopsis.
>
> >
> > Best
> > Leonore
> >
> > -------------------------------------------------------------------------------
> > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource	FAX: (650) 325-6857
> > Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology		URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------------
> >
> > ---------- Forwarded message ----------
> > Date: Fri, 17 Oct 2003 09:33:42 +0200
> > From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> > To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> > Cc: lstein at cshl.org, po-dev at plantontology.org
> > Subject: RE: plant ontology, cooperation?
> >
> > Dear Leonore (and others),
> >
> > Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?
> >
> > Bye,
> > Paulien
> >
> > -----Original Message-----
> > From: Lincoln Stein [mailto:lstein at cshl.edu]
> > Sent: Thursday, October 16, 2003 16:23
> > To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> > Cc: po-dev at plantontology.org
> > Subject: Re: plant ontology, cooperation?
> >
> >
> > Hello Paulien,
> >
> > As PI of the POC project, I would like to personally express my enthusiasm for
> > building a collaboration with your group to develop plant-wide ontologies to
> > describe plant anatomy and developmental stages.  It would be very good for
> > our groups to meet at the San Diego users' meeting.
> >
> > Lincoln
> >
> > On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> >
> >>Dear Paulien:
> >>
> >>This is wonderful. TAIR is part of a recently funded project to develop
> >>plant ontologies called the "Plant Ontology Consortium". The goals of this
> >>project are exactly what you describe.
> >>
> >>The project website is http://www.plantontology.org/. So far most of the
> >>ontology development has been done by Gramene (rice), TAIR and Maize DB.
> >>The website describes the project and how to access the ontologies. We are
> >>using the DAGeditor and ontology representation developed by the GO
> >>(directed, acyclic graphs). The plan is to make the ontologies as broadly
> >>applicable as we can to accomodate as many organisms as possible. The
> >>ontologies can be accessed without restriction and the GO has made the
> >>DAGeditor freely available. We are using the CVS repository as a
> >>shared development resource and communicating over email primarily for
> >>development.
> >>
> >>It would be fantastic to work with your group to develop the structure and
> >>content of the ontologies.We were planning to have a users meeting in
> >>January, following the PAG meeting in San Diego-will people from your
> >>organization be attending?
> >>
> >>I am ccing this email to the group.We have just hired a coordinator (your
> >>counterpart here)  who will be starting soon. She will be based at TAIR but
> >>will coordinate the efforts for the whole group-in the meantime, I am very
> >>happy to work with you. Best Regards
> >>Leonore Reiser
> >>
> >>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> >>
> >>>Dear Mrs. Reiser,
> >>>
> >>>I hope you are the right person to write to about this, but I will give
> >>>it a try. If I should contact somebody else, please let me know.
> >>>
> >>>I am writing on behalf of seven partner labs in Europe, working together
> >>>to establish a network of plant databases. The project is called PlaNet
> >>>(at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> >>>partners all have databases with information about Arabidopsis (and
> >>>sometimes other plants). Some are working on prediction-tools, others
> >>>have collections of mutantlines (or germplasm or accessions, etc.). The
> >>>goal is to connect them all and build one general access to it, using
> >>>BioMoby. People will be able to query through this site and do not have
> >>>to worry about in which database they have to look for their information.
> >>>
> >>>To be able to query multiple databases with one type of question it is
> >>>very important to standardize the available information as much as
> >>>possible. One important aspect in this is the description of the mutants.
> >>>We set up a working group to compare the different
> >>>ontologies/vocabularies already used by the different partners. I am the
> >>>coordinator of this group. In Wageningen I am in the process of building
> >>>a database for our mutants (WAtDB, not online yet), but we already have a
> >>>wealth of information about mutants, transgenics and natural variants.
> >>>But no standard terminology (yet) for describing them.
> >>>
> >>>This is where my request to you is coming in. We have a lot of phenotype
> >>>descriptions and already noticed that not everything has been covered by
> >>>the TAIR vocabulary. One way to solve that is to send you numerous
> >>>submissions/update requests. But we thought that it might be more useful
> >>>to work together more structural. Are you interested in cooperation with
> >>>our group? If so, what would be a good way to do this? In November our PO
> >>>working group is meeting again here in Wageningen and I would like to
> >>>discuss it with them during that meeting. But it would be very useful to
> >>>know what you think about it and maybe already get some suggestions about
> >>>how we could work together.
> >>>
> >>>I hope you are interested and have time to reply within a few weeks. That
> >>>way I can use your information when I am preparing our coming EU PlaNet
> >>>PO working group meeting.
> >>>
> >>>Thanks in advance!
> >>>
> >>>Best wishes,
> >>>Paulien
> >>>
> >>>
> >>>Dr Paulien Adamse
> >>>BU Bioscience
> >>>Plant Research International,
> >>>P.O. Box 16,
> >>>6700 AA Wageningen,
> >>>The Netherlands.
> >>>
> >>>Tel: +31 317 477001/476830
> >>>FAX: +31 317 418094
> >>>paulien.adamse at wur.nl
> >>>www.plant.wageningen-ur.nl
> >>
> >>---------------------------------------------------------------------------
> >>---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> >>Arabidopsis Information Resource	FAX: (650) 325-6857
> >>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >>Department of Plant Biology		URL: http://arabidopsis.org/
> >>260 Panama St.
> >>Stanford, CA 94305
> >>---------------------------------------------------------------------------
> >>----
> >
> >
>
> --
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Research 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
> ******************************************
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From lreiser at acoma.Stanford.EDU  Fri Oct 17 15:54:07 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 17 Oct 2003 12:54:07 -0700 (PDT)
Subject: plant ontology, cooperation?
In-Reply-To: <D7D87C2E22166045999C9FB3DC656B2906F30E@scomp0017>
Message-ID: <Pine.GSO.4.44.0310171236420.12875-100000@acoma.Stanford.EDU>


Dear Paulien:
It would be great if you can come to San Diego. Turns out the users
meeting is planned for July,not January- but POC collaborators will meet.

As a start- you mentioned that there were some specific areas of the
ontologies that were in need of work. What might be best is to start
working on one of these areas to correct/update the structure and content.
Are you familiar with the DAG structure used by GO and other ontologies??
The GO website has some great information/tutorials about this.
(www.arabidopsis.org). You can also access the DAG editor from there and
download a copy from SourceForge
(http://sourceforge.net/project/showfiles.php?group_id=36855).


Since its easiest to see changes in structure using the DAG editor its a
nice way to change things around and then see how it looks. WE can take a
segment of the ontology and refine the structure and share the flat files
(send them back and forth). Email has been a good mode of communication
and we can certainly arrange to speak on the phone if we need to hash out
a particularly difficult area. It would also  be great if you are coming
to SanDiego to spend some time up at Stanford if your schedule allows.

So bottom line is I think it would be a good idea to start with one node
of the ontologies and move on from there. Are you alright with downloading
DagEdit and working this way?

Best
Leonore



On Fri, 17 Oct 2003, Adamse, Paulien wrote:

> Dear Leonore (and others),
>
> Thanks for the very fast response! I did not plan to attend the PAG conference, but am rethinking that now. It would be the best way to start cooperating. In the mean time, do you have suggestions for our group for issues we should discuss (or find out) before coming to your meeting?
>
> Bye,
> Paulien
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein at cshl.edu]
> Sent: Thursday, October 16, 2003 16:23
> To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> Cc: po-dev at plantontology.org
> Subject: Re: plant ontology, cooperation?
>
>
> Hello Paulien,
>
> As PI of the POC project, I would like to personally express my enthusiasm for
> building a collaboration with your group to develop plant-wide ontologies to
> describe plant anatomy and developmental stages.  It would be very good for
> our groups to meet at the San Diego users' meeting.
>
> Lincoln
>
> On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> > Dear Paulien:
> >
> > This is wonderful. TAIR is part of a recently funded project to develop
> > plant ontologies called the "Plant Ontology Consortium". The goals of this
> > project are exactly what you describe.
> >
> > The project website is http://www.plantontology.org/. So far most of the
> > ontology development has been done by Gramene (rice), TAIR and Maize DB.
> > The website describes the project and how to access the ontologies. We are
> > using the DAGeditor and ontology representation developed by the GO
> > (directed, acyclic graphs). The plan is to make the ontologies as broadly
> > applicable as we can to accomodate as many organisms as possible. The
> > ontologies can be accessed without restriction and the GO has made the
> > DAGeditor freely available. We are using the CVS repository as a
> > shared development resource and communicating over email primarily for
> > development.
> >
> > It would be fantastic to work with your group to develop the structure and
> > content of the ontologies.We were planning to have a users meeting in
> > January, following the PAG meeting in San Diego-will people from your
> > organization be attending?
> >
> > I am ccing this email to the group.We have just hired a coordinator (your
> > counterpart here)  who will be starting soon. She will be based at TAIR but
> > will coordinate the efforts for the whole group-in the meantime, I am very
> > happy to work with you. Best Regards
> > Leonore Reiser
> >
> > On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > > Dear Mrs. Reiser,
> > >
> > > I hope you are the right person to write to about this, but I will give
> > > it a try. If I should contact somebody else, please let me know.
> > >
> > > I am writing on behalf of seven partner labs in Europe, working together
> > > to establish a network of plant databases. The project is called PlaNet
> > > (at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > > partners all have databases with information about Arabidopsis (and
> > > sometimes other plants). Some are working on prediction-tools, others
> > > have collections of mutantlines (or germplasm or accessions, etc.). The
> > > goal is to connect them all and build one general access to it, using
> > > BioMoby. People will be able to query through this site and do not have
> > > to worry about in which database they have to look for their information.
> > >
> > > To be able to query multiple databases with one type of question it is
> > > very important to standardize the available information as much as
> > > possible. One important aspect in this is the description of the mutants.
> > > We set up a working group to compare the different
> > > ontologies/vocabularies already used by the different partners. I am the
> > > coordinator of this group. In Wageningen I am in the process of building
> > > a database for our mutants (WAtDB, not online yet), but we already have a
> > > wealth of information about mutants, transgenics and natural variants.
> > > But no standard terminology (yet) for describing them.
> > >
> > > This is where my request to you is coming in. We have a lot of phenotype
> > > descriptions and already noticed that not everything has been covered by
> > > the TAIR vocabulary. One way to solve that is to send you numerous
> > > submissions/update requests. But we thought that it might be more useful
> > > to work together more structural. Are you interested in cooperation with
> > > our group? If so, what would be a good way to do this? In November our PO
> > > working group is meeting again here in Wageningen and I would like to
> > > discuss it with them during that meeting. But it would be very useful to
> > > know what you think about it and maybe already get some suggestions about
> > > how we could work together.
> > >
> > > I hope you are interested and have time to reply within a few weeks. That
> > > way I can use your information when I am preparing our coming EU PlaNet
> > > PO working group meeting.
> > >
> > > Thanks in advance!
> > >
> > > Best wishes,
> > > Paulien
> > >
> > >
> > > Dr Paulien Adamse
> > > BU Bioscience
> > > Plant Research International,
> > > P.O. Box 16,
> > > 6700 AA Wageningen,
> > > The Netherlands.
> > >
> > > Tel: +31 317 477001/476830
> > > FAX: +31 317 418094
> > > paulien.adamse at wur.nl
> > > www.plant.wageningen-ur.nl
> >
> > ---------------------------------------------------------------------------
> >---- Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu The
> > Arabidopsis Information Resource	FAX: (650) 325-6857
> > Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology		URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > ---------------------------------------------------------------------------
> >----
>
> --
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------





From lstein at cshl.edu  Fri Oct 17 20:36:01 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri, 17 Oct 2003 20:36:01 -0400
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <3F904561.9040005@cornell.edu>
References: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU>
 <3F904561.9040005@cornell.edu>
Message-ID: <200310172036.01540.lstein@cshl.edu>

Since Pauline wasn't planning to go to PAG, we can hold off on meeting her 
until july.  But we should have a teleconference with her sooner.

Lincoln

On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal wrote:
> Hi Leonore,
>
> Meeting Pauline at the PAG will be a great idea. We can have discussion
> with him and other potential target DBs and projects. However, POC's first
> user meeting is in July next year. In Jan at Stanford it will be a GO users
> meeting, where many of the plant people are trying to come, e.g. Deepgene
> group.
>
> Leonore Reiser wrote:
> > Hi Everyone, I assume that ya'll have had a chance to read this email.
> > I'd like to send a response soon but want feedback as to how this should
> > be approached. I dont know anymore about what they are doing than what
> > has been written so obviously need to find out more about the project
> > (Pankaj do you know if this is the one Klaus is working with?).
>
> Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
> Project is at http://mips.gsf.de/proj/thal/phenotype/
>
> > Anyway- can I suggest this for an agenda item on the 22nd. In the
> > meanwhile what is the general feeling about how to proceed. If they have
> > some concrete suggestions/feedback it would be excellent to incorporate
> > this at the outset. It would be great to pick an area of an ontology to
> > work on with them and see how this goes.
>
> I agree with Sue, since their priority is on Arabidopsis.
>
> > Best
> > Leonore
> >
> > -------------------------------------------------------------------------
> >------ Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource	FAX: (650) 325-6857
> > Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology		URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------
> >------
> >
> > ---------- Forwarded message ----------
> > Date: Fri, 17 Oct 2003 09:33:42 +0200
> > From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> > To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> > Cc: lstein at cshl.org, po-dev at plantontology.org
> > Subject: RE: plant ontology, cooperation?
> >
> > Dear Leonore (and others),
> >
> > Thanks for the very fast response! I did not plan to attend the PAG
> > conference, but am rethinking that now. It would be the best way to start
> > cooperating. In the mean time, do you have suggestions for our group for
> > issues we should discuss (or find out) before coming to your meeting?
> >
> > Bye,
> > Paulien
> >
> > -----Original Message-----
> > From: Lincoln Stein [mailto:lstein at cshl.edu]
> > Sent: Thursday, October 16, 2003 16:23
> > To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> > Cc: po-dev at plantontology.org
> > Subject: Re: plant ontology, cooperation?
> >
> >
> > Hello Paulien,
> >
> > As PI of the POC project, I would like to personally express my
> > enthusiasm for building a collaboration with your group to develop
> > plant-wide ontologies to describe plant anatomy and developmental stages.
> >  It would be very good for our groups to meet at the San Diego users'
> > meeting.
> >
> > Lincoln
> >
> > On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> >>Dear Paulien:
> >>
> >>This is wonderful. TAIR is part of a recently funded project to develop
> >>plant ontologies called the "Plant Ontology Consortium". The goals of
> >> this project are exactly what you describe.
> >>
> >>The project website is http://www.plantontology.org/. So far most of the
> >>ontology development has been done by Gramene (rice), TAIR and Maize DB.
> >>The website describes the project and how to access the ontologies. We
> >> are using the DAGeditor and ontology representation developed by the GO
> >> (directed, acyclic graphs). The plan is to make the ontologies as
> >> broadly applicable as we can to accomodate as many organisms as
> >> possible. The ontologies can be accessed without restriction and the GO
> >> has made the DAGeditor freely available. We are using the CVS repository
> >> as a shared development resource and communicating over email primarily
> >> for development.
> >>
> >>It would be fantastic to work with your group to develop the structure
> >> and content of the ontologies.We were planning to have a users meeting
> >> in January, following the PAG meeting in San Diego-will people from your
> >> organization be attending?
> >>
> >>I am ccing this email to the group.We have just hired a coordinator (your
> >>counterpart here)  who will be starting soon. She will be based at TAIR
> >> but will coordinate the efforts for the whole group-in the meantime, I
> >> am very happy to work with you. Best Regards
> >>Leonore Reiser
> >>
> >>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> >>>Dear Mrs. Reiser,
> >>>
> >>>I hope you are the right person to write to about this, but I will give
> >>>it a try. If I should contact somebody else, please let me know.
> >>>
> >>>I am writing on behalf of seven partner labs in Europe, working together
> >>>to establish a network of plant databases. The project is called PlaNet
> >>>(at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> >>>partners all have databases with information about Arabidopsis (and
> >>>sometimes other plants). Some are working on prediction-tools, others
> >>>have collections of mutantlines (or germplasm or accessions, etc.). The
> >>>goal is to connect them all and build one general access to it, using
> >>>BioMoby. People will be able to query through this site and do not have
> >>>to worry about in which database they have to look for their
> >>> information.
> >>>
> >>>To be able to query multiple databases with one type of question it is
> >>>very important to standardize the available information as much as
> >>>possible. One important aspect in this is the description of the
> >>> mutants. We set up a working group to compare the different
> >>>ontologies/vocabularies already used by the different partners. I am the
> >>>coordinator of this group. In Wageningen I am in the process of building
> >>>a database for our mutants (WAtDB, not online yet), but we already have
> >>> a wealth of information about mutants, transgenics and natural
> >>> variants. But no standard terminology (yet) for describing them.
> >>>
> >>>This is where my request to you is coming in. We have a lot of phenotype
> >>>descriptions and already noticed that not everything has been covered by
> >>>the TAIR vocabulary. One way to solve that is to send you numerous
> >>>submissions/update requests. But we thought that it might be more useful
> >>>to work together more structural. Are you interested in cooperation with
> >>>our group? If so, what would be a good way to do this? In November our
> >>> PO working group is meeting again here in Wageningen and I would like
> >>> to discuss it with them during that meeting. But it would be very
> >>> useful to know what you think about it and maybe already get some
> >>> suggestions about how we could work together.
> >>>
> >>>I hope you are interested and have time to reply within a few weeks.
> >>> That way I can use your information when I am preparing our coming EU
> >>> PlaNet PO working group meeting.
> >>>
> >>>Thanks in advance!
> >>>
> >>>Best wishes,
> >>>Paulien
> >>>
> >>>
> >>>Dr Paulien Adamse
> >>>BU Bioscience
> >>>Plant Research International,
> >>>P.O. Box 16,
> >>>6700 AA Wageningen,
> >>>The Netherlands.
> >>>
> >>>Tel: +31 317 477001/476830
> >>>FAX: +31 317 418094
> >>>paulien.adamse at wur.nl
> >>>www.plant.wageningen-ur.nl
> >>
> >>-------------------------------------------------------------------------
> >>-- ---- Leonore Reiser, Ph.D.                  
> >> lreiser at acoma.stanford.edu The Arabidopsis Information Resource	FAX:
> >> (650) 325-6857
> >>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >>Department of Plant Biology		URL: http://arabidopsis.org/
> >>260 Panama St.
> >>Stanford, CA 94305
> >>-------------------------------------------------------------------------
> >>-- ----

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)


From pj37 at cornell.edu  Sat Oct 18 13:14:19 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Sat, 18 Oct 2003 13:14:19 -0400
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <200310172036.01540.lstein@cshl.edu>
References: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU> <3F904561.9040005@cornell.edu> <200310172036.01540.lstein@cshl.edu>
Message-ID: <3F9174EB.1060209@cornell.edu>

I agree. Leonore, do you want to go ahead and arrange a conf. call with Pauline.

Thanks
Pankaj


Lincoln Stein wrote:
> Since Pauline wasn't planning to go to PAG, we can hold off on meeting her 
> until july.  But we should have a teleconference with her sooner.
> 
> Lincoln
> 
> On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal wrote:
> 
>>Hi Leonore,
>>
>>Meeting Pauline at the PAG will be a great idea. We can have discussion
>>with him and other potential target DBs and projects. However, POC's first
>>user meeting is in July next year. In Jan at Stanford it will be a GO users
>>meeting, where many of the plant people are trying to come, e.g. Deepgene
>>group.
>>
>>Leonore Reiser wrote:
>>
>>>Hi Everyone, I assume that ya'll have had a chance to read this email.
>>>I'd like to send a response soon but want feedback as to how this should
>>>be approached. I dont know anymore about what they are doing than what
>>>has been written so obviously need to find out more about the project
>>>(Pankaj do you know if this is the one Klaus is working with?).
>>
>>Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
>>Project is at http://mips.gsf.de/proj/thal/phenotype/
>>
>>
>>>Anyway- can I suggest this for an agenda item on the 22nd. In the
>>>meanwhile what is the general feeling about how to proceed. If they have
>>>some concrete suggestions/feedback it would be excellent to incorporate
>>>this at the outset. It would be great to pick an area of an ontology to
>>>work on with them and see how this goes.
>>
>>I agree with Sue, since their priority is on Arabidopsis.
>>
>>
>>>Best
>>>Leonore
>>>
>>>-------------------------------------------------------------------------
>>>------ Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
>>>The Arabidopsis Information Resource	FAX: (650) 325-6857
>>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>>>Department of Plant Biology		URL: http://arabidopsis.org/
>>>260 Panama St.
>>>Stanford, CA 94305
>>>-------------------------------------------------------------------------
>>>------
>>>
>>>---------- Forwarded message ----------
>>>Date: Fri, 17 Oct 2003 09:33:42 +0200
>>>From: "Adamse, Paulien" <paulien.adamse at wur.nl>
>>>To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
>>>Cc: lstein at cshl.org, po-dev at plantontology.org
>>>Subject: RE: plant ontology, cooperation?
>>>
>>>Dear Leonore (and others),
>>>
>>>Thanks for the very fast response! I did not plan to attend the PAG
>>>conference, but am rethinking that now. It would be the best way to start
>>>cooperating. In the mean time, do you have suggestions for our group for
>>>issues we should discuss (or find out) before coming to your meeting?
>>>
>>>Bye,
>>>Paulien
>>>
>>>-----Original Message-----
>>>From: Lincoln Stein [mailto:lstein at cshl.edu]
>>>Sent: Thursday, October 16, 2003 16:23
>>>To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
>>>Cc: po-dev at plantontology.org
>>>Subject: Re: plant ontology, cooperation?
>>>
>>>
>>>Hello Paulien,
>>>
>>>As PI of the POC project, I would like to personally express my
>>>enthusiasm for building a collaboration with your group to develop
>>>plant-wide ontologies to describe plant anatomy and developmental stages.
>>> It would be very good for our groups to meet at the San Diego users'
>>>meeting.
>>>
>>>Lincoln
>>>
>>>On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
>>>
>>>>Dear Paulien:
>>>>
>>>>This is wonderful. TAIR is part of a recently funded project to develop
>>>>plant ontologies called the "Plant Ontology Consortium". The goals of
>>>>this project are exactly what you describe.
>>>>
>>>>The project website is http://www.plantontology.org/. So far most of the
>>>>ontology development has been done by Gramene (rice), TAIR and Maize DB.
>>>>The website describes the project and how to access the ontologies. We
>>>>are using the DAGeditor and ontology representation developed by the GO
>>>>(directed, acyclic graphs). The plan is to make the ontologies as
>>>>broadly applicable as we can to accomodate as many organisms as
>>>>possible. The ontologies can be accessed without restriction and the GO
>>>>has made the DAGeditor freely available. We are using the CVS repository
>>>>as a shared development resource and communicating over email primarily
>>>>for development.
>>>>
>>>>It would be fantastic to work with your group to develop the structure
>>>>and content of the ontologies.We were planning to have a users meeting
>>>>in January, following the PAG meeting in San Diego-will people from your
>>>>organization be attending?
>>>>
>>>>I am ccing this email to the group.We have just hired a coordinator (your
>>>>counterpart here)  who will be starting soon. She will be based at TAIR
>>>>but will coordinate the efforts for the whole group-in the meantime, I
>>>>am very happy to work with you. Best Regards
>>>>Leonore Reiser
>>>>
>>>>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
>>>>
>>>>>Dear Mrs. Reiser,
>>>>>
>>>>>I hope you are the right person to write to about this, but I will give
>>>>>it a try. If I should contact somebody else, please let me know.
>>>>>
>>>>>I am writing on behalf of seven partner labs in Europe, working together
>>>>>to establish a network of plant databases. The project is called PlaNet
>>>>>(at the moment the address is http://mips.gsf.de/proj/planet/). The 7
>>>>>partners all have databases with information about Arabidopsis (and
>>>>>sometimes other plants). Some are working on prediction-tools, others
>>>>>have collections of mutantlines (or germplasm or accessions, etc.). The
>>>>>goal is to connect them all and build one general access to it, using
>>>>>BioMoby. People will be able to query through this site and do not have
>>>>>to worry about in which database they have to look for their
>>>>>information.
>>>>>
>>>>>To be able to query multiple databases with one type of question it is
>>>>>very important to standardize the available information as much as
>>>>>possible. One important aspect in this is the description of the
>>>>>mutants. We set up a working group to compare the different
>>>>>ontologies/vocabularies already used by the different partners. I am the
>>>>>coordinator of this group. In Wageningen I am in the process of building
>>>>>a database for our mutants (WAtDB, not online yet), but we already have
>>>>>a wealth of information about mutants, transgenics and natural
>>>>>variants. But no standard terminology (yet) for describing them.
>>>>>
>>>>>This is where my request to you is coming in. We have a lot of phenotype
>>>>>descriptions and already noticed that not everything has been covered by
>>>>>the TAIR vocabulary. One way to solve that is to send you numerous
>>>>>submissions/update requests. But we thought that it might be more useful
>>>>>to work together more structural. Are you interested in cooperation with
>>>>>our group? If so, what would be a good way to do this? In November our
>>>>>PO working group is meeting again here in Wageningen and I would like
>>>>>to discuss it with them during that meeting. But it would be very
>>>>>useful to know what you think about it and maybe already get some
>>>>>suggestions about how we could work together.
>>>>>
>>>>>I hope you are interested and have time to reply within a few weeks.
>>>>>That way I can use your information when I am preparing our coming EU
>>>>>PlaNet PO working group meeting.
>>>>>
>>>>>Thanks in advance!
>>>>>
>>>>>Best wishes,
>>>>>Paulien
>>>>>
>>>>>
>>>>>Dr Paulien Adamse
>>>>>BU Bioscience
>>>>>Plant Research International,
>>>>>P.O. Box 16,
>>>>>6700 AA Wageningen,
>>>>>The Netherlands.
>>>>>
>>>>>Tel: +31 317 477001/476830
>>>>>FAX: +31 317 418094
>>>>>paulien.adamse at wur.nl
>>>>>www.plant.wageningen-ur.nl
>>>>
>>>>-------------------------------------------------------------------------
>>>>-- ---- Leonore Reiser, Ph.D.                  
>>>>lreiser at acoma.stanford.edu The Arabidopsis Information Resource	FAX:
>>>>(650) 325-6857
>>>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
>>>>Department of Plant Biology		URL: http://arabidopsis.org/
>>>>260 Panama St.
>>>>Stanford, CA 94305
>>>>-------------------------------------------------------------------------
>>>>-- ----
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research 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 lstein at cshl.edu  Sat Oct 18 13:47:16 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat, 18 Oct 2003 13:47:16 -0400
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <3F9174EB.1060209@cornell.edu>
References: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU>
 <200310172036.01540.lstein@cshl.edu> <3F9174EB.1060209@cornell.edu>
Message-ID: <200310181347.16270.lstein@cshl.edu>

Hi Folks,

Just a warning.  We've started mangling Paulien's name.  I 
might have started it.

Lincoln

On Saturday 18 October 2003 01:14 pm, Pankaj Jaiswal wrote:
> I agree. Leonore, do you want to go ahead and arrange a
> conf. call with Pauline.
>
> Thanks
> Pankaj
>
> Lincoln Stein wrote:
> > Since Pauline wasn't planning to go to PAG, we can hold
> > off on meeting her until july.  But we should have a
> > teleconference with her sooner.
> >
> > Lincoln
> >
> > On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal 
wrote:
> >>Hi Leonore,
> >>
> >>Meeting Pauline at the PAG will be a great idea. We can
> >> have discussion with him and other potential target
> >> DBs and projects. However, POC's first user meeting is
> >> in July next year. In Jan at Stanford it will be a GO
> >> users meeting, where many of the plant people are
> >> trying to come, e.g. Deepgene group.
> >>
> >>Leonore Reiser wrote:
> >>>Hi Everyone, I assume that ya'll have had a chance to
> >>> read this email. I'd like to send a response soon but
> >>> want feedback as to how this should be approached. I
> >>> dont know anymore about what they are doing than what
> >>> has been written so obviously need to find out more
> >>> about the project (Pankaj do you know if this is the
> >>> one Klaus is working with?).
> >>
> >>Klaus has a different project and the person is Heidrun
> >>  (gundlach at gsf.de) Project is at
> >> http://mips.gsf.de/proj/thal/phenotype/
> >>
> >>>Anyway- can I suggest this for an agenda item on the
> >>> 22nd. In the meanwhile what is the general feeling
> >>> about how to proceed. If they have some concrete
> >>> suggestions/feedback it would be excellent to
> >>> incorporate this at the outset. It would be great to
> >>> pick an area of an ontology to work on with them and
> >>> see how this goes.
> >>
> >>I agree with Sue, since their priority is on
> >> Arabidopsis.
> >>
> >>>Best
> >>>Leonore
> >>>
> >>>------------------------------------------------------
> >>>------------------- ------ Leonore Reiser, Ph.D.      
> >>>             lreiser at acoma.stanford.edu The
> >>> Arabidopsis Information Resource	FAX: (650) 325-6857
> >>> Carnegie Institution of Washington	Tel: (650)
> >>> 325-1521 ext. 311 Department of Plant Biology		URL:
> >>> http://arabidopsis.org/ 260 Panama St.
> >>>Stanford, CA 94305
> >>>------------------------------------------------------
> >>>------------------- ------
> >>>
> >>>---------- Forwarded message ----------
> >>>Date: Fri, 17 Oct 2003 09:33:42 +0200
> >>>From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> >>>To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> >>>Cc: lstein at cshl.org, po-dev at plantontology.org
> >>>Subject: RE: plant ontology, cooperation?
> >>>
> >>>Dear Leonore (and others),
> >>>
> >>>Thanks for the very fast response! I did not plan to
> >>> attend the PAG conference, but am rethinking that
> >>> now. It would be the best way to start cooperating.
> >>> In the mean time, do you have suggestions for our
> >>> group for issues we should discuss (or find out)
> >>> before coming to your meeting?
> >>>
> >>>Bye,
> >>>Paulien
> >>>
> >>>-----Original Message-----
> >>>From: Lincoln Stein [mailto:lstein at cshl.edu]
> >>>Sent: Thursday, October 16, 2003 16:23
> >>>To: po-dev at plantontology.org; Leonore Reiser; Adamse,
> >>> Paulien Cc: po-dev at plantontology.org
> >>>Subject: Re: plant ontology, cooperation?
> >>>
> >>>
> >>>Hello Paulien,
> >>>
> >>>As PI of the POC project, I would like to personally
> >>> express my enthusiasm for building a collaboration
> >>> with your group to develop plant-wide ontologies to
> >>> describe plant anatomy and developmental stages. It
> >>> would be very good for our groups to meet at the San
> >>> Diego users' meeting.
> >>>
> >>>Lincoln
> >>>
> >>>On Thursday 16 October 2003 09:54 am, Leonore Reiser 
wrote:
> >>>>Dear Paulien:
> >>>>
> >>>>This is wonderful. TAIR is part of a recently funded
> >>>> project to develop plant ontologies called the
> >>>> "Plant Ontology Consortium". The goals of this
> >>>> project are exactly what you describe.
> >>>>
> >>>>The project website is http://www.plantontology.org/.
> >>>> So far most of the ontology development has been
> >>>> done by Gramene (rice), TAIR and Maize DB. The
> >>>> website describes the project and how to access the
> >>>> ontologies. We are using the DAGeditor and ontology
> >>>> representation developed by the GO (directed,
> >>>> acyclic graphs). The plan is to make the ontologies
> >>>> as broadly applicable as we can to accomodate as
> >>>> many organisms as possible. The ontologies can be
> >>>> accessed without restriction and the GO has made the
> >>>> DAGeditor freely available. We are using the CVS
> >>>> repository as a shared development resource and
> >>>> communicating over email primarily for development.
> >>>>
> >>>>It would be fantastic to work with your group to
> >>>> develop the structure and content of the
> >>>> ontologies.We were planning to have a users meeting
> >>>> in January, following the PAG meeting in San
> >>>> Diego-will people from your organization be
> >>>> attending?
> >>>>
> >>>>I am ccing this email to the group.We have just hired
> >>>> a coordinator (your counterpart here)  who will be
> >>>> starting soon. She will be based at TAIR but will
> >>>> coordinate the efforts for the whole group-in the
> >>>> meantime, I am very happy to work with you. Best
> >>>> Regards Leonore Reiser
> >>>>
> >>>>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> >>>>>Dear Mrs. Reiser,
> >>>>>
> >>>>>I hope you are the right person to write to about
> >>>>> this, but I will give it a try. If I should contact
> >>>>> somebody else, please let me know.
> >>>>>
> >>>>>I am writing on behalf of seven partner labs in
> >>>>> Europe, working together to establish a network of
> >>>>> plant databases. The project is called PlaNet (at
> >>>>> the moment the address is
> >>>>> http://mips.gsf.de/proj/planet/). The 7 partners
> >>>>> all have databases with information about
> >>>>> Arabidopsis (and sometimes other plants). Some are
> >>>>> working on prediction-tools, others have
> >>>>> collections of mutantlines (or germplasm or
> >>>>> accessions, etc.). The goal is to connect them all
> >>>>> and build one general access to it, using BioMoby.
> >>>>> People will be able to query through this site and
> >>>>> do not have to worry about in which database they
> >>>>> have to look for their information.
> >>>>>
> >>>>>To be able to query multiple databases with one type
> >>>>> of question it is very important to standardize the
> >>>>> available information as much as possible. One
> >>>>> important aspect in this is the description of the
> >>>>> mutants. We set up a working group to compare the
> >>>>> different ontologies/vocabularies already used by
> >>>>> the different partners. I am the coordinator of
> >>>>> this group. In Wageningen I am in the process of
> >>>>> building a database for our mutants (WAtDB, not
> >>>>> online yet), but we already have a wealth of
> >>>>> information about mutants, transgenics and natural
> >>>>> variants. But no standard terminology (yet) for
> >>>>> describing them.
> >>>>>
> >>>>>This is where my request to you is coming in. We
> >>>>> have a lot of phenotype descriptions and already
> >>>>> noticed that not everything has been covered by the
> >>>>> TAIR vocabulary. One way to solve that is to send
> >>>>> you numerous submissions/update requests. But we
> >>>>> thought that it might be more useful to work
> >>>>> together more structural. Are you interested in
> >>>>> cooperation with our group? If so, what would be a
> >>>>> good way to do this? In November our PO working
> >>>>> group is meeting again here in Wageningen and I
> >>>>> would like to discuss it with them during that
> >>>>> meeting. But it would be very useful to know what
> >>>>> you think about it and maybe already get some
> >>>>> suggestions about how we could work together.
> >>>>>
> >>>>>I hope you are interested and have time to reply
> >>>>> within a few weeks. That way I can use your
> >>>>> information when I am preparing our coming EU
> >>>>> PlaNet PO working group meeting.
> >>>>>
> >>>>>Thanks in advance!
> >>>>>
> >>>>>Best wishes,
> >>>>>Paulien
> >>>>>
> >>>>>
> >>>>>Dr Paulien Adamse
> >>>>>BU Bioscience
> >>>>>Plant Research International,
> >>>>>P.O. Box 16,
> >>>>>6700 AA Wageningen,
> >>>>>The Netherlands.
> >>>>>
> >>>>>Tel: +31 317 477001/476830
> >>>>>FAX: +31 317 418094
> >>>>>paulien.adamse at wur.nl
> >>>>>www.plant.wageningen-ur.nl
> >>>>
> >>>>-----------------------------------------------------
> >>>>-------------------- -- ---- Leonore Reiser, Ph.D.
> >>>>lreiser at acoma.stanford.edu The Arabidopsis
> >>>> Information Resource	FAX: (650) 325-6857
> >>>>Carnegie Institution of Washington	Tel: (650)
> >>>> 325-1521 ext. 311 Department of Plant Biology		URL:
> >>>> http://arabidopsis.org/ 260 Panama St.
> >>>>Stanford, CA 94305
> >>>>-----------------------------------------------------
> >>>>-------------------- -- ----


From pj37 at cornell.edu  Sat Oct 18 13:52:36 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Sat, 18 Oct 2003 13:52:36 -0400
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <200310181347.16270.lstein@cshl.edu>
References: <Pine.GSO.4.44.0310171133020.12875-100000@acoma.Stanford.EDU> <200310172036.01540.lstein@cshl.edu> <3F9174EB.1060209@cornell.edu> <200310181347.16270.lstein@cshl.edu>
Message-ID: <3F917DE4.70808@cornell.edu>

I guess it was me. Sorry for that. I will be careful next time

Thanks for pointing it.
Pankaj

Lincoln Stein wrote:

> Hi Folks,
> 
> Just a warning.  We've started mangling Paulien's name.  I 
> might have started it.
> 
> Lincoln
> 
> On Saturday 18 October 2003 01:14 pm, Pankaj Jaiswal wrote:
> 
>>I agree. Leonore, do you want to go ahead and arrange a
>>conf. call with Pauline.
>>
>>Thanks
>>Pankaj
>>
>>Lincoln Stein wrote:
>>
>>>Since Pauline wasn't planning to go to PAG, we can hold
>>>off on meeting her until july.  But we should have a
>>>teleconference with her sooner.
>>>
>>>Lincoln
>>>
>>>On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal 
> 
> wrote:
> 
>>>>Hi Leonore,
>>>>
>>>>Meeting Pauline at the PAG will be a great idea. We can
>>>>have discussion with him and other potential target
>>>>DBs and projects. However, POC's first user meeting is
>>>>in July next year. In Jan at Stanford it will be a GO
>>>>users meeting, where many of the plant people are
>>>>trying to come, e.g. Deepgene group.
>>>>
>>>>Leonore Reiser wrote:
>>>>
>>>>>Hi Everyone, I assume that ya'll have had a chance to
>>>>>read this email. I'd like to send a response soon but
>>>>>want feedback as to how this should be approached. I
>>>>>dont know anymore about what they are doing than what
>>>>>has been written so obviously need to find out more
>>>>>about the project (Pankaj do you know if this is the
>>>>>one Klaus is working with?).
>>>>
>>>>Klaus has a different project and the person is Heidrun
>>>> (gundlach at gsf.de) Project is at
>>>>http://mips.gsf.de/proj/thal/phenotype/
>>>>
>>>>
>>>>>Anyway- can I suggest this for an agenda item on the
>>>>>22nd. In the meanwhile what is the general feeling
>>>>>about how to proceed. If they have some concrete
>>>>>suggestions/feedback it would be excellent to
>>>>>incorporate this at the outset. It would be great to
>>>>>pick an area of an ontology to work on with them and
>>>>>see how this goes.
>>>>
>>>>I agree with Sue, since their priority is on
>>>>Arabidopsis.




From lreiser at acoma.Stanford.EDU  Mon Oct 20 08:17:02 2003
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Mon, 20 Oct 2003 05:17:02 -0700 (PDT)
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <3F9174EB.1060209@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310200514061.17944-100000@acoma.Stanford.EDU>

Haven't yet heard back regarding the last email from
Paulien. I'll suggest it- but maybe lets see what we can resolve/deal with
over email first. If we're all going to go to the trrouble of a conference
call with this many time zones- we should have a very defined agenda
(IMHO).
Leonore


On Sat, 18 Oct 2003, Pankaj Jaiswal wrote:

> I agree. Leonore, do you want to go ahead and arrange a conf. call with Pauline.
>
> Thanks
> Pankaj
>
>
> Lincoln Stein wrote:
> > Since Pauline wasn't planning to go to PAG, we can hold off on meeting her
> > until july.  But we should have a teleconference with her sooner.
> >
> > Lincoln
> >
> > On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal wrote:
> >
> >>Hi Leonore,
> >>
> >>Meeting Pauline at the PAG will be a great idea. We can have discussion
> >>with him and other potential target DBs and projects. However, POC's first
> >>user meeting is in July next year. In Jan at Stanford it will be a GO users
> >>meeting, where many of the plant people are trying to come, e.g. Deepgene
> >>group.
> >>
> >>Leonore Reiser wrote:
> >>
> >>>Hi Everyone, I assume that ya'll have had a chance to read this email.
> >>>I'd like to send a response soon but want feedback as to how this should
> >>>be approached. I dont know anymore about what they are doing than what
> >>>has been written so obviously need to find out more about the project
> >>>(Pankaj do you know if this is the one Klaus is working with?).
> >>
> >>Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
> >>Project is at http://mips.gsf.de/proj/thal/phenotype/
> >>
> >>
> >>>Anyway- can I suggest this for an agenda item on the 22nd. In the
> >>>meanwhile what is the general feeling about how to proceed. If they have
> >>>some concrete suggestions/feedback it would be excellent to incorporate
> >>>this at the outset. It would be great to pick an area of an ontology to
> >>>work on with them and see how this goes.
> >>
> >>I agree with Sue, since their priority is on Arabidopsis.
> >>
> >>
> >>>Best
> >>>Leonore
> >>>
> >>>-------------------------------------------------------------------------
> >>>------ Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> >>>The Arabidopsis Information Resource	FAX: (650) 325-6857
> >>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >>>Department of Plant Biology		URL: http://arabidopsis.org/
> >>>260 Panama St.
> >>>Stanford, CA 94305
> >>>-------------------------------------------------------------------------
> >>>------
> >>>
> >>>---------- Forwarded message ----------
> >>>Date: Fri, 17 Oct 2003 09:33:42 +0200
> >>>From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> >>>To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> >>>Cc: lstein at cshl.org, po-dev at plantontology.org
> >>>Subject: RE: plant ontology, cooperation?
> >>>
> >>>Dear Leonore (and others),
> >>>
> >>>Thanks for the very fast response! I did not plan to attend the PAG
> >>>conference, but am rethinking that now. It would be the best way to start
> >>>cooperating. In the mean time, do you have suggestions for our group for
> >>>issues we should discuss (or find out) before coming to your meeting?
> >>>
> >>>Bye,
> >>>Paulien
> >>>
> >>>-----Original Message-----
> >>>From: Lincoln Stein [mailto:lstein at cshl.edu]
> >>>Sent: Thursday, October 16, 2003 16:23
> >>>To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> >>>Cc: po-dev at plantontology.org
> >>>Subject: Re: plant ontology, cooperation?
> >>>
> >>>
> >>>Hello Paulien,
> >>>
> >>>As PI of the POC project, I would like to personally express my
> >>>enthusiasm for building a collaboration with your group to develop
> >>>plant-wide ontologies to describe plant anatomy and developmental stages.
> >>> It would be very good for our groups to meet at the San Diego users'
> >>>meeting.
> >>>
> >>>Lincoln
> >>>
> >>>On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> >>>
> >>>>Dear Paulien:
> >>>>
> >>>>This is wonderful. TAIR is part of a recently funded project to develop
> >>>>plant ontologies called the "Plant Ontology Consortium". The goals of
> >>>>this project are exactly what you describe.
> >>>>
> >>>>The project website is http://www.plantontology.org/. So far most of the
> >>>>ontology development has been done by Gramene (rice), TAIR and Maize DB.
> >>>>The website describes the project and how to access the ontologies. We
> >>>>are using the DAGeditor and ontology representation developed by the GO
> >>>>(directed, acyclic graphs). The plan is to make the ontologies as
> >>>>broadly applicable as we can to accomodate as many organisms as
> >>>>possible. The ontologies can be accessed without restriction and the GO
> >>>>has made the DAGeditor freely available. We are using the CVS repository
> >>>>as a shared development resource and communicating over email primarily
> >>>>for development.
> >>>>
> >>>>It would be fantastic to work with your group to develop the structure
> >>>>and content of the ontologies.We were planning to have a users meeting
> >>>>in January, following the PAG meeting in San Diego-will people from your
> >>>>organization be attending?
> >>>>
> >>>>I am ccing this email to the group.We have just hired a coordinator (your
> >>>>counterpart here)  who will be starting soon. She will be based at TAIR
> >>>>but will coordinate the efforts for the whole group-in the meantime, I
> >>>>am very happy to work with you. Best Regards
> >>>>Leonore Reiser
> >>>>
> >>>>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> >>>>
> >>>>>Dear Mrs. Reiser,
> >>>>>
> >>>>>I hope you are the right person to write to about this, but I will give
> >>>>>it a try. If I should contact somebody else, please let me know.
> >>>>>
> >>>>>I am writing on behalf of seven partner labs in Europe, working together
> >>>>>to establish a network of plant databases. The project is called PlaNet
> >>>>>(at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> >>>>>partners all have databases with information about Arabidopsis (and
> >>>>>sometimes other plants). Some are working on prediction-tools, others
> >>>>>have collections of mutantlines (or germplasm or accessions, etc.). The
> >>>>>goal is to connect them all and build one general access to it, using
> >>>>>BioMoby. People will be able to query through this site and do not have
> >>>>>to worry about in which database they have to look for their
> >>>>>information.
> >>>>>
> >>>>>To be able to query multiple databases with one type of question it is
> >>>>>very important to standardize the available information as much as
> >>>>>possible. One important aspect in this is the description of the
> >>>>>mutants. We set up a working group to compare the different
> >>>>>ontologies/vocabularies already used by the different partners. I am the
> >>>>>coordinator of this group. In Wageningen I am in the process of building
> >>>>>a database for our mutants (WAtDB, not online yet), but we already have
> >>>>>a wealth of information about mutants, transgenics and natural
> >>>>>variants. But no standard terminology (yet) for describing them.
> >>>>>
> >>>>>This is where my request to you is coming in. We have a lot of phenotype
> >>>>>descriptions and already noticed that not everything has been covered by
> >>>>>the TAIR vocabulary. One way to solve that is to send you numerous
> >>>>>submissions/update requests. But we thought that it might be more useful
> >>>>>to work together more structural. Are you interested in cooperation with
> >>>>>our group? If so, what would be a good way to do this? In November our
> >>>>>PO working group is meeting again here in Wageningen and I would like
> >>>>>to discuss it with them during that meeting. But it would be very
> >>>>>useful to know what you think about it and maybe already get some
> >>>>>suggestions about how we could work together.
> >>>>>
> >>>>>I hope you are interested and have time to reply within a few weeks.
> >>>>>That way I can use your information when I am preparing our coming EU
> >>>>>PlaNet PO working group meeting.
> >>>>>
> >>>>>Thanks in advance!
> >>>>>
> >>>>>Best wishes,
> >>>>>Paulien
> >>>>>
> >>>>>
> >>>>>Dr Paulien Adamse
> >>>>>BU Bioscience
> >>>>>Plant Research International,
> >>>>>P.O. Box 16,
> >>>>>6700 AA Wageningen,
> >>>>>The Netherlands.
> >>>>>
> >>>>>Tel: +31 317 477001/476830
> >>>>>FAX: +31 317 418094
> >>>>>paulien.adamse at wur.nl
> >>>>>www.plant.wageningen-ur.nl
> >>>>
> >>>>-------------------------------------------------------------------------
> >>>>-- ---- Leonore Reiser, Ph.D.
> >>>>lreiser at acoma.stanford.edu The Arabidopsis Information Resource	FAX:
> >>>>(650) 325-6857
> >>>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> >>>>Department of Plant Biology		URL: http://arabidopsis.org/
> >>>>260 Panama St.
> >>>>Stanford, CA 94305
> >>>>-------------------------------------------------------------------------
> >>>>-- ----
> >
> >
>
> --
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Research 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
> ******************************************
>
>
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From rhee at acoma.Stanford.EDU  Mon Oct 20 12:56:07 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Mon, 20 Oct 2003 09:56:07 -0700 (PDT)
Subject: About (RE: plant ontology, cooperation? (fwd))
In-Reply-To: <Pine.GSO.4.44.0310200514061.17944-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0310200955590.18902-100000@acoma.Stanford.EDU>

i totally agree.
sue

On Mon, 20 Oct 2003, Leonore Reiser wrote:

> Haven't yet heard back regarding the last email from
> Paulien. I'll suggest it- but maybe lets see what we can resolve/deal with
> over email first. If we're all going to go to the trrouble of a conference
> call with this many time zones- we should have a very defined agenda
> (IMHO).
> Leonore
>
>
> On Sat, 18 Oct 2003, Pankaj Jaiswal wrote:
>
> > I agree. Leonore, do you want to go ahead and arrange a conf. call with Pauline.
> >
> > Thanks
> > Pankaj
> >
> >
> > Lincoln Stein wrote:
> > > Since Pauline wasn't planning to go to PAG, we can hold off on meeting her
> > > until july.  But we should have a teleconference with her sooner.
> > >
> > > Lincoln
> > >
> > > On Friday 17 October 2003 03:39 pm, Pankaj Jaiswal wrote:
> > >
> > >>Hi Leonore,
> > >>
> > >>Meeting Pauline at the PAG will be a great idea. We can have discussion
> > >>with him and other potential target DBs and projects. However, POC's first
> > >>user meeting is in July next year. In Jan at Stanford it will be a GO users
> > >>meeting, where many of the plant people are trying to come, e.g. Deepgene
> > >>group.
> > >>
> > >>Leonore Reiser wrote:
> > >>
> > >>>Hi Everyone, I assume that ya'll have had a chance to read this email.
> > >>>I'd like to send a response soon but want feedback as to how this should
> > >>>be approached. I dont know anymore about what they are doing than what
> > >>>has been written so obviously need to find out more about the project
> > >>>(Pankaj do you know if this is the one Klaus is working with?).
> > >>
> > >>Klaus has a different project and the person is Heidrun  (gundlach at gsf.de)
> > >>Project is at http://mips.gsf.de/proj/thal/phenotype/
> > >>
> > >>
> > >>>Anyway- can I suggest this for an agenda item on the 22nd. In the
> > >>>meanwhile what is the general feeling about how to proceed. If they have
> > >>>some concrete suggestions/feedback it would be excellent to incorporate
> > >>>this at the outset. It would be great to pick an area of an ontology to
> > >>>work on with them and see how this goes.
> > >>
> > >>I agree with Sue, since their priority is on Arabidopsis.
> > >>
> > >>
> > >>>Best
> > >>>Leonore
> > >>>
> > >>>-------------------------------------------------------------------------
> > >>>------ Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > >>>The Arabidopsis Information Resource	FAX: (650) 325-6857
> > >>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > >>>Department of Plant Biology		URL: http://arabidopsis.org/
> > >>>260 Panama St.
> > >>>Stanford, CA 94305
> > >>>-------------------------------------------------------------------------
> > >>>------
> > >>>
> > >>>---------- Forwarded message ----------
> > >>>Date: Fri, 17 Oct 2003 09:33:42 +0200
> > >>>From: "Adamse, Paulien" <paulien.adamse at wur.nl>
> > >>>To: Leonore Reiser <lreiser at acoma.Stanford.EDU>
> > >>>Cc: lstein at cshl.org, po-dev at plantontology.org
> > >>>Subject: RE: plant ontology, cooperation?
> > >>>
> > >>>Dear Leonore (and others),
> > >>>
> > >>>Thanks for the very fast response! I did not plan to attend the PAG
> > >>>conference, but am rethinking that now. It would be the best way to start
> > >>>cooperating. In the mean time, do you have suggestions for our group for
> > >>>issues we should discuss (or find out) before coming to your meeting?
> > >>>
> > >>>Bye,
> > >>>Paulien
> > >>>
> > >>>-----Original Message-----
> > >>>From: Lincoln Stein [mailto:lstein at cshl.edu]
> > >>>Sent: Thursday, October 16, 2003 16:23
> > >>>To: po-dev at plantontology.org; Leonore Reiser; Adamse, Paulien
> > >>>Cc: po-dev at plantontology.org
> > >>>Subject: Re: plant ontology, cooperation?
> > >>>
> > >>>
> > >>>Hello Paulien,
> > >>>
> > >>>As PI of the POC project, I would like to personally express my
> > >>>enthusiasm for building a collaboration with your group to develop
> > >>>plant-wide ontologies to describe plant anatomy and developmental stages.
> > >>> It would be very good for our groups to meet at the San Diego users'
> > >>>meeting.
> > >>>
> > >>>Lincoln
> > >>>
> > >>>On Thursday 16 October 2003 09:54 am, Leonore Reiser wrote:
> > >>>
> > >>>>Dear Paulien:
> > >>>>
> > >>>>This is wonderful. TAIR is part of a recently funded project to develop
> > >>>>plant ontologies called the "Plant Ontology Consortium". The goals of
> > >>>>this project are exactly what you describe.
> > >>>>
> > >>>>The project website is http://www.plantontology.org/. So far most of the
> > >>>>ontology development has been done by Gramene (rice), TAIR and Maize DB.
> > >>>>The website describes the project and how to access the ontologies. We
> > >>>>are using the DAGeditor and ontology representation developed by the GO
> > >>>>(directed, acyclic graphs). The plan is to make the ontologies as
> > >>>>broadly applicable as we can to accomodate as many organisms as
> > >>>>possible. The ontologies can be accessed without restriction and the GO
> > >>>>has made the DAGeditor freely available. We are using the CVS repository
> > >>>>as a shared development resource and communicating over email primarily
> > >>>>for development.
> > >>>>
> > >>>>It would be fantastic to work with your group to develop the structure
> > >>>>and content of the ontologies.We were planning to have a users meeting
> > >>>>in January, following the PAG meeting in San Diego-will people from your
> > >>>>organization be attending?
> > >>>>
> > >>>>I am ccing this email to the group.We have just hired a coordinator (your
> > >>>>counterpart here)  who will be starting soon. She will be based at TAIR
> > >>>>but will coordinate the efforts for the whole group-in the meantime, I
> > >>>>am very happy to work with you. Best Regards
> > >>>>Leonore Reiser
> > >>>>
> > >>>>On Thu, 16 Oct 2003, Adamse, Paulien wrote:
> > >>>>
> > >>>>>Dear Mrs. Reiser,
> > >>>>>
> > >>>>>I hope you are the right person to write to about this, but I will give
> > >>>>>it a try. If I should contact somebody else, please let me know.
> > >>>>>
> > >>>>>I am writing on behalf of seven partner labs in Europe, working together
> > >>>>>to establish a network of plant databases. The project is called PlaNet
> > >>>>>(at the moment the address is http://mips.gsf.de/proj/planet/). The 7
> > >>>>>partners all have databases with information about Arabidopsis (and
> > >>>>>sometimes other plants). Some are working on prediction-tools, others
> > >>>>>have collections of mutantlines (or germplasm or accessions, etc.). The
> > >>>>>goal is to connect them all and build one general access to it, using
> > >>>>>BioMoby. People will be able to query through this site and do not have
> > >>>>>to worry about in which database they have to look for their
> > >>>>>information.
> > >>>>>
> > >>>>>To be able to query multiple databases with one type of question it is
> > >>>>>very important to standardize the available information as much as
> > >>>>>possible. One important aspect in this is the description of the
> > >>>>>mutants. We set up a working group to compare the different
> > >>>>>ontologies/vocabularies already used by the different partners. I am the
> > >>>>>coordinator of this group. In Wageningen I am in the process of building
> > >>>>>a database for our mutants (WAtDB, not online yet), but we already have
> > >>>>>a wealth of information about mutants, transgenics and natural
> > >>>>>variants. But no standard terminology (yet) for describing them.
> > >>>>>
> > >>>>>This is where my request to you is coming in. We have a lot of phenotype
> > >>>>>descriptions and already noticed that not everything has been covered by
> > >>>>>the TAIR vocabulary. One way to solve that is to send you numerous
> > >>>>>submissions/update requests. But we thought that it might be more useful
> > >>>>>to work together more structural. Are you interested in cooperation with
> > >>>>>our group? If so, what would be a good way to do this? In November our
> > >>>>>PO working group is meeting again here in Wageningen and I would like
> > >>>>>to discuss it with them during that meeting. But it would be very
> > >>>>>useful to know what you think about it and maybe already get some
> > >>>>>suggestions about how we could work together.
> > >>>>>
> > >>>>>I hope you are interested and have time to reply within a few weeks.
> > >>>>>That way I can use your information when I am preparing our coming EU
> > >>>>>PlaNet PO working group meeting.
> > >>>>>
> > >>>>>Thanks in advance!
> > >>>>>
> > >>>>>Best wishes,
> > >>>>>Paulien
> > >>>>>
> > >>>>>
> > >>>>>Dr Paulien Adamse
> > >>>>>BU Bioscience
> > >>>>>Plant Research International,
> > >>>>>P.O. Box 16,
> > >>>>>6700 AA Wageningen,
> > >>>>>The Netherlands.
> > >>>>>
> > >>>>>Tel: +31 317 477001/476830
> > >>>>>FAX: +31 317 418094
> > >>>>>paulien.adamse at wur.nl
> > >>>>>www.plant.wageningen-ur.nl
> > >>>>
> > >>>>-------------------------------------------------------------------------
> > >>>>-- ---- Leonore Reiser, Ph.D.
> > >>>>lreiser at acoma.stanford.edu The Arabidopsis Information Resource	FAX:
> > >>>>(650) 325-6857
> > >>>>Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> > >>>>Department of Plant Biology		URL: http://arabidopsis.org/
> > >>>>260 Panama St.
> > >>>>Stanford, CA 94305
> > >>>>-------------------------------------------------------------------------
> > >>>>-- ----
> > >
> > >
> >
> > --
> > ******************************************
> > Pankaj Jaiswal, Ph.D.
> > Research 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
> > ******************************************
> >
> >
> >
>
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource	FAX: (650) 325-6857
> Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
> Department of Plant Biology		URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------
>
>

-----------------------------------------------------------------------------
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 rhee at acoma.Stanford.EDU  Mon Oct 20 13:58:29 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Mon, 20 Oct 2003 10:58:29 -0700 (PDT)
Subject: an invitation to participate in a PSB panel (fwd)
Message-ID: <Pine.GSO.4.44.0310201056470.18902-100000@acoma.Stanford.EDU>

Is anyone planning on going to the PSB meeting and interested in
participaing in this panel? Unfortunatley I have a grant due 1/14 and
wasn't planning on going to this, but I think this would be a nice
opportunity for someone to represent the plant groups...

Sue

---------- Forwarded message ----------
Date: Sun, 19 Oct 2003 11:59:35 -0500
From: "Mitchell, Joyce A." <MitchellJo at health.missouri.edu>
To: rhee at acoma.Stanford.EDU
Subject: an invitation to participate in a PSB panel

Dear Dr. Rhee,

I am extending an invitation on behalf of my myself and my two colleagues
(Alexa McCray and Olivier Bodenreider, both from the National Library of
Medicine) to participate in a panel discussion at the Pacific Symposium on
Biocomputing.  We are the organizers of the session on Biomedical
Ontologies.  The session has two parts:  contributed papers and a panel
discussion.  The panel is called, "Biomedical Ontologies:  Burning Needs
and Flame-Retardant Infrastructure".

We would like you to discuss some of the "burning needs" with regard to
ontologies of the plant genomics community and any infrastructure being
developed.  We are aware of your work from the SOFG conference and the
leadership role you play in the TAIR resource.  Several of my
bioinformatics colleagues at the University of Missouri speak highly of
you and your work. This would not be a long talk (5-10 minutes maximum,
depending on the number of other participants) because we would like the
panelists to outline the burning needs and/or the work at flame-retardant
infrastructure and then have a lengthy discussion among the audience and
the panelists.  Last year we had a very lively discussion with the
audience, considered by some among the high points of the conference, and
we hope to continue that tradition.

I have included a link to the PSB meeting so you can get details of place,
time, cost, etc.  Unfortunately, our invitation does not include paying
your expenses or an honorarium.  Hopefully you have already been planning
to attend.  Please let us know of your thoughts on this invitation and
whether you might be able to participate on the panel.

http://psb.stanford.edu/

Regards,

Joyce A. Mitchell, Ph.D.
Professor, Department of Health Management and Informatics
Director, Biomedical and Health Informatics Research Training
427 Clark Hall
School of Medicine
University of Missouri
Columbia, MO  65211

573-882-7077 (voice)
573-882-6158 (fax)
mitchelljo at health.missouri.edu





From Leszek at missouri.edu  Tue Oct 21 11:19:36 2003
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Tue, 21 Oct 2003 10:19:36 -0500
Subject: files on CVS
Message-ID: <3D4AD7F06881FD42A720D33D8E399DF3010ECC84@COL-EMAIL4.col.missouri.edu>

Hi Pankaj,

The Zea ontology files have been moved as requested - now visible in the
CVS via the webview URL (below). I haven't been able to delete the
Poc/Zea_mays/ directory. Hopefully someone who administers the CVS
facility can do this for me.

Please elaborate on what you mean by "converting the flat file format
similar to TAIR & Gramene."

- Leszek
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 215 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
Yahoo! Messenger: leszekvincent
Plant Systematist on The Plant Ontology Consortium - NSF award 0321666
Associate Curator, Dunn-Palmer Herbarium (UMO)
Research Associate, Missouri Botanical Garden (MO), USA
CEO - PhytoSynergy, LLC
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Pankaj Jaiswal
> Sent: Wednesday, October 15, 2003 1:34 PM
> To: POC-dev
> Subject: files on CVS
> 
> 
> 
> Hi Everyone,
> 
> I think we should try to be consistent in the file locations 
> on CVS and flat 
> file format. Therefore, Leszek, would you mind putting the 
> maize ontology files 
> under respective directories on CVS.
> 
> Poc/anatomy/ --->for anatomy ontology
> Poc/definitions/--->for definitions
> 
> Right now they are under Poc/Zea_mays/.
> 
> Also try converting the flat file format similar to TAIR & Gramene.
> 
> This will help the developers and any potential users in the 
> long run. Also can 
> everyone point me to the most relevant files from their 
> projects.  I will be 
> cleaning up the CVS directories next week.
> 
> For the webview of CVS go to http://gorgonzola.cshl.org/viewcvs/Poc/
> 
> Thanks
> Pankaj
> 
> 



From pj37 at cornell.edu  Tue Oct 21 12:02:06 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 21 Oct 2003 12:02:06 -0400
Subject: files on CVS
In-Reply-To: <3D4AD7F06881FD42A720D33D8E399DF3010ECC84@COL-EMAIL4.col.missouri.edu>
References: <3D4AD7F06881FD42A720D33D8E399DF3010ECC84@COL-EMAIL4.col.missouri.edu>
Message-ID: <3F95587E.2000100@cornell.edu>



Vincent, Leszek wrote:

> Hi Pankaj,
> 
> The Zea ontology files have been moved as requested - now visible in the
> CVS via the webview URL (below). I haven't been able to delete the
> Poc/Zea_mays/ directory. Hopefully someone who administers the CVS
> facility can do this for me.
> 
Hi Leszek,
Thank you for taking care of it. We will do the rest.


> Please elaborate on what you mean by "converting the flat file format
> similar to TAIR & Gramene."

I meant using the standard symbols for the different relationship types (%, <, ~).

Thanks again,

Pankaj






From shuly at cshl.org  Wed Oct 22 16:05:54 2003
From: shuly at cshl.org (Shuly)
Date: Wed, 22 Oct 2003 16:05:54 -0400
Subject: DAG editor and MySQL
Message-ID: <3F96E322.2010204@cshl.org>

Following our conference call -

MySQL (versions 4.0 and above) does support transactions.

http://www.mysql.com/doc/en/ANSI_diff_Transactions.html

So, there might be a way to commit changes straight to the db using the 
DAG editor (if that's the limitation).

Shuly.



From pj37 at cornell.edu  Wed Oct 22 16:16:57 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 22 Oct 2003 16:16:57 -0400
Subject: DAG editor and MySQL
In-Reply-To: <3F96E322.2010204@cshl.org>
References: <3F96E322.2010204@cshl.org>
Message-ID: <3F96E5B9.4040508@cornell.edu>

Hi Shuly,

Talk to Chris Mungall <cjm at fruitfly.bdgp.berkeley.edu> and John Richter 
<jrichter at bdgp.lbl.gov> before getting started. Possibly Chris has something in 
place to do those kind of things.

At the last GO meeting, Chris told me that if the "associations" are not 
involved, then it is fairly easy to implement.

Pankaj



Shuly wrote:

> Following our conference call -
> 
> MySQL (versions 4.0 and above) does support transactions.
> 
> http://www.mysql.com/doc/en/ANSI_diff_Transactions.html
> 
> So, there might be a way to commit changes straight to the db using the 
> DAG editor (if that's the limitation).
> 
> Shuly.
> 
> 




From PolaccoM at missouri.edu  Wed Oct 22 17:14:59 2003
From: PolaccoM at missouri.edu (Mary Polacco)
Date: Wed, 22 Oct 2003 16:14:59 -0500
Subject: Postgres has other
In-Reply-To: <3F96E322.2010204@cshl.org>
Message-ID: <BBBC5D83.995D%PolaccoM@missouri.edu>

Re database software - you might wish to consider Postgres which has more
open license than the MySQl and a tad more utility, eg stored procedures.

http://www.postgres.org

I've not used it, but a developer with our maize group has, after using
MySQL - and he prefers Postgres.
   mary

On 10/22/03 3:05 PM, "Shuly" <shuly at cshl.org> wrote:

> Following our conference call -
> 
> MySQL (versions 4.0 and above) does support transactions.
> 
> http://www.mysql.com/doc/en/ANSI_diff_Transactions.html
> 
> So, there might be a way to commit changes straight to the db using the
> DAG editor (if that's the limitation).
> 
> Shuly.
> 
> 



From rhee at acoma.Stanford.EDU  Wed Oct 22 18:53:11 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Wed, 22 Oct 2003 15:53:11 -0700 (PDT)
Subject: DAG editor and MySQL
In-Reply-To: <3F96E5B9.4040508@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310221550370.4284-100000@acoma.Stanford.EDU>

Great suggestions. I thought the problem with the 'assoications' was the
large size of the human annotations, which is not something we will have
to deal with.. It would be great to find out exactly what the issues have
been with using the GO database to make live updates.

Thanks,
Sue

On Wed, 22 Oct 2003, Pankaj Jaiswal wrote:

> Hi Shuly,
>
> Talk to Chris Mungall <cjm at fruitfly.bdgp.berkeley.edu> and John Richter
> <jrichter at bdgp.lbl.gov> before getting started. Possibly Chris has something in
> place to do those kind of things.
>
> At the last GO meeting, Chris told me that if the "associations" are not
> involved, then it is fairly easy to implement.
>
> Pankaj
>
>
>
> Shuly wrote:
>
> > Following our conference call -
> >
> > MySQL (versions 4.0 and above) does support transactions.
> >
> > http://www.mysql.com/doc/en/ANSI_diff_Transactions.html
> >
> > So, there might be a way to commit changes straight to the db using the
> > DAG editor (if that's the limitation).
> >
> > Shuly.
> >
> >
>
>
>

-----------------------------------------------------------------------------
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 fzqhd at studentmail.umsl.edu  Fri Oct 24 12:49:45 2003
From: fzqhd at studentmail.umsl.edu (Felipe Zapata)
Date: Fri, 24 Oct 2003 11:49:45 -0500
Subject: CVS-running!
Message-ID: <1067014185.3f99582915ff1@studentmail.umsl.edu>

Hi,

Well, we gave up to MacCVS (different versions) and decided to use the 
standard CVS (UNIX based) for MacOS X 10.2.  At least it worked as expected under 
the pserver method for checkouts.

Thanks to all of you for your help and suggestions.

Felipe
PS: yes Ken,  MacOS X is a fairly rockin' UNIX system!

_____________
Felipe Zapata
University of Missouri-St.Louis
Department of Biology
8001 Natural Bridge Rd.
St. Louis MO, 63121
Phone: (314) 516-6200
Fax: (314) 516-6233


From pj37 at cornell.edu  Tue Oct 28 12:34:55 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 28 Oct 2003 12:34:55 -0500
Subject: Source forge tracking system for POC--Info required
Message-ID: <3F9EA8BF.7050505@cornell.edu>


Hi Everyone,

Can you answer the following questions. I need them in order to get the 
registration process complete for opening a POC project on sourceforge.net.

Pankaj

Please add a comment to this support request, providing the
following information:

1. A technical description (at least two paragraphs in
length) of the software you are developing, including the
programming language(s) used in its development and its
major features.

2. Details of the Open Source license (either the name of an
OSI-approved license, or the exact terms of the license if
it is not an OSI-approved license) which will be used by
your project.






From shuly at cshl.org  Tue Oct 28 22:51:32 2003
From: shuly at cshl.org (Shuly)
Date: Tue, 28 Oct 2003 22:51:32 -0500
Subject: Source forge tracking system for POC--Info required
References: <3F9EA8BF.7050505@cornell.edu>
Message-ID: <3F9F3944.90409@cshl.org>

Hey Pankaj,

Technical info for source forge -
we are basically using GO tools -
operating system: unix / linux
programming language: perl,  cgi scripts
database: MySQL

As far as I understand, we are not supposed to develop new software - so 
we might want to mention that...

I understand from your email that you got a reply from Source Forge -
so, shell we go on with your subscription, or should I continue with 
mine and take over the plantontology unix name ? I got a reply from them 
pointing you as the one who is using the plantontology unix name -
and asking weather we are from the same group.

I talked to Doreen today about source forge - and there was a debate 
weather we should create plant ontology as an open source project on 
source forge or not. After consulting Lincoln, the decision was that we 
should go ahead and do so.

I have changed the ip for the plantontology dev site to:

brie.cshl.org:8000  

so, you can use that to view the dev site.
Please take a look and let me know what you think.
Many things are still missing.

About the database  - to get the latest db schema I went here -
http://www.godatabase.org/dev/database/archive/latest/
there are 4 datasets (see documentation after the downloads):

termdb

assocdb

seqdb

seqdblite

Do you have an idea which ones we need ?

I contacted Chris Mungal in regards to the DAG editor - and I am waiting 
for his response.

About the Search - are we going to use something that's already exist, 
or develop a new search tool ?
It seems to me like this search that you are talking about might involve 
developing new scripts - to search our own db - I guess...

Mailing Lists - should I remove all the subscribers from the digests lists ?
(I would rather keep those mailing lists for awhile till we decide that 
we do/don't need them rather than remove them and then re-create them 
later on).

Shuly.

Pankaj Jaiswal wrote:

>
> Hi Everyone,
>
> Can you answer the following questions. I need them in order to get 
> the registration process complete for opening a POC project on 
> sourceforge.net.
>
> Pankaj
>
> Please add a comment to this support request, providing the
> following information:
>
> 1. A technical description (at least two paragraphs in
> length) of the software you are developing, including the
> programming language(s) used in its development and its
> major features.
>
> 2. Details of the Open Source license (either the name of an
> OSI-approved license, or the exact terms of the license if
> it is not an OSI-approved license) which will be used by
> your project.
>
>
>
>




From pj37 at cornell.edu  Wed Oct 29 10:25:48 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 29 Oct 2003 10:25:48 -0500
Subject: Source forge tracking system for POC--Info required
In-Reply-To: <3F9F3944.90409@cshl.org>
References: <3F9EA8BF.7050505@cornell.edu> <3F9F3944.90409@cshl.org>
Message-ID: <3F9FDBFC.50103@cornell.edu>

Hi Shuly,

Wait until I hear from them, in the meantime tell them it's the same group.

Here is what I told them in reference to those 2 questions raised by 
Sourceforge. The following statements were mentioned in the original grant 
proposal, except that we will use the Sourceforge, which we have now chosen to 
be an additional mirror site for distribution. Actually, we wanted to have a bug 
tracking system only, but we need to furnish all these details in order to have it.

 >
 > 1. A technical description (at least two paragraphs in
 > length) of the software you are developing, including the
 > programming language(s) used in its development and its
 > major features.
 >

the ontologies will be made available both as flat file DAG-Edit format, and as 
richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http:// 
www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of other GO 
Consortium tools can process.  Diagrams used to supplement the text definitions 
will be downloadable in common archive formats (tar-gzip and zip).
Although this project is not primarily directed at software development, any 
software developed in support of the Plant Ontology Consortium 
(http://www.plantontology.org) will be available under an open source license.

Technical info for source forge -
we are using tools developed by the Gene Ontology Project
operating system: unix / linux
programming language: perl,  cgi scripts
database: MySQL


 > 2. Details of the Open Source license (either the name of an
 > OSI-approved license, or the exact terms of the license if
 > it is not an OSI-approved license) which will be used by
 > your project.
 >

All ontologies, associations and software will be released to the public under 
an open source license that allows free use and distribution 
(http://www.opensource.org).  Releases of ontologies will be made following a 
quarterly schedule as outlined in the project description.  Releases of 
associations will follow the release schedules of TAIR and Gramene, software 
will be released as soon as it is judged minimally useable by third parties. The 
manner and mode of release will be as described in the project description.
In accordance with common open source practice, all works will be copyrighted 
jointly by the members of the Plant Ontology Consortium solely for the purpose 
of protecting the integrity of the work.

 >





From ware at cshl.edu  Wed Oct 29 10:50:34 2003
From: ware at cshl.edu (Ware, Doreen)
Date: Wed, 29 Oct 2003 10:50:34 -0500
Subject: Source forge tracking system for POC--Info required
Message-ID: <39FDE54A4920D411AE0C0090274602F202D0A183@exch01>

Hi Pankaj,

I am not sure if sorceforge is usually used for bug tracking purposes.  

Shuly is taking care of the documentation.  We will use sorceforge as our
CVS repository.  Shuly will be writting up the documentation. I will reveiw
this with her at the end of the week. I do not plan on running a mirror but
maintaining one repository structure.  If we will be using Source forge then
our CVS should be located there.   

Doreen

-----Original Message-----
From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
Sent: Wednesday, October 29, 2003 10:26 AM
To: po-dev at plantontology.org
Subject: Re: Source forge tracking system for POC--Info required


Hi Shuly,

Wait until I hear from them, in the meantime tell them it's the same group.

Here is what I told them in reference to those 2 questions raised by 
Sourceforge. The following statements were mentioned in the original grant 
proposal, except that we will use the Sourceforge, which we have now chosen
to 
be an additional mirror site for distribution. Actually, we wanted to have a
bug 
tracking system only, but we need to furnish all these details in order to
have it.

 >
 > 1. A technical description (at least two paragraphs in
 > length) of the software you are developing, including the
 > programming language(s) used in its development and its
 > major features.
 >

the ontologies will be made available both as flat file DAG-Edit format, and
as 
richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http:// 
www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of
other GO 
Consortium tools can process.  Diagrams used to supplement the text
definitions 
will be downloadable in common archive formats (tar-gzip and zip).
Although this project is not primarily directed at software development, any

software developed in support of the Plant Ontology Consortium 
(http://www.plantontology.org) will be available under an open source
license.

Technical info for source forge -
we are using tools developed by the Gene Ontology Project
operating system: unix / linux
programming language: perl,  cgi scripts
database: MySQL


 > 2. Details of the Open Source license (either the name of an
 > OSI-approved license, or the exact terms of the license if
 > it is not an OSI-approved license) which will be used by
 > your project.
 >

All ontologies, associations and software will be released to the public
under 
an open source license that allows free use and distribution 
(http://www.opensource.org).  Releases of ontologies will be made following
a 
quarterly schedule as outlined in the project description.  Releases of 
associations will follow the release schedules of TAIR and Gramene, software

will be released as soon as it is judged minimally useable by third parties.
The 
manner and mode of release will be as described in the project description.
In accordance with common open source practice, all works will be
copyrighted 
jointly by the members of the Plant Ontology Consortium solely for the
purpose 
of protecting the integrity of the work.

 >




From lstein at cshl.edu  Wed Oct 29 10:59:17 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 29 Oct 2003 10:59:17 -0500
Subject: Source forge tracking system for POC--Info required
In-Reply-To: <39FDE54A4920D411AE0C0090274602F202D0A183@exch01>
References: <39FDE54A4920D411AE0C0090274602F202D0A183@exch01>
Message-ID: <200310291059.17103.lstein@cshl.edu>

Sourceforge has a reasonable bug tracking system.  You have to activate it.

Lincoln

On Wednesday 29 October 2003 10:50 am, Ware, Doreen wrote:
> Hi Pankaj,
>
> I am not sure if sorceforge is usually used for bug tracking purposes.
>
> Shuly is taking care of the documentation.  We will use sorceforge as our
> CVS repository.  Shuly will be writting up the documentation. I will reveiw
> this with her at the end of the week. I do not plan on running a mirror but
> maintaining one repository structure.  If we will be using Source forge
> then our CVS should be located there.
>
> Doreen
>
> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Wednesday, October 29, 2003 10:26 AM
> To: po-dev at plantontology.org
> Subject: Re: Source forge tracking system for POC--Info required
>
>
> Hi Shuly,
>
> Wait until I hear from them, in the meantime tell them it's the same group.
>
> Here is what I told them in reference to those 2 questions raised by
> Sourceforge. The following statements were mentioned in the original grant
> proposal, except that we will use the Sourceforge, which we have now chosen
> to
> be an additional mirror site for distribution. Actually, we wanted to have
> a bug
> tracking system only, but we need to furnish all these details in order to
> have it.
>
>  > 1. A technical description (at least two paragraphs in
>  > length) of the software you are developing, including the
>  > programming language(s) used in its development and its
>  > major features.
>
> the ontologies will be made available both as flat file DAG-Edit format,
> and as
> richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http://
> www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of
> other GO
> Consortium tools can process.  Diagrams used to supplement the text
> definitions
> will be downloadable in common archive formats (tar-gzip and zip).
> Although this project is not primarily directed at software development,
> any
>
> software developed in support of the Plant Ontology Consortium
> (http://www.plantontology.org) will be available under an open source
> license.
>
> Technical info for source forge -
> we are using tools developed by the Gene Ontology Project
> operating system: unix / linux
> programming language: perl,  cgi scripts
> database: MySQL
>
>  > 2. Details of the Open Source license (either the name of an
>  > OSI-approved license, or the exact terms of the license if
>  > it is not an OSI-approved license) which will be used by
>  > your project.
>
> All ontologies, associations and software will be released to the public
> under
> an open source license that allows free use and distribution
> (http://www.opensource.org).  Releases of ontologies will be made following
> a
> quarterly schedule as outlined in the project description.  Releases of
> associations will follow the release schedules of TAIR and Gramene,
> software
>
> will be released as soon as it is judged minimally useable by third
> parties. The
> manner and mode of release will be as described in the project description.
> In accordance with common open source practice, all works will be
> copyrighted
> jointly by the members of the Plant Ontology Consortium solely for the
> purpose
> of protecting the integrity of the work.

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From rhee at acoma.Stanford.EDU  Wed Oct 29 11:03:46 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Wed, 29 Oct 2003 08:03:46 -0800 (PST)
Subject: Source forge tracking system for POC--Info required
In-Reply-To: <39FDE54A4920D411AE0C0090274602F202D0A183@exch01>
Message-ID: <Pine.GSO.4.44.0310290800190.9291-100000@acoma.Stanford.EDU>

On Wed, 29 Oct 2003, Ware, Doreen wrote:

> Hi Pankaj,
>
> I am not sure if sorceforge is usually used for bug tracking purposes.

I know of two projects that are heavily using the bug tracking feature of
Sorceforge: GO and GMOD.

> Shuly is taking care of the documentation.  We will use sorceforge as our
> CVS repository.  Shuly will be writting up the documentation. I will reveiw
> this with her at the end of the week. I do not plan on running a mirror but
> maintaining one repository structure.  If we will be using Source forge then
> our CVS should be located there.

Do you think there should be a backup server, in case Sorceforge is
temporaily down etc?

Sue

> Doreen
>
> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Wednesday, October 29, 2003 10:26 AM
> To: po-dev at plantontology.org
> Subject: Re: Source forge tracking system for POC--Info required
>
>
> Hi Shuly,
>
> Wait until I hear from them, in the meantime tell them it's the same group.
>
> Here is what I told them in reference to those 2 questions raised by
> Sourceforge. The following statements were mentioned in the original grant
> proposal, except that we will use the Sourceforge, which we have now chosen
> to
> be an additional mirror site for distribution. Actually, we wanted to have a
> bug
> tracking system only, but we need to furnish all these details in order to
> have it.
>
>  >
>  > 1. A technical description (at least two paragraphs in
>  > length) of the software you are developing, including the
>  > programming language(s) used in its development and its
>  > major features.
>  >
>
> the ontologies will be made available both as flat file DAG-Edit format, and
> as
> richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http://
> www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of
> other GO
> Consortium tools can process.  Diagrams used to supplement the text
> definitions
> will be downloadable in common archive formats (tar-gzip and zip).
> Although this project is not primarily directed at software development, any
>
> software developed in support of the Plant Ontology Consortium
> (http://www.plantontology.org) will be available under an open source
> license.
>
> Technical info for source forge -
> we are using tools developed by the Gene Ontology Project
> operating system: unix / linux
> programming language: perl,  cgi scripts
> database: MySQL
>
>
>  > 2. Details of the Open Source license (either the name of an
>  > OSI-approved license, or the exact terms of the license if
>  > it is not an OSI-approved license) which will be used by
>  > your project.
>  >
>
> All ontologies, associations and software will be released to the public
> under
> an open source license that allows free use and distribution
> (http://www.opensource.org).  Releases of ontologies will be made following
> a
> quarterly schedule as outlined in the project description.  Releases of
> associations will follow the release schedules of TAIR and Gramene, software
>
> will be released as soon as it is judged minimally useable by third parties.
> The
> manner and mode of release will be as described in the project description.
> In accordance with common open source practice, all works will be
> copyrighted
> jointly by the members of the Plant Ontology Consortium solely for the
> purpose
> of protecting the integrity of the work.
>
>  >
>
>
>

-----------------------------------------------------------------------------
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 pj37 at cornell.edu  Wed Oct 29 11:16:54 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 29 Oct 2003 11:16:54 -0500
Subject: Source forge tracking system for POC--Info required
In-Reply-To: <Pine.GSO.4.44.0310290800190.9291-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310290800190.9291-100000@acoma.Stanford.EDU>
Message-ID: <3F9FE7F6.3070000@cornell.edu>

My impression is that we will use sourceforge primarily for the bug tracking 
system and doing a mirror of the ontology cvs from Gorgonzola (should be done in 
an automated way). Simultaneously, all the ontology files are maintained on 
primary cvs on Gorgonzola. The developers should work on these files only.

Pankaj

Sue Rhee wrote:

> On Wed, 29 Oct 2003, Ware, Doreen wrote:
> 
> 
>>Hi Pankaj,
>>
>>I am not sure if sorceforge is usually used for bug tracking purposes.
> 
> 
> I know of two projects that are heavily using the bug tracking feature of
> Sorceforge: GO and GMOD.
> 
> 
>>Shuly is taking care of the documentation.  We will use sorceforge as our
>>CVS repository.  Shuly will be writting up the documentation. I will reveiw
>>this with her at the end of the week. I do not plan on running a mirror but
>>maintaining one repository structure.  If we will be using Source forge then
>>our CVS should be located there.
> 
> 
> Do you think there should be a backup server, in case Sorceforge is
> temporaily down etc?
> 
> Sue
> 
> 
>>Doreen
>>
>>-----Original Message-----
>>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
>>Sent: Wednesday, October 29, 2003 10:26 AM
>>To: po-dev at plantontology.org
>>Subject: Re: Source forge tracking system for POC--Info required
>>
>>
>>Hi Shuly,
>>
>>Wait until I hear from them, in the meantime tell them it's the same group.
>>
>>Here is what I told them in reference to those 2 questions raised by
>>Sourceforge. The following statements were mentioned in the original grant
>>proposal, except that we will use the Sourceforge, which we have now chosen
>>to
>>be an additional mirror site for distribution. Actually, we wanted to have a
>>bug
>>tracking system only, but we need to furnish all these details in order to
>>have it.
>>
>> >
>> > 1. A technical description (at least two paragraphs in
>> > length) of the software you are developing, including the
>> > programming language(s) used in its development and its
>> > major features.
>> >
>>
>>the ontologies will be made available both as flat file DAG-Edit format, and
>>as
>>richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http://
>>www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of
>>other GO
>>Consortium tools can process.  Diagrams used to supplement the text
>>definitions
>>will be downloadable in common archive formats (tar-gzip and zip).
>>Although this project is not primarily directed at software development, any
>>
>>software developed in support of the Plant Ontology Consortium
>>(http://www.plantontology.org) will be available under an open source
>>license.
>>
>>Technical info for source forge -
>>we are using tools developed by the Gene Ontology Project
>>operating system: unix / linux
>>programming language: perl,  cgi scripts
>>database: MySQL
>>
>>
>> > 2. Details of the Open Source license (either the name of an
>> > OSI-approved license, or the exact terms of the license if
>> > it is not an OSI-approved license) which will be used by
>> > your project.
>> >
>>
>>All ontologies, associations and software will be released to the public
>>under
>>an open source license that allows free use and distribution
>>(http://www.opensource.org).  Releases of ontologies will be made following
>>a
>>quarterly schedule as outlined in the project description.  Releases of
>>associations will follow the release schedules of TAIR and Gramene, software
>>
>>will be released as soon as it is judged minimally useable by third parties.
>>The
>>manner and mode of release will be as described in the project description.
>>In accordance with common open source practice, all works will be
>>copyrighted
>>jointly by the members of the Plant Ontology Consortium solely for the
>>purpose
>>of protecting the integrity of the work.
>>
>> >
>>
>>
>>
> 
> -----------------------------------------------------------------------------
> 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.
Research 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 lstein at cshl.edu  Wed Oct 29 11:33:19 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 29 Oct 2003 11:33:19 -0500
Subject: Source forge tracking system for POC--Info required
In-Reply-To: <3F9FE7F6.3070000@cornell.edu>
References: <Pine.GSO.4.44.0310290800190.9291-100000@acoma.Stanford.EDU> <3F9FE7F6.3070000@cornell.edu>
Message-ID: <200310291133.19049.lstein@cshl.edu>

Any reason not to use Sourceforge as the primary CVS and mirror it to 
Gorgonzola?  I prefer it for security issues.

Lincoln


On Wednesday 29 October 2003 11:16 am, Pankaj Jaiswal wrote:
> My impression is that we will use sourceforge primarily for the bug
> tracking system and doing a mirror of the ontology cvs from Gorgonzola
> (should be done in an automated way). Simultaneously, all the ontology
> files are maintained on primary cvs on Gorgonzola. The developers should
> work on these files only.
>
> Pankaj
>
> Sue Rhee wrote:
> > On Wed, 29 Oct 2003, Ware, Doreen wrote:
> >>Hi Pankaj,
> >>
> >>I am not sure if sorceforge is usually used for bug tracking purposes.
> >
> > I know of two projects that are heavily using the bug tracking feature of
> > Sorceforge: GO and GMOD.
> >
> >>Shuly is taking care of the documentation.  We will use sorceforge as our
> >>CVS repository.  Shuly will be writting up the documentation. I will
> >> reveiw this with her at the end of the week. I do not plan on running a
> >> mirror but maintaining one repository structure.  If we will be using
> >> Source forge then our CVS should be located there.
> >
> > Do you think there should be a backup server, in case Sorceforge is
> > temporaily down etc?
> >
> > Sue
> >
> >>Doreen
> >>
> >>-----Original Message-----
> >>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> >>Sent: Wednesday, October 29, 2003 10:26 AM
> >>To: po-dev at plantontology.org
> >>Subject: Re: Source forge tracking system for POC--Info required
> >>
> >>
> >>Hi Shuly,
> >>
> >>Wait until I hear from them, in the meantime tell them it's the same
> >> group.
> >>
> >>Here is what I told them in reference to those 2 questions raised by
> >>Sourceforge. The following statements were mentioned in the original
> >> grant proposal, except that we will use the Sourceforge, which we have
> >> now chosen to
> >>be an additional mirror site for distribution. Actually, we wanted to
> >> have a bug
> >>tracking system only, but we need to furnish all these details in order
> >> to have it.
> >>
> >> > 1. A technical description (at least two paragraphs in
> >> > length) of the software you are developing, including the
> >> > programming language(s) used in its development and its
> >> > major features.
> >>
> >>the ontologies will be made available both as flat file DAG-Edit format,
> >> and as
> >>richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http://
> >>www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of
> >>other GO
> >>Consortium tools can process.  Diagrams used to supplement the text
> >>definitions
> >>will be downloadable in common archive formats (tar-gzip and zip).
> >>Although this project is not primarily directed at software development,
> >> any
> >>
> >>software developed in support of the Plant Ontology Consortium
> >>(http://www.plantontology.org) will be available under an open source
> >>license.
> >>
> >>Technical info for source forge -
> >>we are using tools developed by the Gene Ontology Project
> >>operating system: unix / linux
> >>programming language: perl,  cgi scripts
> >>database: MySQL
> >>
> >> > 2. Details of the Open Source license (either the name of an
> >> > OSI-approved license, or the exact terms of the license if
> >> > it is not an OSI-approved license) which will be used by
> >> > your project.
> >>
> >>All ontologies, associations and software will be released to the public
> >>under
> >>an open source license that allows free use and distribution
> >>(http://www.opensource.org).  Releases of ontologies will be made
> >> following a
> >>quarterly schedule as outlined in the project description.  Releases of
> >>associations will follow the release schedules of TAIR and Gramene,
> >> software
> >>
> >>will be released as soon as it is judged minimally useable by third
> >> parties. The
> >>manner and mode of release will be as described in the project
> >> description. In accordance with common open source practice, all works
> >> will be copyrighted
> >>jointly by the members of the Plant Ontology Consortium solely for the
> >>purpose
> >>of protecting the integrity of the work.
> >
> > -------------------------------------------------------------------------
> >---- 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.
> > -------------------------------------------------------------------------
> >----

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From pj37 at cornell.edu  Wed Oct 29 12:56:56 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 29 Oct 2003 12:56:56 -0500
Subject: Source forge tracking system for POC--Info required
In-Reply-To: <200310291133.19049.lstein@cshl.edu>
References: <Pine.GSO.4.44.0310290800190.9291-100000@acoma.Stanford.EDU> <3F9FE7F6.3070000@cornell.edu> <200310291133.19049.lstein@cshl.edu>
Message-ID: <3F9FFF68.2090709@cornell.edu>

Hi Lincoln,

We already have files in several  repositories on both internal and external CVS 
servers for Gramene/OBO/TAIR. I agree with you on having only one, personally I 
would like to work on gorgonzola server because most of the development has been 
done on this. Secondly, I am not that confident on using SF CVS, because of 
inconsistencies and errors. Probably that was Sue's concern and just now I 
learnt from Doreen that Ken also faced similar problems in the past for his CMap 
project.


Pankaj



Lincoln Stein wrote:

> Any reason not to use Sourceforge as the primary CVS and mirror it to 
> Gorgonzola?  I prefer it for security issues.
> 
> Lincoln
> 
> 
> On Wednesday 29 October 2003 11:16 am, Pankaj Jaiswal wrote:
> 
>>My impression is that we will use sourceforge primarily for the bug
>>tracking system and doing a mirror of the ontology cvs from Gorgonzola
>>(should be done in an automated way). Simultaneously, all the ontology
>>files are maintained on primary cvs on Gorgonzola. The developers should
>>work on these files only.
>>
>>Pankaj
>>
>>Sue Rhee wrote:
>>
>>>On Wed, 29 Oct 2003, Ware, Doreen wrote:
>>>
>>>>Hi Pankaj,
>>>>
>>>>I am not sure if sorceforge is usually used for bug tracking purposes.
>>>
>>>I know of two projects that are heavily using the bug tracking feature of
>>>Sorceforge: GO and GMOD.
>>>
>>>
>>>>Shuly is taking care of the documentation.  We will use sorceforge as our
>>>>CVS repository.  Shuly will be writting up the documentation. I will
>>>>reveiw this with her at the end of the week. I do not plan on running a
>>>>mirror but maintaining one repository structure.  If we will be using
>>>>Source forge then our CVS should be located there.
>>>
>>>Do you think there should be a backup server, in case Sorceforge is
>>>temporaily down etc?
>>>
>>>Sue
>>>
>>>
>>>>Doreen
>>>>
>>>>-----Original Message-----
>>>>From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
>>>>Sent: Wednesday, October 29, 2003 10:26 AM
>>>>To: po-dev at plantontology.org
>>>>Subject: Re: Source forge tracking system for POC--Info required
>>>>
>>>>
>>>>Hi Shuly,
>>>>
>>>>Wait until I hear from them, in the meantime tell them it's the same
>>>>group.
>>>>
>>>>Here is what I told them in reference to those 2 questions raised by
>>>>Sourceforge. The following statements were mentioned in the original
>>>>grant proposal, except that we will use the Sourceforge, which we have
>>>>now chosen to
>>>>be an additional mirror site for distribution. Actually, we wanted to
>>>>have a bug
>>>>tracking system only, but we need to furnish all these details in order
>>>>to have it.
>>>>
>>>>
>>>>>1. A technical description (at least two paragraphs in
>>>>>length) of the software you are developing, including the
>>>>>programming language(s) used in its development and its
>>>>>major features.
>>>>
>>>>the ontologies will be made available both as flat file DAG-Edit format,
>>>>and as
>>>>richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http://
>>>>www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a number of
>>>>other GO
>>>>Consortium tools can process.  Diagrams used to supplement the text
>>>>definitions
>>>>will be downloadable in common archive formats (tar-gzip and zip).
>>>>Although this project is not primarily directed at software development,
>>>>any
>>>>
>>>>software developed in support of the Plant Ontology Consortium
>>>>(http://www.plantontology.org) will be available under an open source
>>>>license.
>>>>
>>>>Technical info for source forge -
>>>>we are using tools developed by the Gene Ontology Project
>>>>operating system: unix / linux
>>>>programming language: perl,  cgi scripts
>>>>database: MySQL
>>>>
>>>>
>>>>>2. Details of the Open Source license (either the name of an
>>>>>OSI-approved license, or the exact terms of the license if
>>>>>it is not an OSI-approved license) which will be used by
>>>>>your project.
>>>>
>>>>All ontologies, associations and software will be released to the public
>>>>under
>>>>an open source license that allows free use and distribution
>>>>(http://www.opensource.org).  Releases of ontologies will be made
>>>>following a
>>>>quarterly schedule as outlined in the project description.  Releases of
>>>>associations will follow the release schedules of TAIR and Gramene,
>>>>software
>>>>
>>>>will be released as soon as it is judged minimally useable by third
>>>>parties. The
>>>>manner and mode of release will be as described in the project
>>>>description. In accordance with common open source practice, all works
>>>>will be copyrighted
>>>>jointly by the members of the Plant Ontology Consortium solely for the
>>>>purpose
>>>>of protecting the integrity of the work.
>>>




From shuly at cshl.org  Wed Oct 29 14:04:05 2003
From: shuly at cshl.org (Shuly)
Date: Wed, 29 Oct 2003 14:04:05 -0500
Subject: Source forge tracking system for POC--Info required
References: <Pine.GSO.4.44.0310290800190.9291-100000@acoma.Stanford.EDU> <3F9FE7F6.3070000@cornell.edu> <200310291133.19049.lstein@cshl.edu> <3F9FFF68.2090709@cornell.edu>
Message-ID: <3FA00F25.60906@cshl.org>

Peter, out IT guy, sais that gorgonzola is an old machine with little 
memory and it would be a good idea not to use it, or use it less.

Pankaj Jaiswal wrote:

> Hi Lincoln,
>
> We already have files in several  repositories on both internal and 
> external CVS servers for Gramene/OBO/TAIR. I agree with you on having 
> only one, personally I would like to work on gorgonzola server because 
> most of the development has been done on this. Secondly, I am not that 
> confident on using SF CVS, because of inconsistencies and errors. 
> Probably that was Sue's concern and just now I learnt from Doreen that 
> Ken also faced similar problems in the past for his CMap project.
>
>
> Pankaj
>
>
>
> Lincoln Stein wrote:
>
>> Any reason not to use Sourceforge as the primary CVS and mirror it to 
>> Gorgonzola?  I prefer it for security issues.
>>
>> Lincoln
>>
>>
>> On Wednesday 29 October 2003 11:16 am, Pankaj Jaiswal wrote:
>>
>>> My impression is that we will use sourceforge primarily for the bug
>>> tracking system and doing a mirror of the ontology cvs from Gorgonzola
>>> (should be done in an automated way). Simultaneously, all the ontology
>>> files are maintained on primary cvs on Gorgonzola. The developers 
>>> should
>>> work on these files only.
>>>
>>> Pankaj
>>>
>>> Sue Rhee wrote:
>>>
>>>> On Wed, 29 Oct 2003, Ware, Doreen wrote:
>>>>
>>>>> Hi Pankaj,
>>>>>
>>>>> I am not sure if sorceforge is usually used for bug tracking 
>>>>> purposes.
>>>>
>>>>
>>>> I know of two projects that are heavily using the bug tracking 
>>>> feature of
>>>> Sorceforge: GO and GMOD.
>>>>
>>>>
>>>>> Shuly is taking care of the documentation.  We will use sorceforge 
>>>>> as our
>>>>> CVS repository.  Shuly will be writting up the documentation. I will
>>>>> reveiw this with her at the end of the week. I do not plan on 
>>>>> running a
>>>>> mirror but maintaining one repository structure.  If we will be using
>>>>> Source forge then our CVS should be located there.
>>>>
>>>>
>>>> Do you think there should be a backup server, in case Sorceforge is
>>>> temporaily down etc?
>>>>
>>>> Sue
>>>>
>>>>
>>>>> Doreen
>>>>>
>>>>> -----Original Message-----
>>>>> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
>>>>> Sent: Wednesday, October 29, 2003 10:26 AM
>>>>> To: po-dev at plantontology.org
>>>>> Subject: Re: Source forge tracking system for POC--Info required
>>>>>
>>>>>
>>>>> Hi Shuly,
>>>>>
>>>>> Wait until I hear from them, in the meantime tell them it's the same
>>>>> group.
>>>>>
>>>>> Here is what I told them in reference to those 2 questions raised by
>>>>> Sourceforge. The following statements were mentioned in the original
>>>>> grant proposal, except that we will use the Sourceforge, which we 
>>>>> have
>>>>> now chosen to
>>>>> be an additional mirror site for distribution. Actually, we wanted to
>>>>> have a bug
>>>>> tracking system only, but we need to furnish all these details in 
>>>>> order
>>>>> to have it.
>>>>>
>>>>>
>>>>>> 1. A technical description (at least two paragraphs in
>>>>>> length) of the software you are developing, including the
>>>>>> programming language(s) used in its development and its
>>>>>> major features.
>>>>>
>>>>>
>>>>> the ontologies will be made available both as flat file DAG-Edit 
>>>>> format,
>>>>> and as
>>>>> richer RDF [http:// www.w3.org/RDF/] and DAML-OIL [http://
>>>>> www.w3.org/TR/daml+oil-reference] formats that DAG-Edit and a 
>>>>> number of
>>>>> other GO
>>>>> Consortium tools can process.  Diagrams used to supplement the text
>>>>> definitions
>>>>> will be downloadable in common archive formats (tar-gzip and zip).
>>>>> Although this project is not primarily directed at software 
>>>>> development,
>>>>> any
>>>>>
>>>>> software developed in support of the Plant Ontology Consortium
>>>>> (http://www.plantontology.org) will be available under an open source
>>>>> license.
>>>>>
>>>>> Technical info for source forge -
>>>>> we are using tools developed by the Gene Ontology Project
>>>>> operating system: unix / linux
>>>>> programming language: perl,  cgi scripts
>>>>> database: MySQL
>>>>>
>>>>>
>>>>>> 2. Details of the Open Source license (either the name of an
>>>>>> OSI-approved license, or the exact terms of the license if
>>>>>> it is not an OSI-approved license) which will be used by
>>>>>> your project.
>>>>>
>>>>>
>>>>> All ontologies, associations and software will be released to the 
>>>>> public
>>>>> under
>>>>> an open source license that allows free use and distribution
>>>>> (http://www.opensource.org).  Releases of ontologies will be made
>>>>> following a
>>>>> quarterly schedule as outlined in the project description.  
>>>>> Releases of
>>>>> associations will follow the release schedules of TAIR and Gramene,
>>>>> software
>>>>>
>>>>> will be released as soon as it is judged minimally useable by third
>>>>> parties. The
>>>>> manner and mode of release will be as described in the project
>>>>> description. In accordance with common open source practice, all 
>>>>> works
>>>>> will be copyrighted
>>>>> jointly by the members of the Plant Ontology Consortium solely for 
>>>>> the
>>>>> purpose
>>>>> of protecting the integrity of the work.
>>>>
>>>>
>
>




From pj37 at cornell.edu  Fri Oct 31 11:41:53 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 31 Oct 2003 11:41:53 -0500
Subject: First meeting of POC core members
In-Reply-To: <200310131241.38055.lstein@cshl.edu>
References: <3F8AC47F.6010402@cornell.edu> <200310131241.38055.lstein@cshl.edu>
Message-ID: <3FA290D1.7070307@cornell.edu>

Okay,

Can we hold this meeting on Sunday - January 11, 2004

How about Morning 9-11 am

looks like rest of the afternoon is having good workshops.
Let me know and I will try to confirm with organizers to reserve a room.

BTW, do we actually need a room reservation. If everyone agrees we can get 
together at some place in that arena for a couple of hrs.

Pankaj


The PAG schedule for the day is...

     Sunday - January 11, 2004:

     Registration: 7:00 am - 5:00 pm
     Breakfast 7:00 am - 9:00 am

     Workshops -
     All Day Workshops: 8:00 am - 5:40 pm
     Equine
     Cattle/Sheep
     Forest Trees
     Poultry (Part 3)
     Sugar Cane

     8:00 am - 10:40 am:
     Large Insert Libraries
     Legumes

     Lunch (on your own): 11:00 am - 12:00 noon

     12:00 noon - 2:40 pm
     Abiotic Stress
     Plant Cytogenetics
     Rice
     Statistical Genomics

     3:00 pm - 5:40 pm
     Cotton
     International Grape Genome Project
     Comparative Genomics of Plant Reproduction
     Rice Blast

Lincoln Stein wrote:
> The 11th January is better for me.
> 
> Lincoln
> 
> On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
> 
>>Hi Everyone,
>>
>>Can we finalize the first consortium meeting scheduled for PAG. Sue
>>suggested for holding it on either 10th or 11th January.
>>
>>Thanks
>>Pankaj
> 
> 



From rhee at acoma.Stanford.EDU  Fri Oct 31 11:45:12 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Fri, 31 Oct 2003 08:45:12 -0800 (PST)
Subject: First meeting of POC core members
In-Reply-To: <3FA290D1.7070307@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310310844160.25027-100000@acoma.Stanford.EDU>

What do you want to cover in two hours? It seems a bit too short for all
the groups to be getting together in person for...

Sue

On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:

> Okay,
>
> Can we hold this meeting on Sunday - January 11, 2004
>
> How about Morning 9-11 am
>
> looks like rest of the afternoon is having good workshops.
> Let me know and I will try to confirm with organizers to reserve a room.
>
> BTW, do we actually need a room reservation. If everyone agrees we can get
> together at some place in that arena for a couple of hrs.
>
> Pankaj
>
>
> The PAG schedule for the day is...
>
>      Sunday - January 11, 2004:
>
>      Registration: 7:00 am - 5:00 pm
>      Breakfast 7:00 am - 9:00 am
>
>      Workshops -
>      All Day Workshops: 8:00 am - 5:40 pm
>      Equine
>      Cattle/Sheep
>      Forest Trees
>      Poultry (Part 3)
>      Sugar Cane
>
>      8:00 am - 10:40 am:
>      Large Insert Libraries
>      Legumes
>
>      Lunch (on your own): 11:00 am - 12:00 noon
>
>      12:00 noon - 2:40 pm
>      Abiotic Stress
>      Plant Cytogenetics
>      Rice
>      Statistical Genomics
>
>      3:00 pm - 5:40 pm
>      Cotton
>      International Grape Genome Project
>      Comparative Genomics of Plant Reproduction
>      Rice Blast
>
> Lincoln Stein wrote:
> > The 11th January is better for me.
> >
> > Lincoln
> >
> > On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
> >
> >>Hi Everyone,
> >>
> >>Can we finalize the first consortium meeting scheduled for PAG. Sue
> >>suggested for holding it on either 10th or 11th January.
> >>
> >>Thanks
> >>Pankaj
> >
> >
>
>

-----------------------------------------------------------------------------
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 pj37 at cornell.edu  Fri Oct 31 11:59:51 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 31 Oct 2003 11:59:51 -0500
Subject: First meeting of POC core members
In-Reply-To: <Pine.GSO.4.44.0310310844160.25027-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310310844160.25027-100000@acoma.Stanford.EDU>
Message-ID: <3FA29507.4080804@cornell.edu>

I have no objections on having a whole day for it. These are the primary thoughts..
-discussion on establishing a firm top level structure
-integration process
-organization of working groups

Please have a look at the complete schedule and let me know.
http://www.intl-pag.org/12/12-pag.html

Pankaj

Sue Rhee wrote:

> What do you want to cover in two hours? It seems a bit too short for all
> the groups to be getting together in person for...
> 
> Sue
> 
> On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> 
> 
>>Okay,
>>
>>Can we hold this meeting on Sunday - January 11, 2004
>>
>>How about Morning 9-11 am
>>
>>looks like rest of the afternoon is having good workshops.
>>Let me know and I will try to confirm with organizers to reserve a room.
>>
>>BTW, do we actually need a room reservation. If everyone agrees we can get
>>together at some place in that arena for a couple of hrs.
>>
>>Pankaj
>>
>>
>>The PAG schedule for the day is...
>>
>>     Sunday - January 11, 2004:
>>
>>     Registration: 7:00 am - 5:00 pm
>>     Breakfast 7:00 am - 9:00 am
>>
>>     Workshops -
>>     All Day Workshops: 8:00 am - 5:40 pm
>>     Equine
>>     Cattle/Sheep
>>     Forest Trees
>>     Poultry (Part 3)
>>     Sugar Cane
>>
>>     8:00 am - 10:40 am:
>>     Large Insert Libraries
>>     Legumes
>>
>>     Lunch (on your own): 11:00 am - 12:00 noon
>>
>>     12:00 noon - 2:40 pm
>>     Abiotic Stress
>>     Plant Cytogenetics
>>     Rice
>>     Statistical Genomics
>>
>>     3:00 pm - 5:40 pm
>>     Cotton
>>     International Grape Genome Project
>>     Comparative Genomics of Plant Reproduction
>>     Rice Blast
>>
>>Lincoln Stein wrote:
>>
>>>The 11th January is better for me.
>>>
>>>Lincoln
>>>
>>>On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
>>>
>>>
>>>>Hi Everyone,
>>>>
>>>>Can we finalize the first consortium meeting scheduled for PAG. Sue
>>>>suggested for holding it on either 10th or 11th January.
>>>>
>>>>Thanks
>>>>Pankaj
>>>
>>>
>>




From lstein at cshl.edu  Fri Oct 31 14:36:36 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri, 31 Oct 2003 14:36:36 -0500
Subject: First meeting of POC core members
In-Reply-To: <Pine.GSO.4.44.0310310844160.25027-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310310844160.25027-100000@acoma.Stanford.EDU>
Message-ID: <200310311436.36101.lstein@cshl.edu>

Either time is fine for me.  I would prefer the Sunday.

Lincoln

On Friday 31 October 2003 11:45 am, Sue Rhee wrote:
> What do you want to cover in two hours? It seems a bit too short for all
> the groups to be getting together in person for...
>
> Sue
>
> On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> > Okay,
> >
> > Can we hold this meeting on Sunday - January 11, 2004
> >
> > How about Morning 9-11 am
> >
> > looks like rest of the afternoon is having good workshops.
> > Let me know and I will try to confirm with organizers to reserve a room.
> >
> > BTW, do we actually need a room reservation. If everyone agrees we can
> > get together at some place in that arena for a couple of hrs.
> >
> > Pankaj
> >
> >
> > The PAG schedule for the day is...
> >
> >      Sunday - January 11, 2004:
> >
> >      Registration: 7:00 am - 5:00 pm
> >      Breakfast 7:00 am - 9:00 am
> >
> >      Workshops -
> >      All Day Workshops: 8:00 am - 5:40 pm
> >      Equine
> >      Cattle/Sheep
> >      Forest Trees
> >      Poultry (Part 3)
> >      Sugar Cane
> >
> >      8:00 am - 10:40 am:
> >      Large Insert Libraries
> >      Legumes
> >
> >      Lunch (on your own): 11:00 am - 12:00 noon
> >
> >      12:00 noon - 2:40 pm
> >      Abiotic Stress
> >      Plant Cytogenetics
> >      Rice
> >      Statistical Genomics
> >
> >      3:00 pm - 5:40 pm
> >      Cotton
> >      International Grape Genome Project
> >      Comparative Genomics of Plant Reproduction
> >      Rice Blast
> >
> > Lincoln Stein wrote:
> > > The 11th January is better for me.
> > >
> > > Lincoln
> > >
> > > On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
> > >>Hi Everyone,
> > >>
> > >>Can we finalize the first consortium meeting scheduled for PAG. Sue
> > >>suggested for holding it on either 10th or 11th January.
> > >>
> > >>Thanks
> > >>Pankaj
>
> ---------------------------------------------------------------------------
>-- 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.
> ---------------------------------------------------------------------------
>--

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From rhee at acoma.Stanford.EDU  Fri Oct 31 15:14:49 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Fri, 31 Oct 2003 12:14:49 -0800 (PST)
Subject: First meeting of POC core members
In-Reply-To: <3FA29507.4080804@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310311211490.26401-100000@acoma.Stanford.EDU>

i think it would be helpful to meet for the whole day. some additional
agenda items on top of your starting point could be:

1. introductions
2. tair progress report
3. gramene progress report
4. maizegdb progress report
5. kellog group progress report
6. discussion of logic on ontology merging
7. plan for the integration processs
8. organization of working groups
9. wrap up (plan for next meeting, action items)

sue

On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:

> I have no objections on having a whole day for it. These are the primary thoughts..
> -discussion on establishing a firm top level structure
> -integration process
> -organization of working groups
>
> Please have a look at the complete schedule and let me know.
> http://www.intl-pag.org/12/12-pag.html
>
> Pankaj
>
> Sue Rhee wrote:
>
> > What do you want to cover in two hours? It seems a bit too short for all
> > the groups to be getting together in person for...
> >
> > Sue
> >
> > On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> >
> >
> >>Okay,
> >>
> >>Can we hold this meeting on Sunday - January 11, 2004
> >>
> >>How about Morning 9-11 am
> >>
> >>looks like rest of the afternoon is having good workshops.
> >>Let me know and I will try to confirm with organizers to reserve a room.
> >>
> >>BTW, do we actually need a room reservation. If everyone agrees we can get
> >>together at some place in that arena for a couple of hrs.
> >>
> >>Pankaj
> >>
> >>
> >>The PAG schedule for the day is...
> >>
> >>     Sunday - January 11, 2004:
> >>
> >>     Registration: 7:00 am - 5:00 pm
> >>     Breakfast 7:00 am - 9:00 am
> >>
> >>     Workshops -
> >>     All Day Workshops: 8:00 am - 5:40 pm
> >>     Equine
> >>     Cattle/Sheep
> >>     Forest Trees
> >>     Poultry (Part 3)
> >>     Sugar Cane
> >>
> >>     8:00 am - 10:40 am:
> >>     Large Insert Libraries
> >>     Legumes
> >>
> >>     Lunch (on your own): 11:00 am - 12:00 noon
> >>
> >>     12:00 noon - 2:40 pm
> >>     Abiotic Stress
> >>     Plant Cytogenetics
> >>     Rice
> >>     Statistical Genomics
> >>
> >>     3:00 pm - 5:40 pm
> >>     Cotton
> >>     International Grape Genome Project
> >>     Comparative Genomics of Plant Reproduction
> >>     Rice Blast
> >>
> >>Lincoln Stein wrote:
> >>
> >>>The 11th January is better for me.
> >>>
> >>>Lincoln
> >>>
> >>>On Monday 13 October 2003 11:27 am, Pankaj Jaiswal wrote:
> >>>
> >>>
> >>>>Hi Everyone,
> >>>>
> >>>>Can we finalize the first consortium meeting scheduled for PAG. Sue
> >>>>suggested for holding it on either 10th or 11th January.
> >>>>
> >>>>Thanks
> >>>>Pankaj
> >>>
> >>>
> >>
>
>
>

-----------------------------------------------------------------------------
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 pj37 at cornell.edu  Fri Oct 31 15:35:47 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 31 Oct 2003 15:35:47 -0500
Subject: First meeting of POC core members
In-Reply-To: <Pine.GSO.4.44.0310311211490.26401-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310311211490.26401-100000@acoma.Stanford.EDU>
Message-ID: <3FA2C7A3.6050005@cornell.edu>

The agenda looks great. In order to have a full day, we may have to plan it for 
Friday.
Sat and Sunday is all loaded with workshops in post lunch sessions.

Pankaj


Sue Rhee wrote:

> i think it would be helpful to meet for the whole day. some additional
> agenda items on top of your starting point could be:
> 
> 1. introductions
> 2. tair progress report
> 3. gramene progress report
> 4. maizegdb progress report
> 5. kellog group progress report
> 6. discussion of logic on ontology merging
> 7. plan for the integration processs
> 8. organization of working groups
> 9. wrap up (plan for next meeting, action items)
> 
> sue
> 
> On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> 
> 
>>I have no objections on having a whole day for it. These are the primary thoughts..
>>-discussion on establishing a firm top level structure
>>-integration process
>>-organization of working groups
>>
>>Please have a look at the complete schedule and let me know.
>>http://www.intl-pag.org/12/12-pag.html
>>
>>Pankaj
>>
>>Sue Rhee wrote:
>>
>>
>>>What do you want to cover in two hours? It seems a bit too short for all
>>>the groups to be getting together in person for...
>>>
>>>Sue
>>>
>>>On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
>>>
>>>
>>>
>>>>Okay,
>>>>
>>>>Can we hold this meeting on Sunday - January 11, 2004
>>>>
>>>>How about Morning 9-11 am
>>>>
>>>>looks like rest of the afternoon is having good workshops.
>>>>Let me know and I will try to confirm with organizers to reserve a room.
>>>>
>>>>BTW, do we actually need a room reservation. If everyone agrees we can get
>>>>together at some place in that arena for a couple of hrs.
>>>>
>>>>Pankaj




From rhee at acoma.Stanford.EDU  Fri Oct 31 16:29:58 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Fri, 31 Oct 2003 13:29:58 -0800 (PST)
Subject: First meeting of POC core members
In-Reply-To: <3FA2C7A3.6050005@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310311329200.26401-100000@acoma.Stanford.EDU>

i thought that we settled on sunday so already went ahead with booking.. i
could change to fri but would prefer sunday.

sue

On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:

> The agenda looks great. In order to have a full day, we may have to plan it for
> Friday.
> Sat and Sunday is all loaded with workshops in post lunch sessions.
>
> Pankaj
>
>
> Sue Rhee wrote:
>
> > i think it would be helpful to meet for the whole day. some additional
> > agenda items on top of your starting point could be:
> >
> > 1. introductions
> > 2. tair progress report
> > 3. gramene progress report
> > 4. maizegdb progress report
> > 5. kellog group progress report
> > 6. discussion of logic on ontology merging
> > 7. plan for the integration processs
> > 8. organization of working groups
> > 9. wrap up (plan for next meeting, action items)
> >
> > sue
> >
> > On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> >
> >
> >>I have no objections on having a whole day for it. These are the primary thoughts..
> >>-discussion on establishing a firm top level structure
> >>-integration process
> >>-organization of working groups
> >>
> >>Please have a look at the complete schedule and let me know.
> >>http://www.intl-pag.org/12/12-pag.html
> >>
> >>Pankaj
> >>
> >>Sue Rhee wrote:
> >>
> >>
> >>>What do you want to cover in two hours? It seems a bit too short for all
> >>>the groups to be getting together in person for...
> >>>
> >>>Sue
> >>>
> >>>On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> >>>
> >>>
> >>>
> >>>>Okay,
> >>>>
> >>>>Can we hold this meeting on Sunday - January 11, 2004
> >>>>
> >>>>How about Morning 9-11 am
> >>>>
> >>>>looks like rest of the afternoon is having good workshops.
> >>>>Let me know and I will try to confirm with organizers to reserve a room.
> >>>>
> >>>>BTW, do we actually need a room reservation. If everyone agrees we can get
> >>>>together at some place in that arena for a couple of hrs.
> >>>>
> >>>>Pankaj
>
>
>

-----------------------------------------------------------------------------
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 lstein at cshl.edu  Fri Oct 31 16:52:40 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri, 31 Oct 2003 16:52:40 -0500
Subject: First meeting of POC core members
In-Reply-To: <Pine.GSO.4.44.0310311329200.26401-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310311329200.26401-100000@acoma.Stanford.EDU>
Message-ID: <200310311652.40746.lstein@cshl.edu>

I prefer Sunday too.  I have a commitment on friday.

Lincoln

On Friday 31 October 2003 04:29 pm, Sue Rhee wrote:
> i thought that we settled on sunday so already went ahead with booking.. i
> could change to fri but would prefer sunday.
>
> sue
>
> On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> > The agenda looks great. In order to have a full day, we may have to plan
> > it for Friday.
> > Sat and Sunday is all loaded with workshops in post lunch sessions.
> >
> > Pankaj
> >
> > Sue Rhee wrote:
> > > i think it would be helpful to meet for the whole day. some additional
> > > agenda items on top of your starting point could be:
> > >
> > > 1. introductions
> > > 2. tair progress report
> > > 3. gramene progress report
> > > 4. maizegdb progress report
> > > 5. kellog group progress report
> > > 6. discussion of logic on ontology merging
> > > 7. plan for the integration processs
> > > 8. organization of working groups
> > > 9. wrap up (plan for next meeting, action items)
> > >
> > > sue
> > >
> > > On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> > >>I have no objections on having a whole day for it. These are the
> > >> primary thoughts.. -discussion on establishing a firm top level
> > >> structure
> > >>-integration process
> > >>-organization of working groups
> > >>
> > >>Please have a look at the complete schedule and let me know.
> > >>http://www.intl-pag.org/12/12-pag.html
> > >>
> > >>Pankaj
> > >>
> > >>Sue Rhee wrote:
> > >>>What do you want to cover in two hours? It seems a bit too short for
> > >>> all the groups to be getting together in person for...
> > >>>
> > >>>Sue
> > >>>
> > >>>On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> > >>>>Okay,
> > >>>>
> > >>>>Can we hold this meeting on Sunday - January 11, 2004
> > >>>>
> > >>>>How about Morning 9-11 am
> > >>>>
> > >>>>looks like rest of the afternoon is having good workshops.
> > >>>>Let me know and I will try to confirm with organizers to reserve a
> > >>>> room.
> > >>>>
> > >>>>BTW, do we actually need a room reservation. If everyone agrees we
> > >>>> can get together at some place in that arena for a couple of hrs.
> > >>>>
> > >>>>Pankaj
>
> ---------------------------------------------------------------------------
>-- 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.
> ---------------------------------------------------------------------------
>--

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================




From pj37 at cornell.edu  Fri Oct 31 17:01:53 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 31 Oct 2003 17:01:53 -0500
Subject: First meeting of POC core members
In-Reply-To: <200310311652.40746.lstein@cshl.edu>
References: <Pine.GSO.4.44.0310311329200.26401-100000@acoma.Stanford.EDU> <200310311652.40746.lstein@cshl.edu>
Message-ID: <3FA2DBD1.3040100@cornell.edu>

The only options left are to have it in 2 parts
Part-I: Morning 9-11 am
Part-II 3.00pm-whatever time it takes

We can have a break during the rice workshop from 12:00 noon - 2:40 pm

Pankaj





From rhee at acoma.Stanford.EDU  Fri Oct 31 17:09:45 2003
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Fri, 31 Oct 2003 14:09:45 -0800 (PST)
Subject: First meeting of POC core members
In-Reply-To: <3FA2DBD1.3040100@cornell.edu>
Message-ID: <Pine.GSO.4.44.0310311408110.26401-100000@acoma.Stanford.EDU>

ok, how about:

8:30-11 and 3-6:30?

sue

On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:

> The only options left are to have it in 2 parts
> Part-I: Morning 9-11 am
> Part-II 3.00pm-whatever time it takes
>
> We can have a break during the rice workshop from 12:00 noon - 2:40 pm
>
> Pankaj
>
>
>
>

-----------------------------------------------------------------------------
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 pj37 at cornell.edu  Fri Oct 31 17:33:15 2003
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 31 Oct 2003 17:33:15 -0500
Subject: First meeting of POC core members
In-Reply-To: <Pine.GSO.4.44.0310311408110.26401-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0310311408110.26401-100000@acoma.Stanford.EDU>
Message-ID: <3FA2E32B.2090506@cornell.edu>

That's fine with me.
Pankaj

Sue Rhee wrote:

> ok, how about:
> 
> 8:30-11 and 3-6:30?
> 
> sue
> 
> On Fri, 31 Oct 2003, Pankaj Jaiswal wrote:
> 
> 
>>The only options left are to have it in 2 parts
>>Part-I: Morning 9-11 am
>>Part-II 3.00pm-whatever time it takes
>>
>>We can have a break during the rice workshop from 12:00 noon - 2:40 pm
>>
>>Pankaj