From feedback_submission at brie4.plantontology.org  Thu Jul  1 16:04:31 2004
From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org)
Date: Thu, 1 Jul 2004 16:04:31 -0400
Subject: Feedback Submission from Plant Ontology Live Site
Message-ID: <200407012004.i61K4Vjv024793@brie4.cshl.org>

    *** Feedback from Plant Ontology Live Site ***

refer_to_url: http://www.plantontology.org/sitemap/sitemap.html

comments: test please ignore

name: Mary Polacco

email: polaccom at missouri.edu

organization: USDA-ARS Plant Genetics Research Unit

send_feedback: Send your feedback



From PolaccoM at missouri.edu  Thu Jul  1 16:21:21 2004
From: PolaccoM at missouri.edu (Mary Polacco)
Date: Thu, 01 Jul 2004 15:21:21 -0500
Subject: test
Message-ID: <BD09DC71.D64A%PolaccoM@missouri.edu>

test of this does it go to po-dev



From tkellogg at umsl.edu  Thu Jul  1 17:57:46 2004
From: tkellogg at umsl.edu (Elizabeth Kellogg)
Date: Thu, 1 Jul 2004 16:57:46 -0500
Subject: test
In-Reply-To: <BD09DC71.D64A%PolaccoM@missouri.edu>
References: <BD09DC71.D64A%PolaccoM@missouri.edu>
Message-ID: <AFD8AE40-CBA9-11D8-8AE1-000393B121A8@umsl.edu>

Yes.
T

On Jul 1, 2004, at 3:21 PM, Mary Polacco wrote:

> test of this does it go to po-dev
>
>
Elizabeth A. Kellogg
E. Desmond Lee and Family Professor of Botanical Studies
Department of Biology
University of Missouri-St. Louis
St. Louis, MO 63121
Tel: 314-516-6217
FAX: 314-516-6233
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/ 
home.html



From katica at acoma.Stanford.EDU  Thu Jul  1 18:08:23 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Thu, 1 Jul 2004 15:08:23 -0700 (PDT)
Subject: test
In-Reply-To: <BD09DC71.D64A%PolaccoM@missouri.edu>
Message-ID: <Pine.GSO.4.44.0407011501420.23658-100000@acoma.Stanford.EDU>

Mary,

Sorry for the delayed response, I went out for a late (and a long one this
time) lunch break and just got back.

The reason I asked you to  do both is because of the 'route' via they get
to po-dev. Feedback actually come to me first, then, I need to approve it,
and after that it goes to po-dev. This way, we prevent any spam to come to
po-dev. Po at plantontology.org comes directly to po-dev. The reason your
feedback came in to po-dev directly, without needing my approval, is
because your address is already on po-dev, and therefore, no filtering was
necessary.

Just in case you were curious about this. That's the way Shuly set it up.

Katica


On Thu, 1 Jul 2004, Mary Polacco wrote:

> test of this does it go to po-dev
>

--------------------------------------------------------------------------
Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------




From katica at acoma.Stanford.EDU  Fri Jul  2 12:58:18 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 2 Jul 2004 09:58:18 -0700 (PDT)
Subject: Trichomes (fwd)
Message-ID: <Pine.GSO.4.44.0407020950330.5306-100000@acoma.Stanford.EDU>

Hi Jan,

I forwarded your message to po-internal (by mistake, it should have been
fwd to po-dev. See below.

Yes, trichomes are multicelular in some plants (for instance, tobacco). In
Arabidopsis, they are unicellular.

Greeetings,

Katica

--------------------------------------------------------------------------
Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
--------------------------------------------------------------------------

---------- Forwarded message ----------
Date: Fri, 2 Jul 2004 10:55:24 -0500
From: Felipe Zapata <fzqhd at studentmail.umsl.edu>
Reply-To: po-internal at plantontology.org
To: po-internal at plantontology.org
Subject: Re: Trichomes (fwd)

Trichomes can even be multicellular in plants.

F
On Jul 2, 2004, at 10:49 AM, Katica Ilic wrote:

> The message below is from Go mailing list (Jane Clark):
>
> ---------- Forwarded message ----------
> Date: Fri, 02 Jul 2004 16:29:35 +0100
> From: J Clark <jclark at ebi.ac.uk>
> To: go list <go at genome.stanford.edu>
> Subject: Trichomes
>
> Hi,
>
> Can anybody tell me if a trichome is always a single cell?
> I know it is in plants but I'm not sure about other organisms.
>
> Thanks,
>
> Jen
>
>
> --
> EMBL - European Bioinformatics Institute,
> Gene Ontology Consortium,
> and Wolfson College, Cambridge.
> http://www.ebi.ac.uk/~jclark/
>



From jclark at ebi.ac.uk  Mon Jul 12 10:35:53 2004
From: jclark at ebi.ac.uk (J Clark)
Date: Mon, 12 Jul 2004 15:35:53 +0100
Subject: grass inflorescence and flower development terms
Message-ID: <40F2A1C9.5030106@ebi.ac.uk>

Hi,

Pankaj and I have been working on some terms to cover grass 
inflorescence and flower development in the Gene Ontology 
Consortium process ontology. I have just put together a 
first draft of a proposal for the addtition of terms and I 
wondered if people with knowledge of grass development could 
possibly have a look (some time in the next two weeks) and 
check that it's heading in the right direction?

[ 966600 ] monocot inflorescence development
https://sourceforge.net/tracker/index.php?func=detail&aid=966600&group_id=36855&atid=440764

Thank you very much for your help.

Best wishes,

Jennifer








-- 
EMBL - European Bioinformatics Institute,
Gene Ontology Consortium,
and Wolfson College, Cambridge.
http://www.ebi.ac.uk/~jclark/



From jclark at ebi.ac.uk  Fri Jul 16 07:05:35 2004
From: jclark at ebi.ac.uk (J Clark)
Date: Fri, 16 Jul 2004 12:05:35 +0100
Subject: RUBISCO terms
Message-ID: <40F7B67F.4030208@ebi.ac.uk>

Hi,

Is there anybody who's work would be affected by changes to 
the Gene Ontology Consortium function ontology RUBISCO terms 
being discussed in:

[ 877848 ] ribulose bisphosphate carboxylase complex
https://sourceforge.net/tracker/index.php?func=detail&aid=877848&group_id=36855&atid=440764

Comments on this sourceforge item would be greatly appreciated.

Thanks,

Jen


-- 
EMBL - European Bioinformatics Institute,
Gene Ontology Consortium,
and Wolfson College, Cambridge.
http://www.ebi.ac.uk/~jclark/



From pj37 at cornell.edu  Tue Jul 20 10:24:46 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 20 Jul 2004 10:24:46 -0400
Subject: flower=floret
Message-ID: <40FD2B2E.6010805@cornell.edu>


Hi Everyone,

As I was working on the monocot flower development part with Jen Clark
from GO, we came up with a discussion point saying flower being
equivalent to floret.
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=966600&group_id=36855

So the question raised by Jen is why not just call it a synonym of
flower. Also taking advantage of the PARTOF relationship which also
means a child is a PART_OF but NOT_ALWAYS a PART_OF, we can have a
structure like this for anatomy ontology

flower; synonym:floret, floret (sensu Poaceae)
-p-corolla
---p-petal
-p-calyx
---p-sepal
-p-tepal
-p-lemma
-p-palea
-p-androecium
---p-stamen
-p-gynoecium
---p-carpel

This may help in retrieving instantiations of most of generic terms for
  sensu poaceae.
However how is it going to effect sensu Zea, I have to think about it.

-Pankaj


************************
Pankaj Jaiswal, PhD
G15-Bradfield Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
************************










From jclark at ebi.ac.uk  Thu Jul 22 04:41:50 2004
From: jclark at ebi.ac.uk (J Clark)
Date: Thu, 22 Jul 2004 09:41:50 +0100
Subject: opinions needed on germination
Message-ID: <40FF7DCE.5050702@ebi.ac.uk>

(Forwarded to po-dev from the go list.)

Hi all,

We (at SGD) have been working on revising the 'germination' 
area of the
process ontology.  There are a couple of major problems with it:

- 'spore germination' currently has 'post-embryonic 
development'
parentage and so cannot be used for Dicty, bacteria, and other
organisms without embryos.

- 'spore germination (sensu Fungi)' has completely different 
parentage;
its direct parent is 'sporulation' (which is pretty much the 
opposite
of germination!).

In making a revised tree it would be helpful to have 
opinions  on a few
specific questions from other folks whose organisms germinate.

1) we're wondering about obsoleting this term:

germination (GO:0009844):  The physiological and 
developmental changes
by a seed, spore, pollen grain (microspore), or zygote that 
occur after
release from dormancy, and encompassing events prior to and 
including
the first visible indications of growth.

Is there really that much in common between these different 
types of
germination that a grouping term is useful?


2) 'pollen germination' currently has 'post-embryonic 
development'
parentage. Should it?  My botany is rusty, but it seems to 
me that this
takes place before an embryo exists.


3) all the germination terms except the 'sensu Fungi' one 
currently
have 'cell differentiation' parentage.  This sounds 
reasonable for seed
or pollen germination, but isn't spore germination really 
just a
resumption of growth, after breakdown of the spore wall and 
protective
structures?


Once I get some feedback on these issues, I'll submit a 
proposal on the
details to SF.

Thanks!
Maria




-- 
EMBL - European Bioinformatics Institute,
Gene Ontology Consortium,
and Wolfson College, Cambridge.
http://www.ebi.ac.uk/~jclark/



From jid1 at cornell.edu  Fri Jul 23 13:56:08 2004
From: jid1 at cornell.edu (Jerrold Davis)
Date: Fri, 23 Jul 2004 13:56:08 -0400
Subject: flower=floret -- NOT
In-Reply-To: <40FD2B2E.6010805@cornell.edu>
Message-ID: <5.2.1.1.2.20040723135032.02f160f8@postoffice8.mail.cornell.edu>

Pankaj:

A flower is most certainly NOT a floret.  This is a common misconception, 
but it isn't so.

A floret is a flower PLUS 1) lemma, 2) palea, 3) the axis on which the 
flower and these two bracts are borne, and 4) lodicules, depending on 
interpretation.  Many or most people interpret the lodicules as perianth 
parts, in which case they are part of the flower, but if they are 
interpreted as additional structures, rather than as part of the flower, 
they are an additional component of the floret.

Now, you can find some literature in which the lemma and palea are 
interpreted as modified floral parts, in which case the flower and floret 
would become identical or nearly identical in meaning, but this is an 
extremely unconventional interpretation.

Jerry


At 10:24 AM 7/20/2004 -0400, you wrote:

>Hi Everyone,
>
>As I was working on the monocot flower development part with Jen Clark
>from GO, we came up with a discussion point saying flower being
>equivalent to floret.
>https://sourceforge.net/tracker/?func=detail&atid=440764&aid=966600&group_id=36855
>
>So the question raised by Jen is why not just call it a synonym of
>flower. Also taking advantage of the PARTOF relationship which also
>means a child is a PART_OF but NOT_ALWAYS a PART_OF, we can have a
>structure like this for anatomy ontology
>
>flower; synonym:floret, floret (sensu Poaceae)
>-p-corolla
>---p-petal
>-p-calyx
>---p-sepal
>-p-tepal
>-p-lemma
>-p-palea
>-p-androecium
>---p-stamen
>-p-gynoecium
>---p-carpel
>
>This may help in retrieving instantiations of most of generic terms for
>  sensu poaceae.
>However how is it going to effect sensu Zea, I have to think about it.
>
>-Pankaj
>
>
>************************
>Pankaj Jaiswal, PhD
>G15-Bradfield Hall
>Dept. of Plant Breeding
>Cornell University
>Ithaca, NY-14853, USA
>
>Tel: +1-607-255-3103
>      +1-607-255-4109
>Fax: +1-607-255-6683
>http://www.gramene.org
>************************
>
>
>
>
>
>
>



From jclark at ebi.ac.uk  Mon Jul 26 09:53:26 2004
From: jclark at ebi.ac.uk (Jennifer I Clark)
Date: Mon, 26 Jul 2004 14:53:26 +0100
Subject: germination
Message-ID: <41050CD6.1090604@ebi.ac.uk>

Would this be of interest to anyone on the po-dev list?


997064 
<http://sourceforge.net/tracker/index.php?func=detail&aid=997064&group_id=36855&atid=440764> 
2004-07-24 06:52 germination node reorganization


Jen

(GO Curator)



From jamal at yopolis.com  Tue Jul 20 00:20:31 2004
From: jamal at yopolis.com (Jamal Saleh)
Date: Tue, 20 Jul 2004 00:20:31 -0400
Subject: Please read...
Message-ID: <seou3kqmb5danj2.200720040020@208.179.70.110>

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