From feedback_submission at filetta.cshl.edu  Thu Mar  3 20:25:46 2005
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Mar 2005 20:25:46 -0500
Subject: Feedback on POC
Message-ID: <200503040125.j241PkUq011079@filetta.cshl.org>

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

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

comments: Hi there

I was wanting to adopt your plant part ontologies in a plant bioinformatics database that I am developing.

My plant parts include stolons and root nodules for white clover (Trifolium repens).  Neither of these parts are cited on the current ontology.  Do you have any recommendations for alternative ontologies?

name: Ross Chapman

email: ross.chapman at dpi.vic.gov.au

organization: 

send_feedback: Send your feedback



From jitterbug at plantontology.org  Fri Mar  4 21:05:08 2005
From: jitterbug at plantontology.org (Katica Ilic)
Date: Fri, 4 Mar 2005 21:05:08 -0500
Subject: Feedback on POC (fwd) (PR#55)
Message-ID: <200503050205.j25258VV005517@brie4.cshl.org>

Dear Ross,

Thank you for contacting us about missing terms in the Plant Ontology. We are
currently in a very preliminary stage of introducing species?specific terms for
legumes, Solanaceae and cereal species (other than maize and rice), and
projected ontology release should take place in the second part of this year.
However, we are open to user's requests and always consider all the suggestions
and comments.

Two terms that you are inquiring, 'stolon' and 'nodule', will be introduced to
the Plant Ontology next week; the next revision in the POC cvs will have these
new terms. We regularly update our Ontology browser on monthly basis (usually at
the end of the month), and the next scheduled update is March 23.  If you are
familiar with GO or OBO flat files, you can simply download the latest ontology
files from the POC cvs next week (URL: http://brebiou.cshl.edu/viewcvs/Poc/)

Thank you again for using Plant ontologies. Please contact us any time you have
question about ontologies, our database or about POC project in general.

Best regards,

Katica Ilic, POC Project Coordinator


-------- Forwarded message ----------
> Date: Thu, 3 Mar 2005 20:25:46 -0500
> From: feedback_submission at filetta.cshl.edu
> Reply-To: po-dev at plantontology.org, feedback_submission at filetta.cshl.edu
> To: po-dev <po-dev at plantontology.org>
> Subject: Feedback on POC
> 
>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: Hi there
> 
> I was wanting to adopt your plant part ontologies in a plant bioinformatics
> database that I am developing.
> 
> My plant parts include stolons and root nodules for white clover (Trifolium
> repens).  Neither of these parts are cited on the current ontology.  Do you
have
> any recommendations for alternative ontologies?
> 
> name: Ross Chapman
> 
> email: ross.chapman at dpi.vic.gov.au
> 
> organization:
> 
> send_feedback: Send your feedback
> 
> 


From katica at acoma.Stanford.EDU  Tue Mar  8 02:23:00 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Mon, 7 Mar 2005 23:23:00 -0800 (PST)
Subject: New terms in PO, stolon and nodule
Message-ID: <Pine.GSO.4.44.0503072320190.7259-100000@acoma.Stanford.EDU>


Hi All,

As a response to a user's request, I am proposing two new terms in
the Plant Structure Ontology, term 'stolon' and term 'nodule'.

Term: stolon (synonym runner)
In the ontology structure, to be placed under 'stem' node:
Stem
 (i) stolon

Proposed definition: A slender, prostrate or trailing above-ground stem
which produces roots and sometimes erect shoots at its nodes.
 (from APWeb, URL:http://www.mobot.org/MOBOT/research/APweb/)

Term: nodule
In the ontology structure, to be placed under 'root' node.
Root
(p) nodule
Proposed definition: Enlargement or swelling on the roots of plants,
particularly in the Fabaceae, inhabited by nitrogen-fixing bacteria. (from
K Esau).

Thanks,

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




From katica at acoma.Stanford.EDU  Fri Mar 11 13:11:02 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 11 Mar 2005 10:11:02 -0800 (PST)
Subject: New terms in PO, stolon and nodule
In-Reply-To: <Pine.GSO.4.44.0503072320190.7259-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0503111009150.18267-100000@acoma.Stanford.EDU>

Hi All,

I committed the new version of Plant Structure ontology file in cvs,
po_anatomy.obo, version 1.3, with two new terms:

PO:0003023
name: nodule
def: Enlargement or swelling on the roots of plants, particularly in the
Fabaceae, inhabited by nitrogen-fixing bacteria.


PO:0003024
name: stolon
synonym: runner
def: A slender, prostrate or trailing above-ground stem which produces
roots and sometimes erect shoots at its nodes.


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




From jjd5 at cornell.edu  Fri Mar 11 14:40:44 2005
From: jjd5 at cornell.edu (Jeff J. Doyle)
Date: Fri, 11 Mar 2005 14:40:44 -0500
Subject: nodule
In-Reply-To: <Pine.GSO.4.44.0503111009150.18267-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0503111009150.18267-100000@acoma.Stanford.EDU>
Message-ID: <p06100518be57a1ff1bd3@[132.236.163.148]>

>
>PO:0003023
>name: nodule
>def: Enlargement or swelling on the roots of plants, particularly in the
>Fabaceae, inhabited by nitrogen-fixing bacteria.

There are also what are called "stem nodules" in some legumes (the 
papilionoid genus Sesbania is the prime example, but the caesalpiniod 
Neptunia also has nodules on floating stems).  Stem nodules are 
associated with adventitious roots, however, so the definition is not 
actually incorrect, even if the position of the roots in question is 
not typical.

--Jeff


-- 
Jeff J. Doyle
Professor, L. H. Bailey Hortorium, Department of Plant Biology, 
Cornell University
office: 259 Plant Science Building
tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
http://www.plantbio.cornell.edu/faculty.php?PB=jjd5

mailing address:

Department of Plant Biology
228 Plant Science Building
Cornell University
Ithaca, NY 14853-4301


From pj37 at cornell.edu  Fri Mar 11 14:54:11 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 11 Mar 2005 14:54:11 -0500
Subject: nodule
In-Reply-To: <p06100518be57a1ff1bd3@[132.236.163.148]>
References: <Pine.GSO.4.44.0503111009150.18267-100000@acoma.Stanford.EDU> <p06100518be57a1ff1bd3@[132.236.163.148]>
Message-ID: <4231F763.80701@cornell.edu>

Perhaps we should rename it to "root nodule" and the ones Jeff is 
suggesting are termed "stem nodules".

This raises a question. Do we need a generic/grouping  term "nodule" of 
which "stem nodule" and "root nodule" are instances. Obviously in the 
ontology these nodules are part_of "stem" and "root" respectively.

-Pankaj

Jeff J. Doyle wrote:

>>
>> PO:0003023
>> name: nodule
>> def: Enlargement or swelling on the roots of plants, particularly in the
>> Fabaceae, inhabited by nitrogen-fixing bacteria.
> 
> 
> There are also what are called "stem nodules" in some legumes (the 
> papilionoid genus Sesbania is the prime example, but the caesalpiniod 
> Neptunia also has nodules on floating stems).  Stem nodules are 
> associated with adventitious roots, however, so the definition is not 
> actually incorrect, even if the position of the roots in question is not 
> typical.
> 
> --Jeff
> 
> 



From katica at acoma.Stanford.EDU  Fri Mar 11 14:58:45 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 11 Mar 2005 11:58:45 -0800 (PST)
Subject: nodule
In-Reply-To: <p06100518be57a1ff1bd3@[132.236.163.148]>
Message-ID: <Pine.GSO.4.44.0503111155550.20047-100000@acoma.Stanford.EDU>

Hi Jeff,

Thanks for your comment.

Would it be more appropriate to have 'root nodule' instead?
Actually to instantiate term 'nodule' to 'root nodule' and 'stem
nodule'?

Katica

On Fri, 11 Mar 2005, Jeff J. Doyle wrote:

> >
> >PO:0003023
> >name: nodule
> >def: Enlargement or swelling on the roots of plants, particularly in the
> >Fabaceae, inhabited by nitrogen-fixing bacteria.
>
> There are also what are called "stem nodules" in some legumes (the
> papilionoid genus Sesbania is the prime example, but the caesalpiniod
> Neptunia also has nodules on floating stems).  Stem nodules are
> associated with adventitious roots, however, so the definition is not
> actually incorrect, even if the position of the roots in question is
> not typical.
>
> --Jeff
>
>
> --
> Jeff J. Doyle
> Professor, L. H. Bailey Hortorium, Department of Plant Biology,
> Cornell University
> office: 259 Plant Science Building
> tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
> http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
>
> mailing address:
>
> Department of Plant Biology
> 228 Plant Science Building
> Cornell University
> Ithaca, NY 14853-4301
>

--------------------------------------------------------------------------
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 Mar 11 15:11:43 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 11 Mar 2005 12:11:43 -0800 (PST)
Subject: nodule
In-Reply-To: <4231F763.80701@cornell.edu>
Message-ID: <Pine.GSO.4.44.0503111206410.20047-100000@acoma.Stanford.EDU>


It seems we do, if we choose to have root nodule and stem nodule, a
grouping term where all annotations to children terms of nodule would show
up.

Now, where to place generic term 'nodule'? If it goes under the
'sporophyte', it will be a sibling of high nodes, root, shoot, seed and
infructescence.

Katica

On Fri, 11 Mar 2005, Pankaj Jaiswal wrote:

> Perhaps we should rename it to "root nodule" and the ones Jeff is
> suggesting are termed "stem nodules".
>
> This raises a question. Do we need a generic/grouping  term "nodule" of
> which "stem nodule" and "root nodule" are instances. Obviously in the
> ontology these nodules are part_of "stem" and "root" respectively.
>
> -Pankaj
>
> Jeff J. Doyle wrote:
>
> >>
> >> PO:0003023
> >> name: nodule
> >> def: Enlargement or swelling on the roots of plants, particularly in the
> >> Fabaceae, inhabited by nitrogen-fixing bacteria.
> >
> >
> > There are also what are called "stem nodules" in some legumes (the
> > papilionoid genus Sesbania is the prime example, but the caesalpiniod
> > Neptunia also has nodules on floating stems).  Stem nodules are
> > associated with adventitious roots, however, so the definition is not
> > actually incorrect, even if the position of the roots in question is not
> > typical.
> >
> > --Jeff
> >
> >
>

--------------------------------------------------------------------------
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 rhee at acoma.Stanford.EDU  Fri Mar 11 15:14:53 2005
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Fri, 11 Mar 2005 12:14:53 -0800 (PST)
Subject: nodule
In-Reply-To: <Pine.GSO.4.44.0503111155550.20047-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0503111204070.20091-100000@acoma.Stanford.EDU>

Are there any anatomical, morphological, lineage differences between the
nodules in the primary/lateral root and the 'stem' nodules in the
adventitious root? It seems like the introduction of 'stem nodule' for the
nodules that are not really part of stem could lead to some confusion.

Sue

On Fri, 11 Mar 2005, Katica Ilic wrote:

> Hi Jeff,
>
> Thanks for your comment.
>
> Would it be more appropriate to have 'root nodule' instead?
> Actually to instantiate term 'nodule' to 'root nodule' and 'stem
> nodule'?
>
> Katica
>
> On Fri, 11 Mar 2005, Jeff J. Doyle wrote:
>
> > >
> > >PO:0003023
> > >name: nodule
> > >def: Enlargement or swelling on the roots of plants, particularly in the
> > >Fabaceae, inhabited by nitrogen-fixing bacteria.
> >
> > There are also what are called "stem nodules" in some legumes (the
> > papilionoid genus Sesbania is the prime example, but the caesalpiniod
> > Neptunia also has nodules on floating stems).  Stem nodules are
> > associated with adventitious roots, however, so the definition is not
> > actually incorrect, even if the position of the roots in question is
> > not typical.
> >
> > --Jeff
> >
> >
> > --
> > Jeff J. Doyle
> > Professor, L. H. Bailey Hortorium, Department of Plant Biology,
> > Cornell University
> > office: 259 Plant Science Building
> > tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
> > http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
> >
> > mailing address:
> >
> > Department of Plant Biology
> > 228 Plant Science Building
> > Cornell University
> > Ithaca, NY 14853-4301
> >
>
> --------------------------------------------------------------------------
> 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.
> --------------------------------------------------------------------------
>
>

-----------------------------------------------------------------------------
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 katica at acoma.Stanford.EDU  Fri Mar 11 15:30:54 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 11 Mar 2005 12:30:54 -0800 (PST)
Subject: nodule
In-Reply-To: <Pine.GSO.4.44.0503111204070.20091-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0503111228000.20047-100000@acoma.Stanford.EDU>


It seems there is. I am not an expert, here is what I found about
Sebastania:

Sesbania rostrata is a native legume of West Africa. It forms a symbiotic
relationship with Azorhizobium caulinodans and is renowned for it's stem
nodulation. Both stem and root nodules fix nitrogen however root nodules
form at the curled root hair while stem nodules occur at the sites of
adventitious root primordia via "crack" entry. The stem nodules unlike the
root nodules contain functioning chloroplasts in the nodule cortex and are
therefore capable of carbon fixation.

http://www.personal.dundee.ac.uk/~rparsons/sesbania.htm


Katica


On Fri, 11 Mar 2005, Sue Rhee wrote:

> Are there any anatomical, morphological, lineage differences between the
> nodules in the primary/lateral root and the 'stem' nodules in the
> adventitious root? It seems like the introduction of 'stem nodule' for the
> nodules that are not really part of stem could lead to some confusion.
>
> Sue
>
> On Fri, 11 Mar 2005, Katica Ilic wrote:
>
> > Hi Jeff,
> >
> > Thanks for your comment.
> >
> > Would it be more appropriate to have 'root nodule' instead?
> > Actually to instantiate term 'nodule' to 'root nodule' and 'stem
> > nodule'?
> >
> > Katica
> >
> > On Fri, 11 Mar 2005, Jeff J. Doyle wrote:
> >
> > > >
> > > >PO:0003023
> > > >name: nodule
> > > >def: Enlargement or swelling on the roots of plants, particularly in the
> > > >Fabaceae, inhabited by nitrogen-fixing bacteria.
> > >
> > > There are also what are called "stem nodules" in some legumes (the
> > > papilionoid genus Sesbania is the prime example, but the caesalpiniod
> > > Neptunia also has nodules on floating stems).  Stem nodules are
> > > associated with adventitious roots, however, so the definition is not
> > > actually incorrect, even if the position of the roots in question is
> > > not typical.
> > >
> > > --Jeff
> > >
> > >
> > > --
> > > Jeff J. Doyle
> > > Professor, L. H. Bailey Hortorium, Department of Plant Biology,
> > > Cornell University
> > > office: 259 Plant Science Building
> > > tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
> > > http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
> > >
> > > mailing address:
> > >
> > > Department of Plant Biology
> > > 228 Plant Science Building
> > > Cornell University
> > > Ithaca, NY 14853-4301
> > >
> >
> > --------------------------------------------------------------------------
> > 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.
> > --------------------------------------------------------------------------
> >
> >
>
> -----------------------------------------------------------------------------
> 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.
> -----------------------------------------------------------------------------
>
>

--------------------------------------------------------------------------
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 pj37 at cornell.edu  Fri Mar 11 16:21:52 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 11 Mar 2005 16:21:52 -0500
Subject: nodule
In-Reply-To: <Pine.GSO.4.44.0503111228000.20047-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0503111228000.20047-100000@acoma.Stanford.EDU>
Message-ID: <42320BF0.30703@cornell.edu>

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9100377
Mol Plant Microbe Interact. 1997 Apr;10(3):316-25.


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9620265
Plant Mol Biol. 1998 May;37(1):67-76.

I am not an expert either, but the above references  are suggesting that 
  the  so called "stem nodules" are developing from the dormant 
adventitious root primordia. Second one is even calling them 
adventitious root nodules. Therefore taking clues from Sue's  question, 
I would say that both are "root nodules" one is a generic one present 
only on the roots which can cite their lineage presumably to the
"basal cell" developing from zygote and other one, "adventitious root 
nodule" has a lineage from "apical cell" developing from zygote.

Jeff can comment on this. My suggestion is as follows
i = instance
p = part of
Read the structure bottom up.

#1
root
--p--root nodule
--i--adventitious root
----p--adventitious root nodule (synonym: stem nodule)

Basal and apical cell lineage will also question the placement of 
adventitious roots under "root"

-Pankaj

Katica Ilic wrote:

> It seems there is. I am not an expert, here is what I found about
> Sebastania:
> 
> Sesbania rostrata is a native legume of West Africa. It forms a symbiotic
> relationship with Azorhizobium caulinodans and is renowned for it's stem
> nodulation. Both stem and root nodules fix nitrogen however root nodules
> form at the curled root hair while stem nodules occur at the sites of
> adventitious root primordia via "crack" entry. The stem nodules unlike the
> root nodules contain functioning chloroplasts in the nodule cortex and are
> therefore capable of carbon fixation.
> 
> http://www.personal.dundee.ac.uk/~rparsons/sesbania.htm



From jjd5 at cornell.edu  Mon Mar 14 08:55:52 2005
From: jjd5 at cornell.edu (Jeff J. Doyle)
Date: Mon, 14 Mar 2005 08:55:52 -0500
Subject: nodule
In-Reply-To: <Pine.GSO.4.44.0503111228000.20047-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0503111228000.20047-100000@acoma.Stanford.EDU>
Message-ID: <p06100507be5b47d5b36d@[132.236.163.148]>

This is as much as I know about these nodules, too.  It has been 
pointed out to me by Ann Hirsch (UCLA) that calling them "stem" 
nodules is somewhat misleading since they still form on roots, albeit 
adventitious ones.  But the differences between these nodule types 
suggest that some distinction may be useful.

--Jeff

>It seems there is. I am not an expert, here is what I found about
>Sebastania:
>
>Sesbania rostrata is a native legume of West Africa. It forms a symbiotic
>relationship with Azorhizobium caulinodans and is renowned for it's stem
>nodulation. Both stem and root nodules fix nitrogen however root nodules
>form at the curled root hair while stem nodules occur at the sites of
>adventitious root primordia via "crack" entry. The stem nodules unlike the
>root nodules contain functioning chloroplasts in the nodule cortex and are
>therefore capable of carbon fixation.
>
>http://www.personal.dundee.ac.uk/~rparsons/sesbania.htm
>
>
>Katica
>
>
>On Fri, 11 Mar 2005, Sue Rhee wrote:
>
>>  Are there any anatomical, morphological, lineage differences between the
>>  nodules in the primary/lateral root and the 'stem' nodules in the
>>  adventitious root? It seems like the introduction of 'stem nodule' for the
>>  nodules that are not really part of stem could lead to some confusion.
>>
>>  Sue
>>
>>  On Fri, 11 Mar 2005, Katica Ilic wrote:
>>
>>  > Hi Jeff,
>>  >
>>  > Thanks for your comment.
>>  >
>>  > Would it be more appropriate to have 'root nodule' instead?
>>  > Actually to instantiate term 'nodule' to 'root nodule' and 'stem
>>  > nodule'?
>>  >
>>  > Katica
>>  >
>>  > On Fri, 11 Mar 2005, Jeff J. Doyle wrote:
>>  >
>>  > > >
>>  > > >PO:0003023
>>  > > >name: nodule
>>  > > >def: Enlargement or swelling on the roots of plants, 
>>particularly in the
>>  > > >Fabaceae, inhabited by nitrogen-fixing bacteria.
>>  > >
>>  > > There are also what are called "stem nodules" in some legumes (the
>>  > > papilionoid genus Sesbania is the prime example, but the caesalpiniod
>>  > > Neptunia also has nodules on floating stems).  Stem nodules are
>>  > > associated with adventitious roots, however, so the definition is not
>>  > > actually incorrect, even if the position of the roots in question is
>>  > > not typical.
>>  > >
>>  > > --Jeff
>>  > >
>>  > >
>>  > > --
>>  > > Jeff J. Doyle
>>  > > Professor, L. H. Bailey Hortorium, Department of Plant Biology,
>>  > > Cornell University
>>  > > office: 259 Plant Science Building
>>  > > tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
>>  > > http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
>>  > >
>>  > > mailing address:
>>  > >
>>  > > Department of Plant Biology
>>  > > 228 Plant Science Building
>>  > > Cornell University
>>  > > Ithaca, NY 14853-4301
>>  > >
>>  >
>>  > --------------------------------------------------------------------------
>>  > 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.
>>  > --------------------------------------------------------------------------
>>  >
>>  >
>>
>> 
>>-----------------------------------------------------------------------------
>>  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.
>> 
>>-----------------------------------------------------------------------------
>>
>>
>
>--------------------------------------------------------------------------
>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.
>--------------------------------------------------------------------------


-- 
Jeff J. Doyle
Professor, L. H. Bailey Hortorium, Department of Plant Biology, 
Cornell University
office: 259 Plant Science Building
tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
http://www.plantbio.cornell.edu/faculty.php?PB=jjd5

mailing address:

Department of Plant Biology
228 Plant Science Building
Cornell University
Ithaca, NY 14853-4301


From rhee at acoma.Stanford.EDU  Mon Mar 14 12:45:51 2005
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Mon, 14 Mar 2005 09:45:51 -0800 (PST)
Subject: nodule
In-Reply-To: <p06100507be5b47d5b36d@[132.236.163.148]>
Message-ID: <Pine.GSO.4.44.0503140943250.11498-100000@acoma.Stanford.EDU>

Hi, Jeff

It seems like Pankaj's latest proposal addresses your comments well. What
are your thoughts on that?

something like:

root
-nodule
--[is a] adventitious root nodule (synonym: stem nodule)

Sue

On Mon, 14 Mar 2005, Jeff J. Doyle wrote:

> This is as much as I know about these nodules, too.  It has been
> pointed out to me by Ann Hirsch (UCLA) that calling them "stem"
> nodules is somewhat misleading since they still form on roots, albeit
> adventitious ones.  But the differences between these nodule types
> suggest that some distinction may be useful.
>
> --Jeff
>
> >It seems there is. I am not an expert, here is what I found about
> >Sebastania:
> >
> >Sesbania rostrata is a native legume of West Africa. It forms a symbiotic
> >relationship with Azorhizobium caulinodans and is renowned for it's stem
> >nodulation. Both stem and root nodules fix nitrogen however root nodules
> >form at the curled root hair while stem nodules occur at the sites of
> >adventitious root primordia via "crack" entry. The stem nodules unlike the
> >root nodules contain functioning chloroplasts in the nodule cortex and are
> >therefore capable of carbon fixation.
> >
> >http://www.personal.dundee.ac.uk/~rparsons/sesbania.htm
> >
> >
> >Katica
> >
> >
> >On Fri, 11 Mar 2005, Sue Rhee wrote:
> >
> >>  Are there any anatomical, morphological, lineage differences between the
> >>  nodules in the primary/lateral root and the 'stem' nodules in the
> >>  adventitious root? It seems like the introduction of 'stem nodule' for the
> >>  nodules that are not really part of stem could lead to some confusion.
> >>
> >>  Sue
> >>
> >>  On Fri, 11 Mar 2005, Katica Ilic wrote:
> >>
> >>  > Hi Jeff,
> >>  >
> >>  > Thanks for your comment.
> >>  >
> >>  > Would it be more appropriate to have 'root nodule' instead?
> >>  > Actually to instantiate term 'nodule' to 'root nodule' and 'stem
> >>  > nodule'?
> >>  >
> >>  > Katica
> >>  >
> >>  > On Fri, 11 Mar 2005, Jeff J. Doyle wrote:
> >>  >
> >>  > > >
> >>  > > >PO:0003023
> >>  > > >name: nodule
> >>  > > >def: Enlargement or swelling on the roots of plants,
> >>particularly in the
> >>  > > >Fabaceae, inhabited by nitrogen-fixing bacteria.
> >>  > >
> >>  > > There are also what are called "stem nodules" in some legumes (the
> >>  > > papilionoid genus Sesbania is the prime example, but the caesalpiniod
> >>  > > Neptunia also has nodules on floating stems).  Stem nodules are
> >>  > > associated with adventitious roots, however, so the definition is not
> >>  > > actually incorrect, even if the position of the roots in question is
> >>  > > not typical.
> >>  > >
> >>  > > --Jeff
> >>  > >
> >>  > >
> >>  > > --
> >>  > > Jeff J. Doyle
> >>  > > Professor, L. H. Bailey Hortorium, Department of Plant Biology,
> >>  > > Cornell University
> >>  > > office: 259 Plant Science Building
> >>  > > tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
> >>  > > http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
> >>  > >
> >>  > > mailing address:
> >>  > >
> >>  > > Department of Plant Biology
> >>  > > 228 Plant Science Building
> >>  > > Cornell University
> >>  > > Ithaca, NY 14853-4301
> >>  > >
> >>  >
> >>  > --------------------------------------------------------------------------
> >>  > 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.
> >>  > --------------------------------------------------------------------------
> >>  >
> >>  >
> >>
> >>
> >>-----------------------------------------------------------------------------
> >>  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.
> >>
> >>-----------------------------------------------------------------------------
> >>
> >>
> >
> >--------------------------------------------------------------------------
> >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.
> >--------------------------------------------------------------------------
>
>
> --
> Jeff J. Doyle
> Professor, L. H. Bailey Hortorium, Department of Plant Biology,
> Cornell University
> office: 259 Plant Science Building
> tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
> http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
>
> mailing address:
>
> Department of Plant Biology
> 228 Plant Science Building
> Cornell University
> Ithaca, NY 14853-4301
>

-----------------------------------------------------------------------------
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 jjd5 at cornell.edu  Mon Mar 14 15:28:52 2005
From: jjd5 at cornell.edu (Jeff J. Doyle)
Date: Mon, 14 Mar 2005 15:28:52 -0500
Subject: nodule
In-Reply-To: <Pine.GSO.4.44.0503140943250.11498-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0503140943250.11498-100000@acoma.Stanford.EDU>
Message-ID: <p0610050fbe5ba4485e9d@[132.236.163.148]>

It looks fine to me, Sue, as best as I can tell.

--Jeff

>Hi, Jeff
>
>It seems like Pankaj's latest proposal addresses your comments well. What
>are your thoughts on that?
>
>something like:
>
>root
>-nodule
>--[is a] adventitious root nodule (synonym: stem nodule)
>
>Sue
>
>On Mon, 14 Mar 2005, Jeff J. Doyle wrote:
>
>>  This is as much as I know about these nodules, too.  It has been
>>  pointed out to me by Ann Hirsch (UCLA) that calling them "stem"
>>  nodules is somewhat misleading since they still form on roots, albeit
>>  adventitious ones.  But the differences between these nodule types
>>  suggest that some distinction may be useful.
>>
>>  --Jeff
>>
>>  >It seems there is. I am not an expert, here is what I found about
>>  >Sebastania:
>>  >
>>  >Sesbania rostrata is a native legume of West Africa. It forms a symbiotic
>>  >relationship with Azorhizobium caulinodans and is renowned for it's stem
>>  >nodulation. Both stem and root nodules fix nitrogen however root nodules
>>  >form at the curled root hair while stem nodules occur at the sites of
>>  >adventitious root primordia via "crack" entry. The stem nodules unlike the
>>  >root nodules contain functioning chloroplasts in the nodule cortex and are
>>  >therefore capable of carbon fixation.
>>  >
>>  >http://www.personal.dundee.ac.uk/~rparsons/sesbania.htm
>>  >
>>  >
>>  >Katica
>>  >
>>  >
>>  >On Fri, 11 Mar 2005, Sue Rhee wrote:
>>  >
>>  >>  Are there any anatomical, morphological, lineage differences between the
>>  >>  nodules in the primary/lateral root and the 'stem' nodules in the
>>  >>  adventitious root? It seems like the introduction of 'stem 
>>nodule' for the
>>  >>  nodules that are not really part of stem could lead to some confusion.
>>  >>
>>  >>  Sue
>>  >>
>>  >>  On Fri, 11 Mar 2005, Katica Ilic wrote:
>>  >>
>>  >>  > Hi Jeff,
>>  >>  >
>>  >>  > Thanks for your comment.
>>  >>  >
>>  >>  > Would it be more appropriate to have 'root nodule' instead?
>>  >>  > Actually to instantiate term 'nodule' to 'root nodule' and 'stem
>>  >>  > nodule'?
>>  >>  >
>>  >>  > Katica
>>  >>  >
>>  >>  > On Fri, 11 Mar 2005, Jeff J. Doyle wrote:
>>  >>  >
>>  >>  > > >
>>  >>  > > >PO:0003023
>>  >>  > > >name: nodule
>>  >>  > > >def: Enlargement or swelling on the roots of plants,
>>  >>particularly in the
>>  >>  > > >Fabaceae, inhabited by nitrogen-fixing bacteria.
>>  >>  > >
>>  >>  > > There are also what are called "stem nodules" in some legumes (the
>>  >>  > > papilionoid genus Sesbania is the prime example, but the 
>>caesalpiniod
>>  >>  > > Neptunia also has nodules on floating stems).  Stem nodules are
>>  >>  > > associated with adventitious roots, however, so the 
>>definition is not
>>  >>  > > actually incorrect, even if the position of the roots in question is
>>  >>  > > not typical.
>>  >>  > >
>>  >>  > > --Jeff
>>  >>  > >
>>  >>  > >
>>  >>  > > --
>>  >>  > > Jeff J. Doyle
>>  >>  > > Professor, L. H. Bailey Hortorium, Department of Plant Biology,
>>  >>  > > Cornell University
>>  >>  > > office: 259 Plant Science Building
>>  >>  > > tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
>>  >>  > > http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
>>  >>  > >
>>  >>  > > mailing address:
>>  >>  > >
>>  >>  > > Department of Plant Biology
>>  >>  > > 228 Plant Science Building
>>  >>  > > Cornell University
>>  >>  > > Ithaca, NY 14853-4301
>>  >>  > >
>>  >>  >
>>  >>  > 
>>--------------------------------------------------------------------------
>>  >>  > 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.
>>  >>  > 
>>--------------------------------------------------------------------------
>>  >>  >
>>  >>  >
>>  >>
>>  >>
>>  >>-----------------------------------------------------------------------------
>>  >>  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.
>>  >>
>>  >>-----------------------------------------------------------------------------
>>  >>
>>  >>
>>  >
>>  >--------------------------------------------------------------------------
>>  >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.
>>  >--------------------------------------------------------------------------
>>
>>
>>  --
>>  Jeff J. Doyle
>>  Professor, L. H. Bailey Hortorium, Department of Plant Biology,
>>  Cornell University
>>  office: 259 Plant Science Building
>>  tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
>>  http://www.plantbio.cornell.edu/faculty.php?PB=jjd5
>>
>>  mailing address:
>>
>>  Department of Plant Biology
>>  228 Plant Science Building
>>  Cornell University
>>  Ithaca, NY 14853-4301
>>
>
>-----------------------------------------------------------------------------
>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.
>-----------------------------------------------------------------------------


-- 
Jeff J. Doyle
Professor, L. H. Bailey Hortorium, Department of Plant Biology, 
Cornell University
office: 259 Plant Science Building
tel: 607 255-7972 (lab: 607 255-1953); fax: 607-255-5407
http://www.plantbio.cornell.edu/faculty.php?PB=jjd5

mailing address:

Department of Plant Biology
228 Plant Science Building
Cornell University
Ithaca, NY 14853-4301


From pj37 at cornell.edu  Thu Mar 17 10:22:16 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 17 Mar 2005 10:22:16 -0500
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <41223D5B.50202@cornell.edu>
References: <4117994D.7010000@cornell.edu> <5ACCB78E-EA21-11D8-8EAD-000393B121A8@umsl.edu> <4117B9DB.20503@cornell.edu> <BF3C2A00-EBD9-11D8-8C17-000393B121A8@umsl.edu> <411BA5BF.5080405@cornell.edu> <BC843E60-F06F-11D8-ABDD-000393B121A8@umsl.edu> <41223D5B.50202@cornell.edu>
Message-ID: <4239A0A8.8040008@cornell.edu>

Hi Everyone,

We had a discussion on this sometime back but the terms never made it to 
the plant structure ontology. Here is it again.

new term : cauline axillary branch
def: an axillary branch that forms  above ground level and on an 
elongated (cauline) internode

new term: basal axillary branch
synonym: tiller, primary tiller, primary basal axillary branch, first 
order basal axillary branch
def: An axillary  branch that forms at ground level, generally from a 
non elongating (basal) internode

new term: second order basal axillary branch
synonym: secondary tiller, secondary basal axillary branch, secondary 
order basal axillary branch
def: An axillary  branch that forms at ground level, generally from a 
non elongating (basal) internode of the first order basal axillary branch

new term: third order basal axillary branch
synonym: tertiary tiller, tertiary basal axillary branch, tertiary basal 
axillary branch
def: An axillary  branch that forms at ground level, generally from a 
non elongating (basal) internode of the second order basal axillary branch

Suggested structure in ontology.
[i] = instance of

--PO:0009006 : shoot
--[i]--PO:0006343 : axillary shoot (this has a synonym tiller)
-------[i]--PO:new : cauline axillary branch
-------[i]--PO:new : basal axillary branch
-----------[i]--PO:new : second order basal axillary branch
-----------[i]--PO:new : third order basal axillary branch


PO:0006343 : axillary shoot term has a synonym "tiller" that will be 
moved to PO:new : basal axillary branch.

PO:0006343 : axillary shoot can then have a new synonyms "branch" and 
"ratoon"

Ratoon:  A shoot sprouting from a plant base, as in the banana, 
pineapple, sugar cane, bamboo, or in rice after the first harvest where 
basal portion of plant is still attached to ground and can generate new 
tillers/axillary shoots.


If you would like to see the discussion Toby and I had on this issues 
please see http://ascus.plbr.cornell.edu/~pankaj/branch/branch.txt

The tillering patterns in rice are called by primary, secondary and 
tertiary names. Please see the scanned document from an IRRI publication
http://ascus.plbr.cornell.edu/~pankaj/branch/rice-tillering.jpg


-Pankaj



From feedback_submission at filetta.cshl.edu  Thu Mar 17 11:09:53 2005
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 17 Mar 2005 11:09:53 -0500
Subject: Feedback on POC
Message-ID: <200503171609.j2HG9rAh027721@filetta.cshl.org>

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

refer_to_url: 

comments: 

http://www.plantontology.org/amigo/go.cgi?action=replace_tree&search_constraint=terms&query=PO:0000256

The develops from relationship icon is missing. I am using netscape 7.1

name: pankaj

email: pj37 at cornell.edu

organization: cu

send_feedback: Send your feedback



From shuly at cshl.edu  Thu Mar 17 11:20:25 2005
From: shuly at cshl.edu (Shuly Avraham)
Date: Thu, 17 Mar 2005 11:20:25 -0500
Subject: Feedback on POC
In-Reply-To: <200503171609.j2HG9rAh027721@filetta.cshl.org>
References: <200503171609.j2HG9rAh027721@filetta.cshl.org>
Message-ID: <4239AE49.8010501@cshl.edu>

That's because the reletionships changed from 'develops_from' to 
'derives_from' - which confused the image name...
Fixed!

Shuly.

feedback_submission at filetta.cshl.edu wrote:

>    *** Feedback from Plant Ontology Live Site ***
>
>refer_to_url: 
>
>comments: 
>
>http://www.plantontology.org/amigo/go.cgi?action=replace_tree&search_constraint=terms&query=PO:0000256
>
>The develops from relationship icon is missing. I am using netscape 7.1
>
>name: pankaj
>
>email: pj37 at cornell.edu
>
>organization: cu
>
>send_feedback: Send your feedback
>
>  
>


From peter.stevens at mobot.org  Thu Mar 17 10:01:49 2005
From: peter.stevens at mobot.org (Peter Stevens)
Date: Thu, 17 Mar 2005 11:01:49 -0400
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <4239A0A8.8040008@cornell.edu>
References: <4117994D.7010000@cornell.edu>
 <5ACCB78E-EA21-11D8-8EAD-000393B121A8@umsl.edu>
 <4117B9DB.20503@cornell.edu>
 <BF3C2A00-EBD9-11D8-8C17-000393B121A8@umsl.edu>
 <411BA5BF.5080405@cornell.edu>
 <BC843E60-F06F-11D8-ABDD-000393B121A8@umsl.edu>
 <41223D5B.50202@cornell.edu> <4239A0A8.8040008@cornell.edu>
Message-ID: <f0433011dbe5f4af34985@[172.16.16.11]>

>Hi Everyone,
>
>We had a discussion on this sometime back but the terms never made 
>it to the plant structure ontology. Here is it again.
>
>new term : cauline axillary branch
>def: an axillary branch that forms  above ground level and on an 
>elongated (cauline) internode


Note that there will nearly always be problems with definitions like 
this that have two independent variables.  What does one do with 
axillary shoots associated with short internodes on above-ground 
branches, e.g. some magnolia, rhododendron, Enkianthus. apple 
relatives?

P.

>
>new term: basal axillary branch
>synonym: tiller, primary tiller, primary basal axillary branch, 
>first order basal axillary branch
>def: An axillary  branch that forms at ground level, generally from 
>a non elongating (basal) internode
>
>new term: second order basal axillary branch
>synonym: secondary tiller, secondary basal axillary branch, 
>secondary order basal axillary branch
>def: An axillary  branch that forms at ground level, generally from 
>a non elongating (basal) internode of the first order basal axillary 
>branch
>
>new term: third order basal axillary branch
>synonym: tertiary tiller, tertiary basal axillary branch, tertiary 
>basal axillary branch
>def: An axillary  branch that forms at ground level, generally from 
>a non elongating (basal) internode of the second order basal 
>axillary branch
>
>Suggested structure in ontology.
>[i] = instance of
>
>--PO:0009006 : shoot
>--[i]--PO:0006343 : axillary shoot (this has a synonym tiller)
>-------[i]--PO:new : cauline axillary branch
>-------[i]--PO:new : basal axillary branch
>-----------[i]--PO:new : second order basal axillary branch
>-----------[i]--PO:new : third order basal axillary branch
>
>
>PO:0006343 : axillary shoot term has a synonym "tiller" that will be 
>moved to PO:new : basal axillary branch.
>
>PO:0006343 : axillary shoot can then have a new synonyms "branch" and "ratoon"
>
>Ratoon:  A shoot sprouting from a plant base, as in the banana, 
>pineapple, sugar cane, bamboo, or in rice after the first harvest 
>where basal portion of plant is still attached to ground and can 
>generate new tillers/axillary shoots.
>
>
>If you would like to see the discussion Toby and I had on this 
>issues please see 
>http://ascus.plbr.cornell.edu/~pankaj/branch/branch.txt
>
>The tillering patterns in rice are called by primary, secondary and 
>tertiary names. Please see the scanned document from an IRRI 
>publication
>http://ascus.plbr.cornell.edu/~pankaj/branch/rice-tillering.jpg
>
>
>-Pankaj



From katica at acoma.Stanford.EDU  Thu Mar 17 12:33:13 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Thu, 17 Mar 2005 09:33:13 -0800 (PST)
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <4239A0A8.8040008@cornell.edu>
Message-ID: <Pine.GSO.4.44.0503170929030.14597-100000@acoma.Stanford.EDU>


Pankaj,

I am not sure about terms 'second order basal axillary branch' and
'third order basal axillary branch', but we can discuss this in St Louis,
I am planning to have an hour-long discussion on several issues from Plant
Structure Ontology, likely on Saturday morning.

Katica

On Thu, 17 Mar 2005, Pankaj Jaiswal wrote:

> Hi Everyone,
>
> We had a discussion on this sometime back but the terms never made it to
> the plant structure ontology. Here is it again.
>
> new term : cauline axillary branch
> def: an axillary branch that forms  above ground level and on an
> elongated (cauline) internode
>
> new term: basal axillary branch
> synonym: tiller, primary tiller, primary basal axillary branch, first
> order basal axillary branch
> def: An axillary  branch that forms at ground level, generally from a
> non elongating (basal) internode
>
> new term: second order basal axillary branch
> synonym: secondary tiller, secondary basal axillary branch, secondary
> order basal axillary branch
> def: An axillary  branch that forms at ground level, generally from a
> non elongating (basal) internode of the first order basal axillary branch
>
> new term: third order basal axillary branch
> synonym: tertiary tiller, tertiary basal axillary branch, tertiary basal
> axillary branch
> def: An axillary  branch that forms at ground level, generally from a
> non elongating (basal) internode of the second order basal axillary branch
>
> Suggested structure in ontology.
> [i] = instance of
>
> --PO:0009006 : shoot
> --[i]--PO:0006343 : axillary shoot (this has a synonym tiller)
> -------[i]--PO:new : cauline axillary branch
> -------[i]--PO:new : basal axillary branch
> -----------[i]--PO:new : second order basal axillary branch
> -----------[i]--PO:new : third order basal axillary branch
>
>
> PO:0006343 : axillary shoot term has a synonym "tiller" that will be
> moved to PO:new : basal axillary branch.
>
> PO:0006343 : axillary shoot can then have a new synonyms "branch" and
> "ratoon"
>
> Ratoon:  A shoot sprouting from a plant base, as in the banana,
> pineapple, sugar cane, bamboo, or in rice after the first harvest where
> basal portion of plant is still attached to ground and can generate new
> tillers/axillary shoots.
>
>
> If you would like to see the discussion Toby and I had on this issues
> please see http://ascus.plbr.cornell.edu/~pankaj/branch/branch.txt
>
> The tillering patterns in rice are called by primary, secondary and
> tertiary names. Please see the scanned document from an IRRI publication
> http://ascus.plbr.cornell.edu/~pankaj/branch/rice-tillering.jpg
>
>
> -Pankaj
>

--------------------------------------------------------------------------
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 pj37 at cornell.edu  Thu Mar 17 13:55:13 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 17 Mar 2005 13:55:13 -0500
Subject: [Fwd: evidence codes in downloadable file]
Message-ID: <4239D291.6000600@cornell.edu>

Hi Everyone,

The forwarded e mail is a GO-specific request. I think we should do it 
for POC as well.

-Pankaj

-------- Original Message --------
Subject: evidence codes in downloadable file
Date: Thu, 17 Mar 2005 12:55:26 -0500


Folks-

It would be helpful if you made available on your download site a file
with the GO evidence codes.

The file could be two columns:

  name    description

This would be used by systems that utilize a fully automated data
acquisition process.  Our system, GUS, represents internally the
evidence codes and their description, and we would like to acquire that
information automatically.




From pj37 at cornell.edu  Thu Mar 17 14:05:17 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 17 Mar 2005 14:05:17 -0500
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <f0433011dbe5f4af34985@[172.16.16.11]>
References: <4117994D.7010000@cornell.edu> <5ACCB78E-EA21-11D8-8EAD-000393B121A8@umsl.edu> <4117B9DB.20503@cornell.edu> <BF3C2A00-EBD9-11D8-8C17-000393B121A8@umsl.edu> <411BA5BF.5080405@cornell.edu> <BC843E60-F06F-11D8-ABDD-000393B121A8@umsl.edu> <41223D5B.50202@cornell.edu> <4239A0A8.8040008@cornell.edu> <f0433011dbe5f4af34985@[172.16.16.11]>
Message-ID: <4239D4ED.4060606@cornell.edu>



Peter Stevens wrote:

>> Hi Everyone,
>>
>> We had a discussion on this sometime back but the terms never made it 
>> to the plant structure ontology. Here is it again.
>>
>> new term : cauline axillary branch
>> def: an axillary branch that forms  above ground level and on an 
>> elongated (cauline) internode
> 
> 
> 
> Note that there will nearly always be problems with definitions like 
> this that have two independent variables.  What does one do with 
> axillary shoots associated with short internodes on above-ground 
> branches, e.g. some magnolia, rhododendron, Enkianthus. apple relatives?
> 
> P.
> 

Any suggestions on alternate definition.

-Pankaj



From peter.stevens at mobot.org  Mon Mar 21 11:17:19 2005
From: peter.stevens at mobot.org (Peter Stevens)
Date: Mon, 21 Mar 2005 12:17:19 -0400
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <4239D4ED.4060606@cornell.edu>
References: <4117994D.7010000@cornell.edu>
 <5ACCB78E-EA21-11D8-8EAD-000393B121A8@umsl.edu>
 <4117B9DB.20503@cornell.edu>
 <BF3C2A00-EBD9-11D8-8C17-000393B121A8@umsl.edu>
 <411BA5BF.5080405@cornell.edu>
 <BC843E60-F06F-11D8-ABDD-000393B121A8@umsl.edu>
 <41223D5B.50202@cornell.edu> <4239A0A8.8040008@cornell.edu>
 <f0433011dbe5f4af34985@[172.16.16.11]> <4239D4ED.4060606@cornell.edu>
Message-ID: <f04330122be64a3d3eaba@[172.16.16.11]>

>Peter Stevens wrote:
>
>>>Hi Everyone,
>>>
>>>We had a discussion on this sometime back but the terms never made 
>>>it to the plant structure ontology. Here is it again.
>>>
>>>new term : cauline axillary branch
>>>def: an axillary branch that forms  above ground level and on an 
>>>elongated (cauline) internode
>>
>>
>>
>>Note that there will nearly always be problems with definitions 
>>like this that have two independent variables.  What does one do 
>>with axillary shoots associated with short internodes on 
>>above-ground branches, e.g. some magnolia, rhododendron, 
>>Enkianthus. apple relatives?
>>
>>P.
>>
>
>Any suggestions on alternate definition.


an axillary branch that forms above ground level?

P.

>
>-Pankaj



From pj37 at cornell.edu  Mon Mar 21 16:37:32 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 21 Mar 2005 16:37:32 -0500
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <f04330122be64a3d3eaba@[172.16.16.11]>
References: <4117994D.7010000@cornell.edu> <5ACCB78E-EA21-11D8-8EAD-000393B121A8@umsl.edu> <4117B9DB.20503@cornell.edu> <BF3C2A00-EBD9-11D8-8C17-000393B121A8@umsl.edu> <411BA5BF.5080405@cornell.edu> <BC843E60-F06F-11D8-ABDD-000393B121A8@umsl.edu> <41223D5B.50202@cornell.edu> <4239A0A8.8040008@cornell.edu> <f0433011dbe5f4af34985@[172.16.16.11]> <4239D4ED.4060606@cornell.edu> <f04330122be64a3d3eaba@[172.16.16.11]>
Message-ID: <423F3E9C.8030900@cornell.edu>



Peter Stevens wrote:
>> Peter Stevens wrote:
>>
>>>> Hi Everyone,
>>>>
>>>> We had a discussion on this sometime back but the terms never made 
>>>> it to the plant structure ontology. Here is it again.
>>>>
>>>> new term : cauline axillary branch
>>>> def: an axillary branch that forms  above ground level and on an 
>>>> elongated (cauline) internode
>>>
>>>
>>>
>>>
>>> Note that there will nearly always be problems with definitions like 
>>> this that have two independent variables.  What does one do with 
>>> axillary shoots associated with short internodes on above-ground 
>>> branches, e.g. some magnolia, rhododendron, Enkianthus. apple relatives?
>>>
>>> P.
>>>
>>
>> Any suggestions on alternate definition.
> 
> 
> 
> an axillary branch that forms above ground level?
> 
> P.
We are back to the same thing. Both cauline and basal are above ground. 
So how can one put this into definition (how much above ground?), making 
sure the definitions are different and apply discretely to cauline and 
basal branches.

We can't stay generic.

-Pankaj



From katica at acoma.Stanford.EDU  Mon Mar 21 17:01:08 2005
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Mon, 21 Mar 2005 14:01:08 -0800 (PST)
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <423F3E9C.8030900@cornell.edu>
Message-ID: <Pine.GSO.4.44.0503211357010.3055-100000@acoma.Stanford.EDU>


Pankaj,

For the St Louis meeting, could you show us a few examples where you need
granular terms that you proposed for the annotation in rice?

It would really help, at least in my case.

Katica



On Mon, 21 Mar 2005, Pankaj Jaiswal
wrote:

>
>
> Peter Stevens wrote:
> >> Peter Stevens wrote:
> >>
> >>>> Hi Everyone,
> >>>>
> >>>> We had a discussion on this sometime back but the terms never made
> >>>> it to the plant structure ontology. Here is it again.
> >>>>
> >>>> new term : cauline axillary branch
> >>>> def: an axillary branch that forms  above ground level and on an
> >>>> elongated (cauline) internode
> >>>
> >>>
> >>>
> >>>
> >>> Note that there will nearly always be problems with definitions like
> >>> this that have two independent variables.  What does one do with
> >>> axillary shoots associated with short internodes on above-ground
> >>> branches, e.g. some magnolia, rhododendron, Enkianthus. apple relatives?
> >>>
> >>> P.
> >>>
> >>
> >> Any suggestions on alternate definition.
> >
> >
> >
> > an axillary branch that forms above ground level?
> >
> > P.
> We are back to the same thing. Both cauline and basal are above ground.
> So how can one put this into definition (how much above ground?), making
> sure the definitions are different and apply discretely to cauline and
> basal branches.
>
> We can't stay generic.
>
> -Pankaj
>

--------------------------------------------------------------------------
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 pj37 at cornell.edu  Mon Mar 21 17:09:21 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 21 Mar 2005 17:09:21 -0500
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <Pine.GSO.4.44.0503211357010.3055-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0503211357010.3055-100000@acoma.Stanford.EDU>
Message-ID: <423F4611.3080109@cornell.edu>

Certainly yes. Here is the reference.

PNAS | June 15, 2004 | vol. 101 | no. 24 | 9045-9050
Genetic control of branching in foxtail millet
Andrew N. Doust *, Katrien M. Devos , , Michael D. Gadberry * , Mike D. 
Gale  and Elizabeth A. Kellogg
http://www.pnas.org/cgi/content/abstract/101/24/9045

We are trying to annotate these QTL to the anatomy terms.

-Pankaj


Katica Ilic wrote:

> Pankaj,
> 
> For the St Louis meeting, could you show us a few examples where you need
> granular terms that you proposed for the annotation in rice?
> 
> It would really help, at least in my case.
> 
> Katica
> 
> 
> 
> On Mon, 21 Mar 2005, Pankaj Jaiswal
> wrote:
> 
> 
>>
>>Peter Stevens wrote:
>>
>>>>Peter Stevens wrote:
>>>>
>>>>
>>>>>>Hi Everyone,
>>>>>>
>>>>>>We had a discussion on this sometime back but the terms never made
>>>>>>it to the plant structure ontology. Here is it again.
>>>>>>
>>>>>>new term : cauline axillary branch
>>>>>>def: an axillary branch that forms  above ground level and on an
>>>>>>elongated (cauline) internode
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>Note that there will nearly always be problems with definitions like
>>>>>this that have two independent variables.  What does one do with
>>>>>axillary shoots associated with short internodes on above-ground
>>>>>branches, e.g. some magnolia, rhododendron, Enkianthus. apple relatives?
>>>>>
>>>>>P.
>>>>>
>>>>
>>>>Any suggestions on alternate definition.
>>>
>>>
>>>
>>>an axillary branch that forms above ground level?
>>>
>>>P.
>>
>>We are back to the same thing. Both cauline and basal are above ground.
>>So how can one put this into definition (how much above ground?), making
>>sure the definitions are different and apply discretely to cauline and
>>basal branches.
>>
>>We can't stay generic.
>>
>>-Pankaj
>>
> 
> 
> --------------------------------------------------------------------------
> 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.
> --------------------------------------------------------------------------
> 
> 
> 

-- 
************************
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 pj37 at cornell.edu  Mon Mar 21 17:12:07 2005
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 21 Mar 2005 17:12:07 -0500
Subject: new term suggestion: cauline & basal axillary branches
In-Reply-To: <423F4611.3080109@cornell.edu>
References: <Pine.GSO.4.44.0503211357010.3055-100000@acoma.Stanford.EDU> <423F4611.3080109@cornell.edu>
Message-ID: <423F46B7.1050408@cornell.edu>

Gramene does curation on some of the non-rice species as well. The 
following example is not from rice but yes we require terms for 
annotations to Millet QTL.

-Pankaj

Pankaj Jaiswal wrote:

> Certainly yes. Here is the reference.
> 
> PNAS | June 15, 2004 | vol. 101 | no. 24 | 9045-9050
> Genetic control of branching in foxtail millet
> Andrew N. Doust *, Katrien M. Devos , , Michael D. Gadberry * , Mike D. 
> Gale  and Elizabeth A. Kellogg
> http://www.pnas.org/cgi/content/abstract/101/24/9045
> 
> We are trying to annotate these QTL to the anatomy terms.
> 
> -Pankaj
> 
> 
> Katica Ilic wrote:
> 
>> Pankaj,
>>
>> For the St Louis meeting, could you show us a few examples where you need
>> granular terms that you proposed for the annotation in rice?
>>
>> It would really help, at least in my case.
>>
>> Katica
>



From feedback_submission at filetta.cshl.edu  Wed Mar 23 10:48:08 2005
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Wed, 23 Mar 2005 10:48:08 -0500
Subject: Feedback on POC
Message-ID: <200503231548.j2NFm8GV012770@filetta.cshl.org>

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

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

comments: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&session_id=8728b1111592599&search_constraint=gp&query=sd1

Shuly,

#1

I think the search result should include gene full name or in other words the
 DB_Object_Name
 DB_Object_Synonym(|Synonym) 
from association tables.

by looking at only the "sd1" a user has no clue what this is until he/she clicks one more step. 

------------
#2

in the last column of the search results where it says "Plant structure", I think the header "aspect" is missing.



name: pankaj

email: pj37 at cornell.edu

organization: cu

send_feedback: Send your feedback