From katica at acoma.Stanford.EDU  Wed Sep  1 02:42:15 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Tue, 31 Aug 2004 23:42:15 -0700 (PDT)
Subject: pericycle
In-Reply-To: <4134C8BC.7070200@cornell.edu>
Message-ID: <Pine.GSO.4.44.0408312332300.25714-100000@acoma.Stanford.EDU>


Pankaj,

Pericycle should be a child of the root stele (as Peter said), as this is
the outermost layer (boundary) of root stele. It's not a part of the
cortex. The innermost layer of the root cortex is endodermis, a layer od
cells next to the pericycle.

Katica

On Tue, 31 Aug 2004, Pankaj Jaiswal wrote:

> Hi,
> Here is what I proposed in response to Alison's mail for pericycle
>
> ---PO:0009075 : plant ontology
> ----i PO:0009011 : plant structure
> -------i PO:0009003 : sporophyte
> -----------p PO:0009005 : root
> --------------p PO:0000258 : root cortex
> --------------p PO:0020124 : root stele
> -------------------p PO:0006203 : pericycle
> -------i PO:0009007 : tissue
> -----------i PO:0005708 : cortex
> --------------i PO:0000258 : root cortex
> --------------i PO:0006203 : pericycle
>
> But this is again leading us into a black hole, which we are trying to
> avoid. The term pericycle is a generic term and we need to create its
> instances such as
> -root pericycle
> -stem pericycle
> -leaf pericycle
>
> In order to make correct lineage the instantiation is required.
>
> Current definition and comments sauugest it so..
>
> # Definition:
>
>      * Part of the tissue of the stele located between the phloem and
> endodermis.
>
> # Comment:
>
>      * In seed plants it is regularly present in roots and absent in
> most stems and leaves.
>
>
>
> -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  Wed Sep  1 13:29:07 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 01 Sep 2004 13:29:07 -0400
Subject: protoderm and procambium
Message-ID: <413606E3.8050303@cornell.edu>

I received, another feedback from Alison Roberts, which was not copied 
to po-dev list. Here it is.

-Pankaj

-------- Original Message --------
Subject: Re: Feedback Submission from Plant Ontology Live Site
Date: Tue, 31 Aug 2004 15:41:37 -0400
From: Alison Roberts <aroberts at uri.edu>
To: Pankaj Jaiswal <pj37 at cornell.edu>
References: <200408311610.i7VGAnSr012557 at brie4.cshl.org> 
<4134C6D4.7010004 at cornell.edu>

Dear Pankaj,

Thank you for your reply. This may be another thing to think about...
"Procambium" is listed a part of an apical meristem in POC, whereas
"protoderm" is listed as part of a meristem. As I understand these terms,
they should both have the same relationship to the same parent term. As for
what that parent and relationship should be? Procambium and protoderm are
sometimes considered part of the "apical meristematic region", but usually
NOT part of the "apical meristem" proper. They fit the definition of
"meristems" in their own right, so to me it would be preferable to list
them as types of meristems that develop from an apical meristem (root or
shoot). I suppose "ground meristem" should be made obsolete like "ground
tissue".

Regards,
Alison Roberts




From nelsonrt at iastate.edu  Wed Sep  1 13:43:15 2004
From: nelsonrt at iastate.edu (Rex Nelson)
Date: Wed, 1 Sep 2004 12:43:15 -0500
Subject: Soybean ontology (PR#24)
In-Reply-To: <200408312223.i7VMN7Uq015162@brie4.cshl.org>
References: <200408312223.i7VMN7Uq015162@brie4.cshl.org>
Message-ID: <p06020434bd5bb8665b11@[129.186.230.13]>

Katica:

I talked with Dr. Shoemaker and we are interested in collaborating 
with the POC on soybean ontologies.  Is there a time I could place a 
call to you to discuss the collaboration and how this will work?  It 
will be too cumbersome to do it by Email.

Please drop me a note on a time that would be convenient for you to 
take the call.  Please indicate if the time is PDT or not. I am 
assuming the phone number is: (650) 325-1521 ext. 253.

Rex


>Hi Rex,
>
>Thanks again for your interest in plant ontologies. It's great that you have
>plans to create a comprehensive ontology for soybean and other 
>legumes that will
>be freely available to the public. I am sure that both, 
>developmental stages and
>anatomy/morphology ontologies for soybean will be used by a large number of
>researchers.
>
>Regarding  a help with DAG-edit, I agree with you, it's not very 
>intuitive tool,
>but after solving few initial problems, it's relatively easy to edit ontology
>using this tool. Of course, I'll be happy to help you with tips and 
>suggestions
>(I had generous help from my colleagues at TAIR). Please feel free 
>to contact me
>any time. To report bugs that you may sometimes discover, especially with new
>released versions of Dag-edit, please contact John Day-Richter
>(john.richter at aya.yale.edu).
>
>I look forward to hearing from you and Dr. Randy Schoemaker about possibility
>for collaboration and joining our efforts at POC.

-- 
Rex Nelson Ph. D.
Postdoctoral Fellow
nelsonrt at iastate.edu



From ap343 at cornell.edu  Wed Sep  1 14:11:23 2004
From: ap343 at cornell.edu (Anuradha Pujar)
Date: Wed, 1 Sep 2004 14:11:23 -0400 (EDT)
Subject: protoderm and procambium
In-Reply-To: <413606E3.8050303@cornell.edu>
References: <413606E3.8050303@cornell.edu>
Message-ID: <4352.128.253.246.53.1094062283.squirrel@128.253.246.53>

 Dr Alison,
 Thank you for  your feedback, the terms protoderm and procambium should
be placed under apical meristem as you have pointed out, and it will be
done. The term 'meristem' in POC is  generic and is not 'ground
meristem'.

Anuradha

> I received, another feedback from Alison Roberts, which was not copied
> to po-dev list. Here it is.
>
> -Pankaj
>
> -------- Original Message --------
> Subject: Re: Feedback Submission from Plant Ontology Live Site
> Date: Tue, 31 Aug 2004 15:41:37 -0400
> From: Alison Roberts <aroberts at uri.edu>
> To: Pankaj Jaiswal <pj37 at cornell.edu>
> References: <200408311610.i7VGAnSr012557 at brie4.cshl.org>
> <4134C6D4.7010004 at cornell.edu>
>
> Dear Pankaj,
>
> Thank you for your reply. This may be another thing to think about...
> "Procambium" is listed a part of an apical meristem in POC, whereas
> "protoderm" is listed as part of a meristem. As I understand these terms,
> they should both have the same relationship to the same parent term. As
> for
> what that parent and relationship should be? Procambium and protoderm are
> sometimes considered part of the "apical meristematic region", but usually
> NOT part of the "apical meristem" proper. They fit the definition of
> "meristems" in their own right, so to me it would be preferable to list
> them as types of meristems that develop from an apical meristem (root or
> shoot). I suppose "ground meristem" should be made obsolete like "ground
> tissue".
>
> Regards,
> Alison Roberts
>
>
>




From jitterbug at plantontology.org  Wed Sep  1 16:17:01 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Wed, 1 Sep 2004 16:17:01 -0400
Subject: Soybean ontology (PR#24)
Message-ID: <200409012017.i81KH1Uq027894@brie4.cshl.org>


Hi Rex,

Great! POC core members have conference call on Sept 09. So next day,
Sept 10 would be good time for a phone call or any other other day after 
Sep 09. Time difference is 2 hours I believe, any time except Tuesday and
Thursday morining 10-12 (PST), when we have regular meetings at TAIR.

Please let me know if this is OK. I hope it's not too 'far-away' date.

Katica

On Wed, 1 Sept 2004 Rex Nelson wrote:

 Katica:
> 
> I talked with Dr. Shoemaker and we are interested in collaborating 
> with the POC on soybean ontologies.  Is there a time I could place a 
> call to you to discuss the collaboration and how this will work?  It 
> will be too cumbersome to do it by Email.
> 
> Please drop me a note on a time that would be convenient for you to 
> take the call.  Please indicate if the time is PDT or not. I am 
> assuming the phone number is: (650) 325-1521 ext. 253.
> 
> Rex
> 
> 
>>Hi Rex,
>>
>>Thanks again for your interest in plant ontologies. It's great that you have
>>plans to create a comprehensive ontology for soybean and other 
>>legumes that will
>>be freely available to the public. I am sure that both, 
>>developmental stages and
>>anatomy/morphology ontologies for soybean will be used by a large number of
>>researchers.
>>
>>Regarding  a help with DAG-edit, I agree with you, it's not very 
>>intuitive tool,
>>but after solving few initial problems, it's relatively easy to edit ontology
>>using this tool. Of course, I'll be happy to help you with tips and 
>>suggestions
>>(I had generous help from my colleagues at TAIR). Please feel free 
>>to contact me
>>any time. To report bugs that you may sometimes discover, especially with new
>>released versions of Dag-edit, please contact John Day-Richter
>>(john.richter at aya.yale.edu).
>>
>>I look forward to hearing from you and Dr. Randy Schoemaker about possibility
>>for collaboration and joining our efforts at POC.
> 
> -- 
> Rex Nelson Ph. D.
> Postdoctoral Fellow
> nelsonrt at iastate.edu
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: 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  Wed Sep  1 16:44:56 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 01 Sep 2004 16:44:56 -0400
Subject: Soybean ontology (PR#24)
In-Reply-To: <200409012017.i81KH1Uq027894@brie4.cshl.org>
References: <200409012017.i81KH1Uq027894@brie4.cshl.org>
Message-ID: <413634C8.2000708@cornell.edu>

Hi Katica,

Please include Anu in your discussions.

Pankaj

Katica Ilic wrote:

> Hi Rex,
> 
> Great! POC core members have conference call on Sept 09. So next day,
> Sept 10 would be good time for a phone call or any other other day after 
> Sep 09. Time difference is 2 hours I believe, any time except Tuesday and
> Thursday morining 10-12 (PST), when we have regular meetings at TAIR.
> 
> Please let me know if this is OK. I hope it's not too 'far-away' date.
> 
> Katica
> 
> On Wed, 1 Sept 2004 Rex Nelson wrote:
> 
>  Katica:
> 
>>I talked with Dr. Shoemaker and we are interested in collaborating 
>>with the POC on soybean ontologies.  Is there a time I could place a 
>>call to you to discuss the collaboration and how this will work?  It 
>>will be too cumbersome to do it by Email.
>>
>>Please drop me a note on a time that would be convenient for you to 
>>take the call.  Please indicate if the time is PDT or not. I am 
>>assuming the phone number is: (650) 325-1521 ext. 253.
>>
>>Rex
>>
>>
>>
>>>Hi Rex,
>>>
>>>Thanks again for your interest in plant ontologies. It's great that you have
>>>plans to create a comprehensive ontology for soybean and other 
>>>legumes that will
>>>be freely available to the public. I am sure that both, 
>>>developmental stages and
>>>anatomy/morphology ontologies for soybean will be used by a large number of
>>>researchers.
>>>
>>>Regarding  a help with DAG-edit, I agree with you, it's not very 
>>>intuitive tool,
>>>but after solving few initial problems, it's relatively easy to edit ontology
>>>using this tool. Of course, I'll be happy to help you with tips and 
>>>suggestions
>>>(I had generous help from my colleagues at TAIR). Please feel free 
>>>to contact me
>>>any time. To report bugs that you may sometimes discover, especially with new
>>>released versions of Dag-edit, please contact John Day-Richter
>>>(john.richter at aya.yale.edu).
>>>
>>>I look forward to hearing from you and Dr. Randy Schoemaker about possibility
>>>for collaboration and joining our efforts at POC.
>>
>>-- 
>>Rex Nelson Ph. D.
>>Postdoctoral Fellow
>>nelsonrt at iastate.edu
>>
>>
> 
> Katica Ilic, TAIR Curator,	     E-mail: 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 nelsonrt at iastate.edu  Thu Sep  2 10:26:06 2004
From: nelsonrt at iastate.edu (Rex Nelson)
Date: Thu, 2 Sep 2004 09:26:06 -0500
Subject: Soybean ontology (PR#24)
In-Reply-To: <200409012017.i81KH1Uq027894@brie4.cshl.org>
References: <200409012017.i81KH1Uq027894@brie4.cshl.org>
Message-ID: <p06020438bd5cdb2d817c@[129.186.230.13]>

Katica:

>Hi Rex,
>
>Great! POC core members have conference call on Sept 09. So next day,
>Sept 10 would be good time for a phone call or any other other day after
>Sep 09. Time difference is 2 hours I believe, any time except Tuesday and
>Thursday morining 10-12 (PST), when we have regular meetings at TAIR.
>
>Please let me know if this is OK. I hope it's not too 'far-away' date.
>
>Katica
>

OK, I guess it will be Friday Sept. 10.  Will 9:00am your time be OK? 
We could do it at 1:00 - 2:00pm your time also.

Drop me a note as to which time is better for you and what phone 
number to call.

PS: Which Email address would you prefer me to use for you - this one 
or katica at acoma.stanford.edu?

Rex

-- 
Rex Nelson Ph. D.
Postdoctoral Fellow
nelsonrt at iastate.edu



From pj37 at cornell.edu  Thu Sep  2 14:40:50 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 02 Sep 2004 14:40:50 -0400
Subject: new version in CVS
Message-ID: <41376932.9080900@cornell.edu>

Hi Everyone,

The new version of anatomy.ontology and anatomy.definition files are 
available from CVS. Please update the files in your sand boxes.

The modifications made were:

PO:0006203 : pericycle is now part_of  PO:0020124 : root stele

Following are now part_of PO:0005708 : cortex
  PO:0000252 : endodermis
  PO:0005051 : hypodermis


-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 katica at acoma.Stanford.EDU  Thu Sep  2 21:47:21 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Thu, 2 Sep 2004 18:47:21 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <p06020438bd5cdb2d817c@[129.186.230.13]>
Message-ID: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU>

Hi all,

We have a user's request to introduce the following terms in PO:

Cauline leaf
Rosette leaf
Hypocotyl hook


Cauline leaf and rosette leaf are both present in TAIR (with several
annotations for both)

Term name: Cauline leaf
ID: TAIR:0000090 (currently 5 genes associated with this term, 5
annotations)
Def: Stem leaf, produced before the transition to flowering, lacking a
petiole.

Term name: Rosette leaf
ID: TAIR:0000089 (currently 11 genes associated with this term, 11
annotations)
Def: Leaf that is part of phyllotactic spiral with little internode
elongation between successive leaves. In Arabidopsis, vegetative
development is characterized by the production of the rosette leaves.

Both terms could be children of 'leaf' or 'simple leaf' (instance
of).
These are the existing terms in PO (under phyllome node), and to my
knowledge, synonymy may not work here:

  PO:0009025 : leaf
  PO:0006340 : adult leaf
  PO:0020103 : flag leaf
  PO:0020043 : compound leaf
  PO:0006338 : embryonic leaf
  PO:0006339 : juvenile leaf
  PO:0020042 : simple leaf


I myself am not very sure about the third proposed term, hypocotyl
hook; it's referring to the region of the seedling in early seedling
development, but this is not dev stage term.

There are few publications (often ethylene response genes) in which the
authors are referring to 'hypocotyl hook'. Here are some:

http://dev.biologists.org/cgi/reprint/126/16/3661
http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-313x.1999.00607.x/full/

What do you think about introducing these three terms?

Pankaj, this node is currently assigned to you.

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 fzqhd at umsl.edu  Thu Sep  2 22:15:36 2004
From: fzqhd at umsl.edu (Felipe Zapata)
Date: Thu, 2 Sep 2004 21:15:36 -0500
Subject: New terms in PO
In-Reply-To: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU>
Message-ID: <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu>

Cauline leaf:
 From the definition it looks like it refers to a regular leaf. Only it  
has a particular name because "is before flowering" and "lacks a  
petiole".  Lacking a petiole shouldn't pose a problem as not all the  
parts of leaf have to be present (we still follow the sometimes part of  
rule, right?). So a leaf may or may not have petiole.  In regards to  
"before flowering" I wonder if this event makes a "regular leaf" (in  
terms of anatomy and structure) a different type of leaf. I don't think  
so.  This is more like a...developmental stage term?

Rosette leaf:
Once again, from the definition, it looks like it refers to a regular  
(normal) leaf growing in certain arrangement, not to a different type  
of leaf.  If the internodes between leaves elongate or not, that's a  
different issue.  Some plants grow characteristically as rosette plants  
(e.g. plants in the high peaks), nonetheless the leaves are "normal  
leaves".  If rosette leaf is introduced to POC, why not alternate leaf?  
opposite leaf?

Hypocothyl hook:
I am not what it refers to, but if it is indispensable...

F

On Sep 2, 2004, at 8:47 PM, Katica Ilic wrote:

> Hi all,
>
> We have a user's request to introduce the following terms in PO:
>
> Cauline leaf
> Rosette leaf
> Hypocotyl hook
>
>
> Cauline leaf and rosette leaf are both present in TAIR (with several
> annotations for both)
>
> Term name: Cauline leaf
> ID: TAIR:0000090 (currently 5 genes associated with this term, 5
> annotations)
> Def: Stem leaf, produced before the transition to flowering, lacking a
> petiole.
>
> Term name: Rosette leaf
> ID: TAIR:0000089 (currently 11 genes associated with this term, 11
> annotations)
> Def: Leaf that is part of phyllotactic spiral with little internode
> elongation between successive leaves. In Arabidopsis, vegetative
> development is characterized by the production of the rosette leaves.
>
> Both terms could be children of 'leaf' or 'simple leaf' (instance
> of).
> These are the existing terms in PO (under phyllome node), and to my
> knowledge, synonymy may not work here:
>
>   PO:0009025 : leaf
>   PO:0006340 : adult leaf
>   PO:0020103 : flag leaf
>   PO:0020043 : compound leaf
>   PO:0006338 : embryonic leaf
>   PO:0006339 : juvenile leaf
>   PO:0020042 : simple leaf
>
>
> I myself am not very sure about the third proposed term, hypocotyl
> hook; it's referring to the region of the seedling in early seedling
> development, but this is not dev stage term.
>
> There are few publications (often ethylene response genes) in which the
> authors are referring to 'hypocotyl hook'. Here are some:
>
> http://dev.biologists.org/cgi/reprint/126/16/3661
> http://www.blackwell-synergy.com/links/doi/10.1046/j.1365 
> -313x.1999.00607.x/full/
>
> What do you think about introducing these three terms?
>
> Pankaj, this node is currently assigned to you.
>
> 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 msachs at uiuc.edu  Thu Sep  2 22:59:19 2004
From: msachs at uiuc.edu (Marty Sachs)
Date: Thu, 2 Sep 2004 21:59:19 -0500
Subject: New terms in PO
In-Reply-To: <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu>
References: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU>
 <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu>
Message-ID: <p06110403bd5d8c85a880@[130.126.89.70]>

At 9:15 PM -0500 9/2/04, Felipe Zapata wrote:
>Rosette leaf:
>Once again, from the definition, it looks like it refers to a 
>regular (normal) leaf growing in certain arrangement, not to a 
>different type of leaf.  If the internodes between leaves elongate 
>or not, that's a different issue.  Some plants grow 
>characteristically as rosette plants (e.g. plants in the high 
>peaks), nonetheless the leaves are "normal leaves".  If rosette leaf 
>is introduced to POC, why not alternate leaf? opposite leaf?

Maize folks use the term 'Rosette leaf' to describe the appearance of 
mutants defective in Gibberellic Acid synthesis or response.

	-Marty


From paulien.adamse at wur.nl  Fri Sep  3 02:09:21 2004
From: paulien.adamse at wur.nl (Adamse, Paulien)
Date: Fri, 3 Sep 2004 08:09:21 +0200
Subject: New terms in PO
Message-ID: <D7D87C2E22166045999C9FB3DC656B29CFF01F@scomp0017>

For describing Arabidopsis it is quite relevant. Not just for mutants, but I needed it a lot to describe Arabidopsis mutants in my database.

Paulien

-----Original Message-----
From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org]On
Behalf Of Marty Sachs
Sent: Friday, September 03, 2004 04:59
To: po-dev at plantontology.org
Subject: Re: New terms in PO


At 9:15 PM -0500 9/2/04, Felipe Zapata wrote:
>Rosette leaf:
>Once again, from the definition, it looks like it refers to a 
>regular (normal) leaf growing in certain arrangement, not to a 
>different type of leaf.  If the internodes between leaves elongate 
>or not, that's a different issue.  Some plants grow 
>characteristically as rosette plants (e.g. plants in the high 
>peaks), nonetheless the leaves are "normal leaves".  If rosette leaf 
>is introduced to POC, why not alternate leaf? opposite leaf?

Maize folks use the term 'Rosette leaf' to describe the appearance of 
mutants defective in Gibberellic Acid synthesis or response.

	-Marty



From lreiser at acoma.Stanford.EDU  Fri Sep  3 10:51:59 2004
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Sep 2004 07:51:59 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu>
Message-ID: <Pine.GSO.4.44.0409030746120.19826-100000@acoma.Stanford.EDU>

On Thu, 2 Sep 2004, Felipe Zapata wrote:

> Cauline leaf:
>  From the definition it looks like it refers to a regular leaf. Only it
> has a particular name because "is before flowering" and "lacks a
> petiole".  Lacking a petiole shouldn't pose a problem as not all the
> parts of leaf have to be present (we still follow the sometimes part of
> rule, right?). So a leaf may or may not have petiole.  In regards to
> "before flowering" I wonder if this event makes a "regular leaf" (in
> terms of anatomy and structure) a different type of leaf. I don't think
> so.  This is more like a...developmental stage term?

This term typically refers to the leaves which are borne on the elongated
inflorescence branches in Arabidopsis. It is a VERY commonly used term in
desrcribing Arabidopsis both wild type and mutant form.They almost always
have 'adult' characteristics.

>
> Rosette leaf:
> Once again, from the definition, it looks like it refers to a regular
> (normal) leaf growing in certain arrangement, not to a different type
> of leaf.  If the internodes between leaves elongate or not, that's a
> different issue.  Some plants grow characteristically as rosette plants
> (e.g. plants in the high peaks), nonetheless the leaves are "normal
> leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
> opposite leaf?
Again- this is a very commonly used term to describe leaves that are
formed prior to elongation of the primary stem. Well, actually, I think
Fred Hempell may have shown that some of these leaves are initiated before
stem elongation. So maybe defining as leaves which are below the elongated
internode.

>
> Hypocothyl hook:
> I am not what it refers to, but if it is indispensable...
>

Oh yes- it is indespensable- particularly when describing ethylene
responses. Part of the so called triple response is hypocotyl hook
curvature. This would be an example of a term that refers to a region
(defined by a physiological response).
Leonore

> F
>
> On Sep 2, 2004, at 8:47 PM, Katica Ilic wrote:
>
> > Hi all,
> >
> > We have a user's request to introduce the following terms in PO:
> >
> > Cauline leaf
> > Rosette leaf
> > Hypocotyl hook
> >
> >
> > Cauline leaf and rosette leaf are both present in TAIR (with several
> > annotations for both)
> >
> > Term name: Cauline leaf
> > ID: TAIR:0000090 (currently 5 genes associated with this term, 5
> > annotations)
> > Def: Stem leaf, produced before the transition to flowering, lacking a
> > petiole.
> >
> > Term name: Rosette leaf
> > ID: TAIR:0000089 (currently 11 genes associated with this term, 11
> > annotations)
> > Def: Leaf that is part of phyllotactic spiral with little internode
> > elongation between successive leaves. In Arabidopsis, vegetative
> > development is characterized by the production of the rosette leaves.
> >
> > Both terms could be children of 'leaf' or 'simple leaf' (instance
> > of).
> > These are the existing terms in PO (under phyllome node), and to my
> > knowledge, synonymy may not work here:
> >
> >   PO:0009025 : leaf
> >   PO:0006340 : adult leaf
> >   PO:0020103 : flag leaf
> >   PO:0020043 : compound leaf
> >   PO:0006338 : embryonic leaf
> >   PO:0006339 : juvenile leaf
> >   PO:0020042 : simple leaf
> >
> >
> > I myself am not very sure about the third proposed term, hypocotyl
> > hook; it's referring to the region of the seedling in early seedling
> > development, but this is not dev stage term.
> >
> > There are few publications (often ethylene response genes) in which the
> > authors are referring to 'hypocotyl hook'. Here are some:
> >
> > http://dev.biologists.org/cgi/reprint/126/16/3661
> > http://www.blackwell-synergy.com/links/doi/10.1046/j.1365
> > -313x.1999.00607.x/full/
> >
> > What do you think about introducing these three terms?
> >
> > Pankaj, this node is currently assigned to you.
> >
> > 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.
> > -----------------------------------------------------------------------
> > ---
> >
> >
>

-------------------------------------------------------------------------------
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 Sep  3 11:56:35 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Sep 2004 11:56:35 -0400
Subject: New terms in PO
In-Reply-To: <Pine.GSO.4.44.0409030746120.19826-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0409030746120.19826-100000@acoma.Stanford.EDU>
Message-ID: <41389433.6030103@cornell.edu>

My comments are follow Leonore's.
-Pankaj

Leonore Reiser wrote:

> On Thu, 2 Sep 2004, Felipe Zapata wrote:
> 
> 
>>Cauline leaf:
>> From the definition it looks like it refers to a regular leaf. Only it
>>has a particular name because "is before flowering" and "lacks a
>>petiole".  Lacking a petiole shouldn't pose a problem as not all the
>>parts of leaf have to be present (we still follow the sometimes part of
>>rule, right?). So a leaf may or may not have petiole.  In regards to
>>"before flowering" I wonder if this event makes a "regular leaf" (in
>>terms of anatomy and structure) a different type of leaf. I don't think
>>so.  This is more like a...developmental stage term?
> 
> 
> This term typically refers to the leaves which are borne on the elongated
> inflorescence branches in Arabidopsis. It is a VERY commonly used term in
> desrcribing Arabidopsis both wild type and mutant form.They almost always
> have 'adult' characteristics.

I consider this as a generic leaf but present on the cauline internodes.
Going by the TAIR definition as follows it is an equivalent of "flag 
leaf" in cereal plants.
Def: Stem leaf, produced before the transition to flowering, lacking a 
petiole.

However, if there are more than one instances of this leaf in a plant 
(answer is possibly YES) , then we can create this as an instance of the 
leaf at the same level as
PO:0006340 : adult leaf
PO:0020103 : flag leaf
PO:0020043 : compound leaf
PO:0006338 : embryonic leaf
PO:0006339 : juvenile leaf
PO:0020042 : simple leaf



>>Rosette leaf:
>>Once again, from the definition, it looks like it refers to a regular
>>(normal) leaf growing in certain arrangement, not to a different type
>>of leaf.  If the internodes between leaves elongate or not, that's a
>>different issue.  Some plants grow characteristically as rosette plants
>>(e.g. plants in the high peaks), nonetheless the leaves are "normal
>>leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
>>opposite leaf?
> 
> Again- this is a very commonly used term to describe leaves that are
> formed prior to elongation of the primary stem. Well, actually, I think
> Fred Hempell may have shown that some of these leaves are initiated before
> stem elongation. So maybe defining as leaves which are below the elongated
> internode.
> 

I think this refers to the generic leaf present in the Arabidopsis or in 
any other organism, often found in the region of stem, where internode 
elongation is either absent or minimal. In cases of Maize as Marty is 
suggesting, it is due to the defective in Gibberellic Acid synthesis, 
where possibly due to this effect the plant may never enters the "stem 
elongation growth stage". However, in case of Arabidopsis this is a 
normal phenomenon and so as in cabbage or many of the other Brassicales. 
These are definitely different than cauline leaves in terms of position 
which are present towards the top of the stalk/stem with elongated 
internodes also called as cauline region.

A generic definition of a rosette leaves is "A group of leaves arising 
closely together from a short stem, forming a radiating cluster on or 
near the ground".

Therefore, I would consider rosette leaves as synonym of the term 
PO:0009025 : leaf.



> 
>>Hypocothyl hook:
>>I am not what it refers to, but if it is indispensable...
>>
> 
> 
> Oh yes- it is indespensable- particularly when describing ethylene
> responses. Part of the so called triple response is hypocotyl hook
> curvature. This would be an example of a term that refers to a region
> (defined by a physiological response).
> Leonore
> 

In most of the descriptions I have found, if refers to the upper region 
of hypocotyl next to the cotyledons, found mainly in the germinating 
seeds of dicots only, that undergo epigeal type of germination. e.g. in 
many beans. However, in those seeds undergoing hypogeal type of 
germination, e.g. in peas, the hook forms in epicotyl and cotyledons 
stay in ground. In these cases it is called "epicotyl hook".

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=epicotyl+hook

Plant Cell Physiol. 2001 Sep;42(9):952-8 says:
...The intensity of the yieldin signal in the hypocotyls was highest in 
the apical pre-elongation region (the hook region) and decreased toward 
the elongated mature base indicating that the yieldin disappeared with 
the ceasing of cell elongation....

Physiol Plant. 2000 Feb;108(2):208-15.  suggests evidence of term usage 
hypocotyl/epicotyl hook.

more on epicotyl hook.
Photochem Photobiol. 1992;55(2):313-8.
Plant Physiol. 1996 Jan;110(1):163-70.

Going by the majority cases, it is part of a hypocotyl or rather it is 
the hypocotyl and the curved portion of the hypocotyl, which straigtens 
out once the cotyledons emerge from the ground/soil. Once it 
straightens, no one calls it s hook, it is hypocotyl. It is just a short 
phase of germination when the hypocotyl is maintained as a hook.

My suggestion is to create a synonym "hypocotyl hook" for hypocotyl.








From lreiser at acoma.Stanford.EDU  Fri Sep  3 12:09:55 2004
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Sep 2004 09:09:55 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <41389433.6030103@cornell.edu>
Message-ID: <Pine.GSO.4.44.0409030859410.19826-100000@acoma.Stanford.EDU>

On Fri, 3 Sep 2004, Pankaj Jaiswal wrote:

> My comments are follow Leonore's.
> -Pankaj
>
> Leonore Reiser wrote:
>
> > On Thu, 2 Sep 2004, Felipe Zapata wrote:
> >
> >
> >>Cauline leaf:
> >> From the definition it looks like it refers to a regular leaf. Only it
> >>has a particular name because "is before flowering" and "lacks a
> >>petiole".  Lacking a petiole shouldn't pose a problem as not all the
> >>parts of leaf have to be present (we still follow the sometimes part of
> >>rule, right?). So a leaf may or may not have petiole.  In regards to
> >>"before flowering" I wonder if this event makes a "regular leaf" (in
> >>terms of anatomy and structure) a different type of leaf. I don't think
> >>so.  This is more like a...developmental stage term?
> >
> >
> > This term typically refers to the leaves which are borne on the elongated
> > inflorescence branches in Arabidopsis. It is a VERY commonly used term in
> > desrcribing Arabidopsis both wild type and mutant form.They almost always
> > have 'adult' characteristics.
>
> I consider this as a generic leaf but present on the cauline internodes.
> Going by the TAIR definition as follows it is an equivalent of "flag
> leaf" in cereal plants.
> Def: Stem leaf, produced before the transition to flowering, lacking a
> petiole.

Gah- no one in the Arabidopsis community would use the term flag leaf to
define this body part. Nor are the leaves produced before the transition
to flowering - most are borne on a flowering plant. The reason I added the
statement about origins/initiation is because its likely that these leaves
are produced AFTER the transition to flowering has occured (though some
are initiated before BOLTING).

>
> However, if there are more than one instances of this leaf in a plant
> (answer is possibly YES) , then we can create this as an instance of the
> leaf at the same level as
> PO:0006340 : adult leaf
> PO:0020103 : flag leaf
> PO:0020043 : compound leaf
> PO:0006338 : embryonic leaf
> PO:0006339 : juvenile leaf
> PO:0020042 : simple leaf
>
>
>
> >>Rosette leaf:
> >>Once again, from the definition, it looks like it refers to a regular
> >>(normal) leaf growing in certain arrangement, not to a different type
> >>of leaf.  If the internodes between leaves elongate or not, that's a
> >>different issue.  Some plants grow characteristically as rosette plants
> >>(e.g. plants in the high peaks), nonetheless the leaves are "normal
> >>leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
> >>opposite leaf?
> >
> > Again- this is a very commonly used term to describe leaves that are
> > formed prior to elongation of the primary stem. Well, actually, I think
> > Fred Hempell may have shown that some of these leaves are initiated before
> > stem elongation. So maybe defining as leaves which are below the elongated
> > internode.
> >
>
> I think this refers to the generic leaf present in the Arabidopsis or in
> any other organism, often found in the region of stem, where internode
> elongation is either absent or minimal. In cases of Maize as Marty is
> suggesting, it is due to the defective in Gibberellic Acid synthesis,
> where possibly due to this effect the plant may never enters the "stem
> elongation growth stage". However, in case of Arabidopsis this is a
> normal phenomenon and so as in cabbage or many of the other Brassicales.
> These are definitely different than cauline leaves in terms of position
> which are present towards the top of the stalk/stem with elongated
> internodes also called as cauline region.
>

Aren't we describing normal development in these ontologies.


> A generic definition of a rosette leaves is "A group of leaves arising
> closely together from a short stem, forming a radiating cluster on or
> near the ground".
>
> Therefore, I would consider rosette leaves as synonym of the term
> PO:0009025 : leaf.
>
>
>
> >
> >>Hypocothyl hook:
> >>I am not what it refers to, but if it is indispensable...
> >>
> >
> >
> > Oh yes- it is indespensable- particularly when describing ethylene
> > responses. Part of the so called triple response is hypocotyl hook
> > curvature. This would be an example of a term that refers to a region
> > (defined by a physiological response).
> > Leonore
> >
>
> In most of the descriptions I have found, if refers to the upper region
> of hypocotyl next to the cotyledons, found mainly in the germinating
> seeds of dicots only, that undergo epigeal type of germination. e.g. in
> many beans. However, in those seeds undergoing hypogeal type of
> germination, e.g. in peas, the hook forms in epicotyl and cotyledons
> stay in ground. In these cases it is called "epicotyl hook".
>
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=epicotyl+hook
>
> Plant Cell Physiol. 2001 Sep;42(9):952-8 says:
> ...The intensity of the yieldin signal in the hypocotyls was highest in
> the apical pre-elongation region (the hook region) and decreased toward
> the elongated mature base indicating that the yieldin disappeared with
> the ceasing of cell elongation....
>
> Physiol Plant. 2000 Feb;108(2):208-15.  suggests evidence of term usage
> hypocotyl/epicotyl hook.
>
> more on epicotyl hook.
> Photochem Photobiol. 1992;55(2):313-8.
> Plant Physiol. 1996 Jan;110(1):163-70.
>
> Going by the majority cases, it is part of a hypocotyl or rather it is
> the hypocotyl and the curved portion of the hypocotyl, which straigtens
> out once the cotyledons emerge from the ground/soil. Once it
> straightens, no one calls it s hook, it is hypocotyl. It is just a short
> phase of germination when the hypocotyl is maintained as a hook.
>
> My suggestion is to create a synonym "hypocotyl hook" for hypocotyl.
>
>
I dont think that is going to work. Yes it is  a region of the hypocotyl
that is curved for a period of time during development. Oh and how about
apical
hook (more commonly used in describing this body part)  with hypocotyl
hook as a synonym. There needs to be some way of describing this very
special part/stage in seedling development. Yes it is a developmental
stage (apical hook formation or whatever) but there are genes that are
expressed specifically in this domain...
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
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Fri Sep  3 12:14:12 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Sep 2004 12:14:12 -0400
Subject: New terms in PO
In-Reply-To: <p06110403bd5d8c85a880@[130.126.89.70]>
References: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU> <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu> <p06110403bd5d8c85a880@[130.126.89.70]>
Message-ID: <41389854.6040601@cornell.edu>



Marty Sachs wrote:

> At 9:15 PM -0500 9/2/04, Felipe Zapata wrote:
> 
>> Rosette leaf:
>> Once again, from the definition, it looks like it refers to a regular 
>> (normal) leaf growing in certain arrangement, not to a different type 
>> of leaf.  If the internodes between leaves elongate or not, that's a 
>> different issue.  Some plants grow characteristically as rosette 
>> plants (e.g. plants in the high peaks), nonetheless the leaves are 
>> "normal leaves".  If rosette leaf is introduced to POC, why not 
>> alternate leaf? opposite leaf?
> 
> 
> Maize folks use the term 'Rosette leaf' to describe the appearance of 
> mutants defective in Gibberellic Acid synthesis or response.
> 
>     -Marty
> 
I think we need to be careful in phenotype annotation. Popularly the 
phenotype could be called as rosette leaf, but I guess the actual traits 
measured would be

Leaf size--small or normal/abnormal
internode length--short/abnormal
plant height--short/abnormal
Gibberellic Acid synthesis--absent/abnormal
Response to Gibberellic Acid--absent/abnormal
Gibberellic Acid content--absent/abnormal


-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 msachs at uiuc.edu  Fri Sep  3 12:39:12 2004
From: msachs at uiuc.edu (Marty Sachs)
Date: Fri, 3 Sep 2004 11:39:12 -0500
Subject: New terms in PO
In-Reply-To: <41389854.6040601@cornell.edu>
References: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU>
 <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu>
 <p06110403bd5d8c85a880@[130.126.89.70]> <41389854.6040601@cornell.edu>
Message-ID: <p06110408bd5e4bf0ef2e@[130.126.89.70]>

At 12:14 PM -0400 9/3/04, Pankaj Jaiswal wrote:
>Marty Sachs wrote:
>
>>At 9:15 PM -0500 9/2/04, Felipe Zapata wrote:
>>
>>>Rosette leaf:
>>>Once again, from the definition, it looks like it refers to a 
>>>regular (normal) leaf growing in certain arrangement, not to a 
>>>different type of leaf.  If the internodes between leaves elongate 
>>>or not, that's a different issue.  Some plants grow 
>>>characteristically as rosette plants (e.g. plants in the high 
>>>peaks), nonetheless the leaves are "normal leaves".  If rosette 
>>>leaf is introduced to POC, why not alternate leaf? opposite leaf?
>>
>>
>>Maize folks use the term 'Rosette leaf' to describe the appearance 
>>of mutants defective in Gibberellic Acid synthesis or response.
>>
>>     -Marty
>>
>I think we need to be careful in phenotype annotation. Popularly the 
>phenotype could be called as rosette leaf, but I guess the actual 
>traits measured would be
>
>Leaf size--small or normal/abnormal
>internode length--short/abnormal
>plant height--short/abnormal
>Gibberellic Acid synthesis--absent/abnormal
>Response to Gibberellic Acid--absent/abnormal
>Gibberellic Acid content--absent/abnormal
>


Pankaj,

I agree.

Also, leaf shape: broad.  See: 
http://www.maizegdb.org/db_images/Variation/coe0022-1683/038.jpg

d1 (Allele) d1, dwarf plants: three paired rows, left two untreated 
(rosettes reaching flowering), next two rows treated weekly with 
gibberellic acid (elongated and reaching flowering)

	-Marty


From pj37 at cornell.edu  Fri Sep  3 12:51:54 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Sep 2004 12:51:54 -0400
Subject: New terms in PO
In-Reply-To: <p06110408bd5e4bf0ef2e@[130.126.89.70]>
References: <Pine.GSO.4.44.0409021824200.14671-100000@acoma.Stanford.EDU> <2497B276-FD4F-11D8-870B-000A95AF2466@umsl.edu> <p06110403bd5d8c85a880@[130.126.89.70]> <41389854.6040601@cornell.edu> <p06110408bd5e4bf0ef2e@[130.126.89.70]>
Message-ID: <4138A12A.30701@cornell.edu>

Great !
So when we do the associations for POC, irrespective of the phenotype, 
the real associations would be to the POC terms
-internode
-leaf

Thus a user can make a statement based on the Object_type associated,
-show me all the maize phenotypes associated with leaf
-show me all the maize phenotypes associated with internode
-show me all the arabidopsis phenotypes associated with leaf
-show me all the arabidopsis phenotypes associated with internode

Thus generating a list of species specific phenotype accessions 
listed/associated for a given POC term. In this case the object_type is 
phenotype.
Other object_types would be
genes
geneproducts
	transcripts
	proteins
alleles
stocks
etc.


-Pankaj

Marty Sachs wrote:
> At 12:14 PM -0400 9/3/04, Pankaj Jaiswal wrote:
> 
>> Marty Sachs wrote:
>>
>>> At 9:15 PM -0500 9/2/04, Felipe Zapata wrote:
>>>
>>>> Rosette leaf:
>>>> Once again, from the definition, it looks like it refers to a 
>>>> regular (normal) leaf growing in certain arrangement, not to a 
>>>> different type of leaf.  If the internodes between leaves elongate 
>>>> or not, that's a different issue.  Some plants grow 
>>>> characteristically as rosette plants (e.g. plants in the high 
>>>> peaks), nonetheless the leaves are "normal leaves".  If rosette leaf 
>>>> is introduced to POC, why not alternate leaf? opposite leaf?
>>>
>>>
>>>
>>> Maize folks use the term 'Rosette leaf' to describe the appearance of 
>>> mutants defective in Gibberellic Acid synthesis or response.
>>>
>>>     -Marty
>>>
>> I think we need to be careful in phenotype annotation. Popularly the 
>> phenotype could be called as rosette leaf, but I guess the actual 
>> traits measured would be
>>
>> Leaf size--small or normal/abnormal
>> internode length--short/abnormal
>> plant height--short/abnormal
>> Gibberellic Acid synthesis--absent/abnormal
>> Response to Gibberellic Acid--absent/abnormal
>> Gibberellic Acid content--absent/abnormal
>>
> 
> 
> Pankaj,
> 
> I agree.
> 
> Also, leaf shape: broad.  See: 
> http://www.maizegdb.org/db_images/Variation/coe0022-1683/038.jpg
> 
> d1 (Allele) d1, dwarf plants: three paired rows, left two untreated 
> (rosettes reaching flowering), next two rows treated weekly with 
> gibberellic acid (elongated and reaching flowering)
> 
>     -Marty
> 

-- 
************************
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 katica at acoma.Stanford.EDU  Fri Sep  3 15:46:21 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 3 Sep 2004 12:46:21 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <41389433.6030103@cornell.edu>
Message-ID: <Pine.GSO.4.44.0409031242320.23238-100000@acoma.Stanford.EDU>

Hi,

I agree with Leonore and here is one more point to the discussion
about hypocotyl hook. If the term 'hypocotyl hook' end up being a synonym
of 'hypocotyl' in PO, (which I think is not right, even with different kinds of synonymy
currently in use by GO), all the annotations to this term would show up
under hypocotyl. So, if curators could use term hypocotyl, we wouldn't
have had their request for this term at the first place.

Cauline and rosette leaf:
Felipe, I understand you rationale, and those were the reasons that these
terms did not make it to the PO in the first round (back in May), but now,
we are talking about a need to facilitate annotations. Perhaps I was not
specific enough when I included info about gene annotations in TAIR. Genes
annotated to the term cauline leaf are not necessarily the same as those
annotated to rosette leaf (although, four out of five genes are expressed
in both, cauline and rosette leaves). They would all show up if you query
term 'leaf', but unless we have the cauline and rosette leaf as separate
terms, we can never see the annotation to each, nor would we be able to
ask which genes are expressed in cauline leaves, but not in rosette leaves
(for instance PPCK1 is expressed in mainly in rosette leaves, while PPCK2
is expressed in roots and cauline leaves, see Plant, Cell and Environment,
2002, 25:115-122). This is the reason it wouldn't work if we make rosette
leaf a synonym of term leaf, as Pankaj suggested.

Katica



On Fri, 3 Sep 2004, Pankaj Jaiswal wrote:

> My comments are follow Leonore's.
> -Pankaj
>
> Leonore Reiser wrote:
>
> > On Thu, 2 Sep 2004, Felipe Zapata wrote:
> >
> >
> >>Cauline leaf:
> >> From the definition it looks like it refers to a regular leaf. Only it
> >>has a particular name because "is before flowering" and "lacks a
> >>petiole".  Lacking a petiole shouldn't pose a problem as not all the
> >>parts of leaf have to be present (we still follow the sometimes part of
> >>rule, right?). So a leaf may or may not have petiole.  In regards to
> >>"before flowering" I wonder if this event makes a "regular leaf" (in
> >>terms of anatomy and structure) a different type of leaf. I don't think
> >>so.  This is more like a...developmental stage term?
> >
> >
> > This term typically refers to the leaves which are borne on the elongated
> > inflorescence branches in Arabidopsis. It is a VERY commonly used term in
> > desrcribing Arabidopsis both wild type and mutant form.They almost always
> > have 'adult' characteristics.
>
> I consider this as a generic leaf but present on the cauline internodes.
> Going by the TAIR definition as follows it is an equivalent of "flag
> leaf" in cereal plants.
> Def: Stem leaf, produced before the transition to flowering, lacking a
> petiole.
>
> However, if there are more than one instances of this leaf in a plant
> (answer is possibly YES) , then we can create this as an instance of the
> leaf at the same level as
> PO:0006340 : adult leaf
> PO:0020103 : flag leaf
> PO:0020043 : compound leaf
> PO:0006338 : embryonic leaf
> PO:0006339 : juvenile leaf
> PO:0020042 : simple leaf
>
>
>
> >>Rosette leaf:
> >>Once again, from the definition, it looks like it refers to a regular
> >>(normal) leaf growing in certain arrangement, not to a different type
> >>of leaf.  If the internodes between leaves elongate or not, that's a
> >>different issue.  Some plants grow characteristically as rosette plants
> >>(e.g. plants in the high peaks), nonetheless the leaves are "normal
> >>leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
> >>opposite leaf?
> >
> > Again- this is a very commonly used term to describe leaves that are
> > formed prior to elongation of the primary stem. Well, actually, I think
> > Fred Hempell may have shown that some of these leaves are initiated before
> > stem elongation. So maybe defining as leaves which are below the elongated
> > internode.
> >
>
> I think this refers to the generic leaf present in the Arabidopsis or in
> any other organism, often found in the region of stem, where internode
> elongation is either absent or minimal. In cases of Maize as Marty is
> suggesting, it is due to the defective in Gibberellic Acid synthesis,
> where possibly due to this effect the plant may never enters the "stem
> elongation growth stage". However, in case of Arabidopsis this is a
> normal phenomenon and so as in cabbage or many of the other Brassicales.
> These are definitely different than cauline leaves in terms of position
> which are present towards the top of the stalk/stem with elongated
> internodes also called as cauline region.
>
> A generic definition of a rosette leaves is "A group of leaves arising
> closely together from a short stem, forming a radiating cluster on or
> near the ground".
>
> Therefore, I would consider rosette leaves as synonym of the term
> PO:0009025 : leaf.
>
>
>
> >
> >>Hypocothyl hook:
> >>I am not what it refers to, but if it is indispensable...
> >>
> >
> >
> > Oh yes- it is indespensable- particularly when describing ethylene
> > responses. Part of the so called triple response is hypocotyl hook
> > curvature. This would be an example of a term that refers to a region
> > (defined by a physiological response).
> > Leonore
> >
>
> In most of the descriptions I have found, if refers to the upper region
> of hypocotyl next to the cotyledons, found mainly in the germinating
> seeds of dicots only, that undergo epigeal type of germination. e.g. in
> many beans. However, in those seeds undergoing hypogeal type of
> germination, e.g. in peas, the hook forms in epicotyl and cotyledons
> stay in ground. In these cases it is called "epicotyl hook".
>
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=epicotyl+hook
>
> Plant Cell Physiol. 2001 Sep;42(9):952-8 says:
> ...The intensity of the yieldin signal in the hypocotyls was highest in
> the apical pre-elongation region (the hook region) and decreased toward
> the elongated mature base indicating that the yieldin disappeared with
> the ceasing of cell elongation....
>
> Physiol Plant. 2000 Feb;108(2):208-15.  suggests evidence of term usage
> hypocotyl/epicotyl hook.
>
> more on epicotyl hook.
> Photochem Photobiol. 1992;55(2):313-8.
> Plant Physiol. 1996 Jan;110(1):163-70.
>
> Going by the majority cases, it is part of a hypocotyl or rather it is
> the hypocotyl and the curved portion of the hypocotyl, which straigtens
> out once the cotyledons emerge from the ground/soil. Once it
> straightens, no one calls it s hook, it is hypocotyl. It is just a short
> phase of germination when the hypocotyl is maintained as a hook.
>
> My suggestion is to create a synonym "hypocotyl hook" for hypocotyl.
>
>
>
>
>
>

--------------------------------------------------------------------------
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 Sep  3 16:11:11 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Sep 2004 16:11:11 -0400
Subject: New terms in PO
In-Reply-To: <Pine.GSO.4.44.0409031242320.23238-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0409031242320.23238-100000@acoma.Stanford.EDU>
Message-ID: <4138CFDF.3040903@cornell.edu>



Katica Ilic wrote:
> Hi,
> 
> I agree with Leonore and here is one more point to the discussion
> about hypocotyl hook. If the term 'hypocotyl hook' end up being a synonym
> of 'hypocotyl' in PO, (which I think is not right, even with different kinds of synonymy
> currently in use by GO), all the annotations to this term would show up
> under hypocotyl. So, if curators could use term hypocotyl, we wouldn't
> have had their request for this term at the first place.
> 

That's a valid case, but I must say it is growth stage dependent. There 
is no hook  after it straightens, whereas if you have a term for a 
region then it may make sense. such as towards apical end of hypocotyl 
(apical pre-elongation region) and elongated mature base.

I am open to this term.


> Cauline and rosette leaf:
> Felipe, I understand you rationale, and those were the reasons that these
> terms did not make it to the PO in the first round (back in May), but now,
> we are talking about a need to facilitate annotations. Perhaps I was not
> specific enough when I included info about gene annotations in TAIR. Genes
> annotated to the term cauline leaf are not necessarily the same as those
> annotated to rosette leaf (although, four out of five genes are expressed
> in both, cauline and rosette leaves). They would all show up if you query
> term 'leaf', but unless we have the cauline and rosette leaf as separate
> terms, we can never see the annotation to each, nor would we be able to
> ask which genes are expressed in cauline leaves, but not in rosette leaves
> (for instance PPCK1 is expressed in mainly in rosette leaves, while PPCK2
> is expressed in roots and cauline leaves, see Plant, Cell and Environment,
> 2002, 25:115-122). This is the reason it wouldn't work if we make rosette
> leaf a synonym of term leaf, as Pankaj suggested.
> 
> Katica
> 

The rosette annotation can go to the generic leaf and the rest to the 
new simple leaf instance cauline leaf. I was just supporting Leonore's 
statement on having a new term for Cauline.

You will be able to generate a statement show me all the genes that are 
expressed in leaves BUT not in cauline leaves.
or
those in cauline leaves BUTNOT in leaves (rosette leaves). Use of 
rosette leaves will work here because its is there as a synonym.

BTW TAIR also has adult leaf in Arabidopsis. How does the adult leaf 
differ from any of the rosette or cauline leaf.

Pankaj



From pj37 at cornell.edu  Fri Sep  3 16:14:58 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 03 Sep 2004 16:14:58 -0400
Subject: New terms in PO
In-Reply-To: <4138CFDF.3040903@cornell.edu>
References: <Pine.GSO.4.44.0409031242320.23238-100000@acoma.Stanford.EDU> <4138CFDF.3040903@cornell.edu>
Message-ID: <4138D0C2.6070709@cornell.edu>



Pankaj Jaiswal wrote:

> 
> BTW TAIR also has adult leaf in Arabidopsis. How does the adult leaf 
> differ from any of the rosette or cauline leaf.
> 
> Pankaj
> 
> 

This question is just out of curiosity, since I am not an expert on 
Arabidopsis.

-Pankaj



From katica at acoma.Stanford.EDU  Fri Sep  3 17:07:20 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 3 Sep 2004 14:07:20 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <4138D0C2.6070709@cornell.edu>
Message-ID: <Pine.GSO.4.44.0409031358040.23238-100000@acoma.Stanford.EDU>

Pankaj,

Quick answer would be that rossete laeves are first juvenile before they
become adult. For the gene expression studies, having a rosette leaf as a
synonym of adult leaf would not work.

Annotations in TAIR for adult leaves are different from those associated
to rosette leaf.

Katica

On Fri, 3 Sep
2004, Pankaj Jaiswal wrote:

>
>
> Pankaj Jaiswal wrote:
>
> >
> > BTW TAIR also has adult leaf in Arabidopsis. How does the adult leaf
> > differ from any of the rosette or cauline leaf.
> >
> > Pankaj
> >
> >
>
> This question is just out of curiosity, since I am not an expert on
> Arabidopsis.
>
> -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 katica at acoma.Stanford.EDU  Fri Sep  3 17:19:27 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Fri, 3 Sep 2004 14:19:27 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <Pine.GSO.4.44.0409030859410.19826-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0409031418190.23238-100000@acoma.Stanford.EDU>


Pankaj,

Currently, the only synonym of term leaf (PO:0009025) is foliage leaf.  If
we add rosette leaf as synonym, it might work, now that I remember
that annotation to the term itself can be separated from the annotation
for the children of that term (where all the cauline leaf annotations
would be, considering that cauline leaf would be an instance of a leaf).

plant structure
- sporophyte
--- shoot
------phyllome
---------leaf
-----------(i) adult leaf
-----------(i) cauline leaf (new term)
-----------(i) coleoptile
-----------(i) compound leaf
-----------(i) embryonic leaf
-----------(i) juvenile leaf
-----------(i) simple leaf

(didn't include part_of children under 'leaf')

Here is suggested definition for cauline leaf:
Stem leaf, often lacking a petiole. In Arabidopsis, refers to the leaves
that are borne on the elongated inflorescence branches.

I'll look up for the definition fr hypocotyls hook, if we agree to
introduce this term to the PO.

Katica


On Fri, 3 Sep 2004, Leonore Reiser wrote:

> On Fri, 3 Sep 2004, Pankaj Jaiswal wrote:
>
> > My comments are follow Leonore's.
> > -Pankaj
> >
> > Leonore Reiser wrote:
> >
> > > On Thu, 2 Sep 2004, Felipe Zapata wrote:
> > >
> > >
> > >>Cauline leaf:
> > >> From the definition it looks like it refers to a regular leaf. Only it
> > >>has a particular name because "is before flowering" and "lacks a
> > >>petiole".  Lacking a petiole shouldn't pose a problem as not all the
> > >>parts of leaf have to be present (we still follow the sometimes part of
> > >>rule, right?). So a leaf may or may not have petiole.  In regards to
> > >>"before flowering" I wonder if this event makes a "regular leaf" (in
> > >>terms of anatomy and structure) a different type of leaf. I don't think
> > >>so.  This is more like a...developmental stage term?
> > >
> > >
> > > This term typically refers to the leaves which are borne on the elongated
> > > inflorescence branches in Arabidopsis. It is a VERY commonly used term in
> > > desrcribing Arabidopsis both wild type and mutant form.They almost always
> > > have 'adult' characteristics.
> >
> > I consider this as a generic leaf but present on the cauline internodes.
> > Going by the TAIR definition as follows it is an equivalent of "flag
> > leaf" in cereal plants.
> > Def: Stem leaf, produced before the transition to flowering, lacking a
> > petiole.
>
> Gah- no one in the Arabidopsis community would use the term flag leaf to
> define this body part. Nor are the leaves produced before the transition
> to flowering - most are borne on a flowering plant. The reason I added the
> statement about origins/initiation is because its likely that these leaves
> are produced AFTER the transition to flowering has occured (though some
> are initiated before BOLTING).
>
> >
> > However, if there are more than one instances of this leaf in a plant
> > (answer is possibly YES) , then we can create this as an instance of the
> > leaf at the same level as
> > PO:0006340 : adult leaf
> > PO:0020103 : flag leaf
> > PO:0020043 : compound leaf
> > PO:0006338 : embryonic leaf
> > PO:0006339 : juvenile leaf
> > PO:0020042 : simple leaf
> >
> >
> >
> > >>Rosette leaf:
> > >>Once again, from the definition, it looks like it refers to a regular
> > >>(normal) leaf growing in certain arrangement, not to a different type
> > >>of leaf.  If the internodes between leaves elongate or not, that's a
> > >>different issue.  Some plants grow characteristically as rosette plants
> > >>(e.g. plants in the high peaks), nonetheless the leaves are "normal
> > >>leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
> > >>opposite leaf?
> > >
> > > Again- this is a very commonly used term to describe leaves that are
> > > formed prior to elongation of the primary stem. Well, actually, I think
> > > Fred Hempell may have shown that some of these leaves are initiated before
> > > stem elongation. So maybe defining as leaves which are below the elongated
> > > internode.
> > >
> >
> > I think this refers to the generic leaf present in the Arabidopsis or in
> > any other organism, often found in the region of stem, where internode
> > elongation is either absent or minimal. In cases of Maize as Marty is
> > suggesting, it is due to the defective in Gibberellic Acid synthesis,
> > where possibly due to this effect the plant may never enters the "stem
> > elongation growth stage". However, in case of Arabidopsis this is a
> > normal phenomenon and so as in cabbage or many of the other Brassicales.
> > These are definitely different than cauline leaves in terms of position
> > which are present towards the top of the stalk/stem with elongated
> > internodes also called as cauline region.
> >
>
> Aren't we describing normal development in these ontologies.
>
>
> > A generic definition of a rosette leaves is "A group of leaves arising
> > closely together from a short stem, forming a radiating cluster on or
> > near the ground".
> >
> > Therefore, I would consider rosette leaves as synonym of the term
> > PO:0009025 : leaf.
> >
> >
> >
> > >
> > >>Hypocothyl hook:
> > >>I am not what it refers to, but if it is indispensable...
> > >>
> > >
> > >
> > > Oh yes- it is indespensable- particularly when describing ethylene
> > > responses. Part of the so called triple response is hypocotyl hook
> > > curvature. This would be an example of a term that refers to a region
> > > (defined by a physiological response).
> > > Leonore
> > >
> >
> > In most of the descriptions I have found, if refers to the upper region
> > of hypocotyl next to the cotyledons, found mainly in the germinating
> > seeds of dicots only, that undergo epigeal type of germination. e.g. in
> > many beans. However, in those seeds undergoing hypogeal type of
> > germination, e.g. in peas, the hook forms in epicotyl and cotyledons
> > stay in ground. In these cases it is called "epicotyl hook".
> >
> > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=epicotyl+hook
> >
> > Plant Cell Physiol. 2001 Sep;42(9):952-8 says:
> > ...The intensity of the yieldin signal in the hypocotyls was highest in
> > the apical pre-elongation region (the hook region) and decreased toward
> > the elongated mature base indicating that the yieldin disappeared with
> > the ceasing of cell elongation....
> >
> > Physiol Plant. 2000 Feb;108(2):208-15.  suggests evidence of term usage
> > hypocotyl/epicotyl hook.
> >
> > more on epicotyl hook.
> > Photochem Photobiol. 1992;55(2):313-8.
> > Plant Physiol. 1996 Jan;110(1):163-70.
> >
> > Going by the majority cases, it is part of a hypocotyl or rather it is
> > the hypocotyl and the curved portion of the hypocotyl, which straigtens
> > out once the cotyledons emerge from the ground/soil. Once it
> > straightens, no one calls it s hook, it is hypocotyl. It is just a short
> > phase of germination when the hypocotyl is maintained as a hook.
> >
> > My suggestion is to create a synonym "hypocotyl hook" for hypocotyl.
> >
> >
> I dont think that is going to work. Yes it is  a region of the hypocotyl
> that is curved for a period of time during development. Oh and how about
> apical
> hook (more commonly used in describing this body part)  with hypocotyl
> hook as a synonym. There needs to be some way of describing this very
> special part/stage in seedling development. Yes it is a developmental
> stage (apical hook formation or whatever) but there are genes that are
> expressed specifically in this domain...
> 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
> -------------------------------------------------------------------------------
>

--------------------------------------------------------------------------
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 lreiser at acoma.Stanford.EDU  Fri Sep  3 20:20:01 2004
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Fri, 3 Sep 2004 17:20:01 -0700 (PDT)
Subject: New terms in PO
In-Reply-To: <Pine.GSO.4.44.0409031418190.23238-100000@acoma.Stanford.EDU>
Message-ID: <Pine.GSO.4.44.0409031718360.25276-100000@acoma.Stanford.EDU>


I think your first statement about rosette leaf !=(not equals) adult leaf
OR juvenile leaf is correct. I believe that rosette leaves can be adult or
juvenile based on things like trichomes. Might be worth asking Tanya about
as she is pretty familiar with phase change markers.
Leonore

On Fri, 3 Sep 2004, Katica Ilic wrote:

>
> Pankaj,
>
> Currently, the only synonym of term leaf (PO:0009025) is foliage leaf.  If
> we add rosette leaf as synonym, it might work, now that I remember
> that annotation to the term itself can be separated from the annotation
> for the children of that term (where all the cauline leaf annotations
> would be, considering that cauline leaf would be an instance of a leaf).
>
> plant structure
> - sporophyte
> --- shoot
> ------phyllome
> ---------leaf
> -----------(i) adult leaf
> -----------(i) cauline leaf (new term)
> -----------(i) coleoptile
> -----------(i) compound leaf
> -----------(i) embryonic leaf
> -----------(i) juvenile leaf
> -----------(i) simple leaf
>
> (didn't include part_of children under 'leaf')
>
> Here is suggested definition for cauline leaf:
> Stem leaf, often lacking a petiole. In Arabidopsis, refers to the leaves
> that are borne on the elongated inflorescence branches.
>
> I'll look up for the definition fr hypocotyls hook, if we agree to
> introduce this term to the PO.
>
> Katica
>
>
> On Fri, 3 Sep 2004, Leonore Reiser wrote:
>
> > On Fri, 3 Sep 2004, Pankaj Jaiswal wrote:
> >
> > > My comments are follow Leonore's.
> > > -Pankaj
> > >
> > > Leonore Reiser wrote:
> > >
> > > > On Thu, 2 Sep 2004, Felipe Zapata wrote:
> > > >
> > > >
> > > >>Cauline leaf:
> > > >> From the definition it looks like it refers to a regular leaf. Only it
> > > >>has a particular name because "is before flowering" and "lacks a
> > > >>petiole".  Lacking a petiole shouldn't pose a problem as not all the
> > > >>parts of leaf have to be present (we still follow the sometimes part of
> > > >>rule, right?). So a leaf may or may not have petiole.  In regards to
> > > >>"before flowering" I wonder if this event makes a "regular leaf" (in
> > > >>terms of anatomy and structure) a different type of leaf. I don't think
> > > >>so.  This is more like a...developmental stage term?
> > > >
> > > >
> > > > This term typically refers to the leaves which are borne on the elongated
> > > > inflorescence branches in Arabidopsis. It is a VERY commonly used term in
> > > > desrcribing Arabidopsis both wild type and mutant form.They almost always
> > > > have 'adult' characteristics.
> > >
> > > I consider this as a generic leaf but present on the cauline internodes.
> > > Going by the TAIR definition as follows it is an equivalent of "flag
> > > leaf" in cereal plants.
> > > Def: Stem leaf, produced before the transition to flowering, lacking a
> > > petiole.
> >
> > Gah- no one in the Arabidopsis community would use the term flag leaf to
> > define this body part. Nor are the leaves produced before the transition
> > to flowering - most are borne on a flowering plant. The reason I added the
> > statement about origins/initiation is because its likely that these leaves
> > are produced AFTER the transition to flowering has occured (though some
> > are initiated before BOLTING).
> >
> > >
> > > However, if there are more than one instances of this leaf in a plant
> > > (answer is possibly YES) , then we can create this as an instance of the
> > > leaf at the same level as
> > > PO:0006340 : adult leaf
> > > PO:0020103 : flag leaf
> > > PO:0020043 : compound leaf
> > > PO:0006338 : embryonic leaf
> > > PO:0006339 : juvenile leaf
> > > PO:0020042 : simple leaf
> > >
> > >
> > >
> > > >>Rosette leaf:
> > > >>Once again, from the definition, it looks like it refers to a regular
> > > >>(normal) leaf growing in certain arrangement, not to a different type
> > > >>of leaf.  If the internodes between leaves elongate or not, that's a
> > > >>different issue.  Some plants grow characteristically as rosette plants
> > > >>(e.g. plants in the high peaks), nonetheless the leaves are "normal
> > > >>leaves".  If rosette leaf is introduced to POC, why not alternate leaf?
> > > >>opposite leaf?
> > > >
> > > > Again- this is a very commonly used term to describe leaves that are
> > > > formed prior to elongation of the primary stem. Well, actually, I think
> > > > Fred Hempell may have shown that some of these leaves are initiated before
> > > > stem elongation. So maybe defining as leaves which are below the elongated
> > > > internode.
> > > >
> > >
> > > I think this refers to the generic leaf present in the Arabidopsis or in
> > > any other organism, often found in the region of stem, where internode
> > > elongation is either absent or minimal. In cases of Maize as Marty is
> > > suggesting, it is due to the defective in Gibberellic Acid synthesis,
> > > where possibly due to this effect the plant may never enters the "stem
> > > elongation growth stage". However, in case of Arabidopsis this is a
> > > normal phenomenon and so as in cabbage or many of the other Brassicales.
> > > These are definitely different than cauline leaves in terms of position
> > > which are present towards the top of the stalk/stem with elongated
> > > internodes also called as cauline region.
> > >
> >
> > Aren't we describing normal development in these ontologies.
> >
> >
> > > A generic definition of a rosette leaves is "A group of leaves arising
> > > closely together from a short stem, forming a radiating cluster on or
> > > near the ground".
> > >
> > > Therefore, I would consider rosette leaves as synonym of the term
> > > PO:0009025 : leaf.
> > >
> > >
> > >
> > > >
> > > >>Hypocothyl hook:
> > > >>I am not what it refers to, but if it is indispensable...
> > > >>
> > > >
> > > >
> > > > Oh yes- it is indespensable- particularly when describing ethylene
> > > > responses. Part of the so called triple response is hypocotyl hook
> > > > curvature. This would be an example of a term that refers to a region
> > > > (defined by a physiological response).
> > > > Leonore
> > > >
> > >
> > > In most of the descriptions I have found, if refers to the upper region
> > > of hypocotyl next to the cotyledons, found mainly in the germinating
> > > seeds of dicots only, that undergo epigeal type of germination. e.g. in
> > > many beans. However, in those seeds undergoing hypogeal type of
> > > germination, e.g. in peas, the hook forms in epicotyl and cotyledons
> > > stay in ground. In these cases it is called "epicotyl hook".
> > >
> > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=epicotyl+hook
> > >
> > > Plant Cell Physiol. 2001 Sep;42(9):952-8 says:
> > > ...The intensity of the yieldin signal in the hypocotyls was highest in
> > > the apical pre-elongation region (the hook region) and decreased toward
> > > the elongated mature base indicating that the yieldin disappeared with
> > > the ceasing of cell elongation....
> > >
> > > Physiol Plant. 2000 Feb;108(2):208-15.  suggests evidence of term usage
> > > hypocotyl/epicotyl hook.
> > >
> > > more on epicotyl hook.
> > > Photochem Photobiol. 1992;55(2):313-8.
> > > Plant Physiol. 1996 Jan;110(1):163-70.
> > >
> > > Going by the majority cases, it is part of a hypocotyl or rather it is
> > > the hypocotyl and the curved portion of the hypocotyl, which straigtens
> > > out once the cotyledons emerge from the ground/soil. Once it
> > > straightens, no one calls it s hook, it is hypocotyl. It is just a short
> > > phase of germination when the hypocotyl is maintained as a hook.
> > >
> > > My suggestion is to create a synonym "hypocotyl hook" for hypocotyl.
> > >
> > >
> > I dont think that is going to work. Yes it is  a region of the hypocotyl
> > that is curved for a period of time during development. Oh and how about
> > apical
> > hook (more commonly used in describing this body part)  with hypocotyl
> > hook as a synonym. There needs to be some way of describing this very
> > special part/stage in seedling development. Yes it is a developmental
> > stage (apical hook formation or whatever) but there are genes that are
> > expressed specifically in this domain...
> > 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
> > -------------------------------------------------------------------------------
> >
>
> --------------------------------------------------------------------------
> 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.
> --------------------------------------------------------------------------
>
>

-------------------------------------------------------------------------------
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 peter.stevens at mobot.org  Sat Sep  4 09:26:13 2004
From: peter.stevens at mobot.org (Peter Stevens)
Date: Sat, 4 Sep 2004 09:26:13 -0400
Subject: New terms in PO
In-Reply-To: <Pine.GSO.4.44.0409031718360.25276-100000@acoma.Stanford.EDU>
References: <Pine.GSO.4.44.0409031718360.25276-100000@acoma.Stanford.EDU>
Message-ID: <f04330111bd5f71f037c7@[172.16.18.52]>

I was not im my office yesterday, and it has been a little hard to 
follow the cauline leaf discussion.  Cauline leaves s. srr. occur 
only when there are rosettes (but not all plants with rosettes have 
cauline leaves), and they have no particular morphology, so the 
definition


>  >
>>  Here is suggested definition for cauline leaf:
>>  Stem leaf, often lacking a petiole. In Arabidopsis, refers to the leaves
>>  that are borne on the elongated inflorescence branches.
>  >

Is overly restictive from that point of view.  Nor are they 
necessarily borne on inflorescence branches, indeed, they would be on 
the scape.

P.


From feedback_submission at brie4.plantontology.org  Mon Sep 13 17:38:02 2004
From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org)
Date: Mon, 13 Sep 2004 17:38:02 -0400
Subject: Feedback Submission from Plant Ontology Live Site
Message-ID: <200409132138.i8DLc28R018413@brie4.cshl.org>

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

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

comments: this is a test by shuly

name: shuly

email: shuly_avraham at hotmail.com

organization: cshl

send_feedback: Send your feedback



From jitterbug at plantontology.org  Mon Sep 13 17:55:13 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Mon, 13 Sep 2004 17:55:13 -0400
Subject: test! Feedback Submission from Plant Ontology Live Site (fwd) (PR#28)
Message-ID: <200409132155.i8DLtDUq018667@brie4.cshl.org>

To po-dev subscribers: 
This is a test message, please delete it.
We apologize for the inconvenience.

Shuly,

Thank you for your fedback to POC. Please reply to this message.

Katica 

> ---------- Forwarded message ----------
> Date: Mon, 13 Sep 2004 17:38:02 -0400
> From: feedback_submission at brie4.plantontology.org
> Reply-To: po-dev at plantontology.org,
feedback_submission at brie4.plantontology.org
> To: po <po-dev at plantontology.org>
> Subject: Feedback Submission from Plant Ontology Live Site
> 
>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: this is a test by shuly
> 
> name: shuly
> 
> email: shuly_avraham at hotmail.com
> 
> organization: cshl
> 
> send_feedback: Send your feedback
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: 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 jitterbug at plantontology.org  Tue Sep 14 00:36:18 2004
From: jitterbug at plantontology.org (Shuly Avraham)
Date: Tue, 14 Sep 2004 00:36:18 -0400
Subject: [Fwd: Feedback Submission from Plant Ontology Live Site] (PR#27)
Message-ID: <200409140436.i8E4aIUq024968@brie4.cshl.org>

po-dev members - please ignore!

this is a test by shuly at cshl.org

> This is a multi-part message in MIME format.
> --------------090507030203090409070408
> Content-Type: text/plain; charset=us-ascii; format=flowed
> Content-Transfer-Encoding: 7bit
> 
> test feed sub - by shuly
> 
> -------- Original Message --------
> Subject: 	Feedback Submission from Plant Ontology Live Site
> Date: 	Mon, 13 Sep 2004 17:38:02 -0400
> From: 	feedback_submission at brie4.plantontology.org
> Reply-To: 	po-dev at plantontology.org, 
> feedback_submission at brie4.plantontology.org
> To: 	po <po-dev at plantontology.org>
> 
> 
> 
>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: this is a test by shuly
> 
> name: shuly
> 
> email: shuly_avraham at hotmail.com
> 
> organization: cshl
> 
> send_feedback: Send your feedback
> 
> 
> 
> --------------090507030203090409070408
> Content-Type: text/html; charset=us-ascii
> Content-Transfer-Encoding: 7bit
> 
> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
> <html>
> <head>
>   <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1">
>   <title></title>
> </head>
> <body text="#000000" bgcolor="#ffffff">
> test feed sub - by shuly<br>
> <br>
> -------- Original Message --------
> <table cellpadding="0" cellspacing="0" border="0">
>   <tbody>
>     <tr>
>       <th valign="baseline" align="right" nowrap="nowrap">Subject: </th>
>       <td>Feedback Submission from Plant Ontology Live Site</td>
>     </tr>
>     <tr>
>       <th valign="baseline" align="right" nowrap="nowrap">Date: </th>
>       <td>Mon, 13 Sep 2004 17:38:02 -0400</td>
>     </tr>
>     <tr>
>       <th valign="baseline" align="right" nowrap="nowrap">From: </th>
>       <td><a class="moz-txt-link-abbreviated"
> href="mailto:feedback_submission at brie4.plantontology.org">feedback_submission at brie4.plantontology.org</a></td>
>     </tr>
>     <tr>
>       <th valign="baseline" align="right" nowrap="nowrap">Reply-To: </th>
>       <td><a class="moz-txt-link-abbreviated"
> href="mailto:po-dev at plantontology.org">po-dev at plantontology.org</a>,
> <a class="moz-txt-link-abbreviated"
> href="mailto:feedback_submission at brie4.plantontology.org">feedback_submission at brie4.plantontology.org</a></td>
>     </tr>
>     <tr>
>       <th valign="baseline" align="right" nowrap="nowrap">To: </th>
>       <td>po <a class="moz-txt-link-rfc2396E"
> href="mailto:po-dev at plantontology.org"><po-dev at plantontology.org></a></td>
>     </tr>
>   </tbody>
> </table>
> <br>
> <br>
> <pre>    *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: <a class="moz-txt-link-freetext"
> href="http://www.plantontology.org/index.html">http://www.plantontology.org/index.html</a>
> 
> comments: this is a test by shuly
> 
> name: shuly
> 
> email: <a class="moz-txt-link-abbreviated"
> href="mailto:shuly_avraham at hotmail.com">shuly_avraham at hotmail.com</a>
> 
> organization: cshl
> 
> send_feedback: Send your feedback
> 
> </pre>
> </body>
> </html>
> 
> --------------090507030203090409070408--
> 
> 


From shuly_avraham at hotmail.com  Tue Sep 14 00:44:17 2004
From: shuly_avraham at hotmail.com (Shuly Avraham)
Date: Tue, 14 Sep 2004 04:44:17 +0000
Subject: [Fwd: Feedback Submission from Plant Ontology Live Site] (PR#27)
Message-ID: <BAY2-F17E6f17ro43pw0000a7d2@hotmail.com>

sorry, po-dev members - please ignore.

this is a test by shuly at cshl.org

&gt;From: Shuly Avraham &lt;jitterbug at plantontology.org&gt;
&gt;To: shuly_avraham at hotmail.com
&gt;CC: po-dev at plantontology.org
&gt;Subject: Re: [Fwd: Feedback Submission from Plant Ontology Live Site] 
(PR#27)
&gt;Date: Tue, 14 Sep 2004 00:36:18 -0400
&gt;
&gt;po-dev members - please ignore!
&gt;
&gt;this is a test by shuly at cshl.org
&gt;
&gt; &gt; This is a multi-part message in MIME format.
&gt; &gt; --------------090507030203090409070408
&gt; &gt; Content-Type: text/plain; charset=us-ascii; format=flowed
&gt; &gt; Content-Transfer-Encoding: 7bit
&gt; &gt;
&gt; &gt; test feed sub - by shuly
&gt; &gt;
&gt; &gt; -------- Original Message --------
&gt; &gt; Subject: 	Feedback Submission from Plant Ontology Live Site
&gt; &gt; Date: 	Mon, 13 Sep 2004 17:38:02 -0400
&gt; &gt; From: 	feedback_submission at brie4.plantontology.org
&gt; &gt; Reply-To: 	po-dev at plantontology.org,
&gt; &gt; feedback_submission at brie4.plantontology.org
&gt; &gt; To: 	po &lt;po-dev at plantontology.org&gt;
&gt; &gt;
&gt; &gt;
&gt; &gt;
&gt; &gt;     *** Feedback from Plant Ontology Live Site ***
&gt; &gt;
&gt; &gt; refer_to_url: http://www.plantontology.org/index.html
&gt; &gt;
&gt; &gt; comments: this is a test by shuly
&gt; &gt;
&gt; &gt; name: shuly
&gt; &gt;
&gt; &gt; email: shuly_avraham at hotmail.com
&gt; &gt;
&gt; &gt; organization: cshl
&gt; &gt;
&gt; &gt; send_feedback: Send your feedback
&gt; &gt;
&gt; &gt;
&gt; &gt;
&gt; &gt; --------------090507030203090409070408
&gt; &gt; Content-Type: text/html; charset=us-ascii
&gt; &gt; Content-Transfer-Encoding: 7bit
&gt; &gt;
&gt; &gt; &lt;!DOCTYPE html PUBLIC &quot;-//W3C//DTD HTML 4.01 
Transitional//EN&quot;&gt;
&gt; &gt; &lt;html&gt;
&gt; &gt; &lt;head&gt;
&gt; &gt;   &lt;meta http-equiv=&quot;Content-Type&quot; 
content=&quot;text/html;charset=ISO-8859-1&quot;&gt;
&gt; &gt;   &lt;title&gt;&lt;/title&gt;
&gt; &gt; &lt;/head&gt;
&gt; &gt; &lt;body text=&quot;#000000&quot; bgcolor=&quot;#ffffff&quot;&gt;
&gt; &gt; test feed sub - by shuly&lt;br&gt;
&gt; &gt; &lt;br&gt;
&gt; &gt; -------- Original Message --------
&gt; &gt; &lt;table cellpadding=&quot;0&quot; cellspacing=&quot;0&quot; 
border=&quot;0&quot;&gt;
&gt; &gt;   &lt;tbody&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;Subject: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;Feedback Submission from Plant Ontology Live 
Site&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;Date: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;Mon, 13 Sep 2004 17:38:02 -0400&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;From: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;&lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:feedback_submission at brie4.plantontology.org&quot;&gt;feedback_submission at brie4.plantontology.org&lt;/a&gt;&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;Reply-To: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;&lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:po-dev at plantontology.org&quot;&gt;po-dev at plantontology.org&lt;/a&gt;,
&gt; &gt; &lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:feedback_submission at brie4.plantontology.org&quot;&gt;feedback_submission at brie4.plantontology.org&lt;/a&gt;&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;To: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;po &lt;a class=&quot;moz-txt-link-rfc2396E&quot;
&gt; &gt; 
href=&quot;mailto:po-dev at plantontology.org&quot;&gt;&lt;po-dev at plantontology.org&gt;&lt;/a&gt;&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;   &lt;/tbody&gt;
&gt; &gt; &lt;/table&gt;
&gt; &gt; &lt;br&gt;
&gt; &gt; &lt;br&gt;
&gt; &gt; &lt;pre&gt;    *** Feedback from Plant Ontology Live Site ***
&gt; &gt;
&gt; &gt; refer_to_url: &lt;a class=&quot;moz-txt-link-freetext&quot;
&gt; &gt; 
href=&quot;http://www.plantontology.org/index.html&quot;&gt;http://www.plantontology.org/index.html&lt;/a&gt;
&gt; &gt;
&gt; &gt; comments: this is a test by shuly
&gt; &gt;
&gt; &gt; name: shuly
&gt; &gt;
&gt; &gt; email: &lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:shuly_avraham at hotmail.com&quot;&gt;shuly_avraham at hotmail.com&lt;/a&gt;
&gt; &gt;
&gt; &gt; organization: cshl
&gt; &gt;
&gt; &gt; send_feedback: Send your feedback
&gt; &gt;
&gt; &gt; &lt;/pre&gt;
&gt; &gt; &lt;/body&gt;
&gt; &gt; &lt;/html&gt;
&gt; &gt;
&gt; &gt; --------------090507030203090409070408--
&gt; &gt;
&gt; &gt;

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From shuly_avraham at hotmail.com  Tue Sep 14 00:58:00 2004
From: shuly_avraham at hotmail.com (Shuly Avraham)
Date: Tue, 14 Sep 2004 04:58:00 +0000
Subject: [Fwd: Feedback Submission from Plant Ontology Live Site] (PR#27)
Message-ID: <BAY2-F12jEiw7fJrBUl000591a5@hotmail.com>


po-dev members - this is a test please ignore!


This message is a reply to jitterbug.

&gt;From: Shuly Avraham &lt;jitterbug at plantontology.org&gt;
&gt;To: shuly_avraham at hotmail.com
&gt;CC: po-dev at plantontology.org
&gt;Subject: Re: [Fwd: Feedback Submission from Plant Ontology Live Site] 
(PR#27)
&gt;Date: Tue, 14 Sep 2004 00:36:18 -0400
&gt;
&gt;po-dev members - please ignore!
&gt;
&gt;this is a test by shuly at cshl.org
&gt;
&gt; &gt; This is a multi-part message in MIME format.
&gt; &gt; --------------090507030203090409070408
&gt; &gt; Content-Type: text/plain; charset=us-ascii; format=flowed
&gt; &gt; Content-Transfer-Encoding: 7bit
&gt; &gt;
&gt; &gt; test feed sub - by shuly
&gt; &gt;
&gt; &gt; -------- Original Message --------
&gt; &gt; Subject: 	Feedback Submission from Plant Ontology Live Site
&gt; &gt; Date: 	Mon, 13 Sep 2004 17:38:02 -0400
&gt; &gt; From: 	feedback_submission at brie4.plantontology.org
&gt; &gt; Reply-To: 	po-dev at plantontology.org,
&gt; &gt; feedback_submission at brie4.plantontology.org
&gt; &gt; To: 	po &lt;po-dev at plantontology.org&gt;
&gt; &gt;
&gt; &gt;
&gt; &gt;
&gt; &gt;     *** Feedback from Plant Ontology Live Site ***
&gt; &gt;
&gt; &gt; refer_to_url: http://www.plantontology.org/index.html
&gt; &gt;
&gt; &gt; comments: this is a test by shuly
&gt; &gt;
&gt; &gt; name: shuly
&gt; &gt;
&gt; &gt; email: shuly_avraham at hotmail.com
&gt; &gt;
&gt; &gt; organization: cshl
&gt; &gt;
&gt; &gt; send_feedback: Send your feedback
&gt; &gt;
&gt; &gt;
&gt; &gt;
&gt; &gt; --------------090507030203090409070408
&gt; &gt; Content-Type: text/html; charset=us-ascii
&gt; &gt; Content-Transfer-Encoding: 7bit
&gt; &gt;
&gt; &gt; &lt;!DOCTYPE html PUBLIC &quot;-//W3C//DTD HTML 4.01 
Transitional//EN&quot;&gt;
&gt; &gt; &lt;html&gt;
&gt; &gt; &lt;head&gt;
&gt; &gt;   &lt;meta http-equiv=&quot;Content-Type&quot; 
content=&quot;text/html;charset=ISO-8859-1&quot;&gt;
&gt; &gt;   &lt;title&gt;&lt;/title&gt;
&gt; &gt; &lt;/head&gt;
&gt; &gt; &lt;body text=&quot;#000000&quot; bgcolor=&quot;#ffffff&quot;&gt;
&gt; &gt; test feed sub - by shuly&lt;br&gt;
&gt; &gt; &lt;br&gt;
&gt; &gt; -------- Original Message --------
&gt; &gt; &lt;table cellpadding=&quot;0&quot; cellspacing=&quot;0&quot; 
border=&quot;0&quot;&gt;
&gt; &gt;   &lt;tbody&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;Subject: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;Feedback Submission from Plant Ontology Live 
Site&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;Date: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;Mon, 13 Sep 2004 17:38:02 -0400&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;From: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;&lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:feedback_submission at brie4.plantontology.org&quot;&gt;feedback_submission at brie4.plantontology.org&lt;/a&gt;&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;Reply-To: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;&lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:po-dev at plantontology.org&quot;&gt;po-dev at plantontology.org&lt;/a&gt;,
&gt; &gt; &lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:feedback_submission at brie4.plantontology.org&quot;&gt;feedback_submission at brie4.plantontology.org&lt;/a&gt;&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;     &lt;tr&gt;
&gt; &gt;       &lt;th valign=&quot;baseline&quot; align=&quot;right&quot; 
nowrap=&quot;nowrap&quot;&gt;To: &lt;/th&gt;
&gt; &gt;       &lt;td&gt;po &lt;a class=&quot;moz-txt-link-rfc2396E&quot;
&gt; &gt; 
href=&quot;mailto:po-dev at plantontology.org&quot;&gt;&lt;po-dev at plantontology.org&gt;&lt;/a&gt;&lt;/td&gt;
&gt; &gt;     &lt;/tr&gt;
&gt; &gt;   &lt;/tbody&gt;
&gt; &gt; &lt;/table&gt;
&gt; &gt; &lt;br&gt;
&gt; &gt; &lt;br&gt;
&gt; &gt; &lt;pre&gt;    *** Feedback from Plant Ontology Live Site ***
&gt; &gt;
&gt; &gt; refer_to_url: &lt;a class=&quot;moz-txt-link-freetext&quot;
&gt; &gt; 
href=&quot;http://www.plantontology.org/index.html&quot;&gt;http://www.plantontology.org/index.html&lt;/a&gt;
&gt; &gt;
&gt; &gt; comments: this is a test by shuly
&gt; &gt;
&gt; &gt; name: shuly
&gt; &gt;
&gt; &gt; email: &lt;a class=&quot;moz-txt-link-abbreviated&quot;
&gt; &gt; 
href=&quot;mailto:shuly_avraham at hotmail.com&quot;&gt;shuly_avraham at hotmail.com&lt;/a&gt;
&gt; &gt;
&gt; &gt; organization: cshl
&gt; &gt;
&gt; &gt; send_feedback: Send your feedback
&gt; &gt;
&gt; &gt; &lt;/pre&gt;
&gt; &gt; &lt;/body&gt;
&gt; &gt; &lt;/html&gt;
&gt; &gt;
&gt; &gt; --------------090507030203090409070408--
&gt; &gt;
&gt; &gt;

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From shuly at cshl.edu  Tue Sep 14 14:50:08 2004
From: shuly at cshl.edu (Shuly)
Date: Tue, 14 Sep 2004 14:50:08 -0400
Subject: test by shuly - please ignire
Message-ID: <41473D60.9010906@cshl.org>

po-dev members - this is a test -
please ignore!



From PolaccoM at missouri.edu  Tue Sep 14 15:13:02 2004
From: PolaccoM at missouri.edu (Mary Polacco)
Date: Tue, 14 Sep 2004 14:13:02 -0500
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
Message-ID: <BD6CACEF.E50C%PolaccoM@missouri.edu>

Katica,

Let me know if this format is OK. I am open to any suggestions on anything
else here.

I will send on soon the ones where we have no annotation yet in MaizeGDB.
Where there was an (in sensu), I used the PO ID for the appropriate match in
maize and picking the sensu ones as appropriate. The accessions listed in
the mapping file are being placed into MaizeGDB to be used for providing
AMIGO with the gene associations.

Some notes.

A.  there are a few terms where the mapping was not precise; I have checked
with Leszek, and would like to propose that we consider adding new terms for
these cases.

MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
**preferred would be mapping to non-existent term: basal axillary shoot

MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
** pollen is a parent term for male gametophyte

MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
**strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
but is considered that way in usage.

MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
**while stem is the major component of maize stalk, it also is composed of
leaf sheath

MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
**mid rib includes more tissue that just the mid vein, but at this time I am
only mapping to mid vein


B. I changed a several terms in MaizeGDB to be equivalent to those in PO:
 culm node to node
 sheath to leaf sheath
 leaf blade to leaf lamina
  etc
  

C. in addition to Part A above, some terms in MaizeGDB should remain
different, but be 'synonymized' with the PO term:
 MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
 MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
 MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
  

-mary

++++++++++++++++++++++++++++++++++++++++++++++++++
 

 

MaizeGDB: 79057 shoot apical meristem > PO: shoot apical meristem ;
PO:0020148

MaizeGDB: 64470 node > PO: node ; PO:0020141

MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139

MaizeGDB: 1861 leaf > PO: leaf ; PO:0009025

MaizeGDB: 24738 leaf apex > PO: leaf apex ; PO:0020137

MaizeGDB: 24736 auricle > PO: auricle ; PO:0020106

MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016

MaizeGDB: 104000 leaf epidermis > PO: leaf epidermis ; PO:0006016

MaizeGDB: 131140 guard cell > PO: guard cell ; PO:0000293

MaizeGDB: 64473 ligule > PO: ligule ; PO:0020105

MaizeGDB: 13810 leaf sheath > PO: leaf sheath ; PO:0020104

MaizeGDB: 894644 leaf base > PO: leaf base ; PO:0020040

MaizeGDB: 24740 leaf lamina > PO: leaf lamina ; PO:0020039

MaizeGDB: 65488 leaf margin > PO: leaf margin ; PO:0020128

MaizeGDB: 11056 coleoptile > PO: coleoptile ; PO:0020033

MaizeGDB: 58047 stalk > PO: stem ; PO:0009047

MaizeGDB: 58047 stalk > PO: leaf sheath ; PO:0020104

MaizeGDB: 60674 stem > PO: stem ; PO:0009047

 

MaizeGDB: 106160 shoot > PO: shoot ; PO:0009006

MaizeGDB: 24734 root > PO: root ; PO:0009005

MaizeGDB: 106152 primary root > PO: primary root ; PO:0020127

MaizeGDB: 40516 root cap > PO: root cap ; PO:0020123

MaizeGDB: 894753 nodal root > PO: nodal root ; PO:0003005

MaizeGDB: 100045 root hair > PO: root hair ; PO:0000256

 

MaizeGDB: 100180 inflorescence > PO: inflorescence ; PO:0009049

MaizeGDB: 64471 glume > PO: glume ; PO:0009039

 

MaizeGDB: 24979 ear > PO: ear ; PO:0020136

MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001

MaizeGDB: 13807 pericarp > PO: pericarp ; PO:0009084

MaizeGDB: 1860 aleurone > PO: aleurone layer ; PO:000536

MaizeGDB: 11053 plumule > PO: plumule ; PO:0020032

MaizeGDB: 894610 cotyledon > PO: cotyledon ; PO:0020030

MaizeGDB: 11087 embryo > PO: embryo ; PO:0009009

MaizeGDB: 86197 embryo axis > PO: embryo axis ; PO:0019018

MaizeGDB: 15814 endosperm > PO: endosperm ; PO:0009089

MaizeGDB: 11042 scutellum > PO: scutellum ; PO:0020110

MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505

MaizeGDB: 167982 glume of ear spikelet > PO: glume of ear spikelet ;
PO:0006367

MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337

MaizeGDB: 64631 female gametophyte > PO: female gametophyte ; PO:0020092

MaizeGDB: 24753 silk > PO: silk ; PO:0006488

 

MaizeGDB: 24990 tassel > PO: tassel ; PO:0020126

MaizeGDB: 64630 male gametophyte > PO: male gametophyte ; PO:0020091

MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091

MaizeGDB: 24749 anther > PO: anther ; PO:0006473

MaizeGDB: 24746 glume of tassel spikelet > PO: glume of tassel spikelet ;
PO:0006368

MaizeGDB: 167379 central spike of tassel > PO: central spike of tassel ;
PO:0006324

 

 

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From schmidt at cshl.edu  Tue Sep 14 15:19:10 2004
From: schmidt at cshl.edu (Steven Schmidt)
Date: Tue, 14 Sep 2004 15:19:10 -0400
Subject: test
Message-ID: <200409141519.10401.schmidt@cshl.edu>

ok?
-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.



From katica at acoma.Stanford.EDU  Tue Sep 14 15:33:48 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Tue, 14 Sep 2004 12:33:48 -0700 (PDT)
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
In-Reply-To: <BD6CACEF.E50C%PolaccoM@missouri.edu>
Message-ID: <Pine.GSO.4.44.0409141223110.29775-100000@acoma.Stanford.EDU>

Hi Mary,

The mapping file looks fine on the first glance (format is OK). There are
47 mapped terms, all clear to me, except in one case, the term stalk (line
17) MaizeGDB 58047,  with mapping term in PO leaf sheath (PO:0020104).
I am not sure about this. Can you send me the definition for stalk in
MaizeGDB?

Also, please remind me again, how many terms are in the maize ontology.
Also, how many terms currently have no definition?


Thanks,

Katica


 On Tue, 14 Sep 2004, Mary Polacco wrote:

> Katica,
>
> Let me know if this format is OK. I am open to any suggestions on anything
> else here.
>
> I will send on soon the ones where we have no annotation yet in MaizeGDB.
> Where there was an (in sensu), I used the PO ID for the appropriate match in
> maize and picking the sensu ones as appropriate. The accessions listed in
> the mapping file are being placed into MaizeGDB to be used for providing
> AMIGO with the gene associations.
>
> Some notes.
>
> A.  there are a few terms where the mapping was not precise; I have checked
> with Leszek, and would like to propose that we consider adding new terms for
> these cases.
>
> MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
> **preferred would be mapping to non-existent term: basal axillary shoot
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
> ** pollen is a parent term for male gametophyte
>
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
> **strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
> but is considered that way in usage.
>
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
> MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
> **while stem is the major component of maize stalk, it also is composed of
> leaf sheath
>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
> **mid rib includes more tissue that just the mid vein, but at this time I am
> only mapping to mid vein
>
>
> B. I changed a several terms in MaizeGDB to be equivalent to those in PO:
>  culm node to node
>  sheath to leaf sheath
>  leaf blade to leaf lamina
>   etc
>
>
> C. in addition to Part A above, some terms in MaizeGDB should remain
> different, but be 'synonymized' with the PO term:
>  MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>  MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>  MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
>
> -mary
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
> MaizeGDB: 79057 shoot apical meristem > PO: shoot apical meristem ;
> PO:0020148
>
> MaizeGDB: 64470 node > PO: node ; PO:0020141
>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
>
> MaizeGDB: 1861 leaf > PO: leaf ; PO:0009025
>
> MaizeGDB: 24738 leaf apex > PO: leaf apex ; PO:0020137
>
> MaizeGDB: 24736 auricle > PO: auricle ; PO:0020106
>
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 104000 leaf epidermis > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 131140 guard cell > PO: guard cell ; PO:0000293
>
> MaizeGDB: 64473 ligule > PO: ligule ; PO:0020105
>
> MaizeGDB: 13810 leaf sheath > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 894644 leaf base > PO: leaf base ; PO:0020040
>
> MaizeGDB: 24740 leaf lamina > PO: leaf lamina ; PO:0020039
>
> MaizeGDB: 65488 leaf margin > PO: leaf margin ; PO:0020128
>
> MaizeGDB: 11056 coleoptile > PO: coleoptile ; PO:0020033
>
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
>
> MaizeGDB: 58047 stalk > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 60674 stem > PO: stem ; PO:0009047
>
>
>
> MaizeGDB: 106160 shoot > PO: shoot ; PO:0009006
>
> MaizeGDB: 24734 root > PO: root ; PO:0009005
>
> MaizeGDB: 106152 primary root > PO: primary root ; PO:0020127
>
> MaizeGDB: 40516 root cap > PO: root cap ; PO:0020123
>
> MaizeGDB: 894753 nodal root > PO: nodal root ; PO:0003005
>
> MaizeGDB: 100045 root hair > PO: root hair ; PO:0000256
>
>
>
> MaizeGDB: 100180 inflorescence > PO: inflorescence ; PO:0009049
>
> MaizeGDB: 64471 glume > PO: glume ; PO:0009039
>
>
>
> MaizeGDB: 24979 ear > PO: ear ; PO:0020136
>
> MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>
> MaizeGDB: 13807 pericarp > PO: pericarp ; PO:0009084
>
> MaizeGDB: 1860 aleurone > PO: aleurone layer ; PO:000536
>
> MaizeGDB: 11053 plumule > PO: plumule ; PO:0020032
>
> MaizeGDB: 894610 cotyledon > PO: cotyledon ; PO:0020030
>
> MaizeGDB: 11087 embryo > PO: embryo ; PO:0009009
>
> MaizeGDB: 86197 embryo axis > PO: embryo axis ; PO:0019018
>
> MaizeGDB: 15814 endosperm > PO: endosperm ; PO:0009089
>
> MaizeGDB: 11042 scutellum > PO: scutellum ; PO:0020110
>
> MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>
> MaizeGDB: 167982 glume of ear spikelet > PO: glume of ear spikelet ;
> PO:0006367
>
> MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
> MaizeGDB: 64631 female gametophyte > PO: female gametophyte ; PO:0020092
>
> MaizeGDB: 24753 silk > PO: silk ; PO:0006488
>
>
>
> MaizeGDB: 24990 tassel > PO: tassel ; PO:0020126
>
> MaizeGDB: 64630 male gametophyte > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 24749 anther > PO: anther ; PO:0006473
>
> MaizeGDB: 24746 glume of tassel spikelet > PO: glume of tassel spikelet ;
> PO:0006368
>
> MaizeGDB: 167379 central spike of tassel > PO: central spike of tassel ;
> PO:0006324
>
>
>
>
>
>

--------------------------------------------------------------------------
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 schmidt at cshl.edu  Tue Sep 14 15:49:44 2004
From: schmidt at cshl.edu (Steven Schmidt)
Date: Tue, 14 Sep 2004 15:49:44 -0400
Subject: reply-to test
Message-ID: <200409141549.44599.schmidt@cshl.edu>

Is sccny at optonline.net in the reply-to?
-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.



From schmidt at cshl.edu  Tue Sep 14 18:23:29 2004
From: schmidt at cshl.edu (Steven Schmidt)
Date: Tue, 14 Sep 2004 18:23:29 -0400
Subject: reply-to in forwarded message  (PR#100000000001)
Message-ID: <200409141823.30250.schmidt@cshl.edu>

po-dev members - please ignore
Shuly: I fixed .procmailrc to send to -outgoing
check the reply-to
-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977
Maybe someday I'll start following my own advice.



From shuly at cshl.edu  Tue Sep 14 20:18:27 2004
From: shuly at cshl.edu (Shuly)
Date: Tue, 14 Sep 2004 20:18:27 -0400
Subject: reply-to in forwarded message  (PR#100000000001)
In-Reply-To: <200409141823.30250.schmidt@cshl.edu>
References: <200409141823.30250.schmidt@cshl.edu>
Message-ID: <41478A53.8090406@cshl.org>

looks good.
Shuly.

Steven Schmidt wrote:

>po-dev members - please ignore
>Shuly: I fixed .procmailrc to send to -outgoing
>check the reply-to
>  
>




From feedback_submission at brie4.plantontology.org  Wed Sep 15 12:42:26 2004
From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org)
Date: Wed, 15 Sep 2004 12:42:26 -0400
Subject: Feedback Submission from Plant Ontology Live Site
Message-ID: <200409151642.i8FGgQxE019558@brie4.cshl.org>

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

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

comments: this is test please ignore

name: Hartmut Foerster

email: hartmut at acoma.stanford.edu

organization: Carnegie Institution

send_feedback: Send your feedback



From jitterbug at plantontology.org  Wed Sep 15 12:56:40 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Wed, 15 Sep 2004 12:56:40 -0400
Subject: test-Hartmut Feedback Submission from Plant Ontology Live Site (fwd) (PR#32)
Message-ID: <200409151656.i8FGueUq019694@brie4.cshl.org>

to po-dev subscribers: This is another test messsage, please ignore it.
 
Dear Hartmut,

Thank you for your interest in plant ontologies.

Katica

> ---------- Forwarded message ----------
> Date: Wed, 15 Sep 2004 12:42:26 -0400
> From: feedback_submission at brie4.plantontology.org
> Reply-To: po-dev at plantontology.org,
feedback_submission at brie4.plantontology.org
> To: po <po-dev at plantontology.org>
> Subject: Feedback Submission from Plant Ontology Live Site
> 
>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: this is test please ignore
> 
> name: Hartmut Foerster
> 
> email: hartmut at acoma.stanford.edu
> 
> organization: Carnegie Institution
> 
> send_feedback: Send your feedback
> 
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: 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 hartmut at acoma.Stanford.EDU  Wed Sep 15 12:57:44 2004
From: hartmut at acoma.Stanford.EDU (hartmut at acoma.Stanford.EDU)
Date: Wed, 15 Sep 2004 09:57:44 -0700 (PDT)
Subject: test-Hartmut Feedback Submission from Plant Ontology Live Site
 (fwd) (PR#32)
In-Reply-To: <200409151656.i8FGueUq019694@brie4.cshl.org>
Message-ID: <Pine.GSO.4.44.0409150956270.12151-100000@acoma.Stanford.EDU>

This is another test, please ignore


Katica please reply


On Wed, 15 Sep 2004, Katica Ilic wrote:

> to po-dev subscribers: This is another test messsage, please ignore it.
>
> Dear Hartmut,
>
> Thank you for your interest in plant ontologies.
>
> Katica
>
> > ---------- Forwarded message ----------
> > Date: Wed, 15 Sep 2004 12:42:26 -0400
> > From: feedback_submission at brie4.plantontology.org
> > Reply-To: po-dev at plantontology.org,
> feedback_submission at brie4.plantontology.org
> > To: po <po-dev at plantontology.org>
> > Subject: Feedback Submission from Plant Ontology Live Site
> >
> >     *** Feedback from Plant Ontology Live Site ***
> >
> > refer_to_url: http://www.plantontology.org/index.html
> >
> > comments: this is test please ignore
> >
> > name: Hartmut Foerster
> >
> > email: hartmut at acoma.stanford.edu
> >
> > organization: Carnegie Institution
> >
> > send_feedback: Send your feedback
> >
> >
> >
> Katica Ilic, TAIR Curator,	     E-mail: 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 jitterbug at plantontology.org  Wed Sep 15 13:01:06 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Wed, 15 Sep 2004 13:01:06 -0400
Subject: test-Hartmut Feedback Submission from Plant Ontology Live Site (fwd) (PR#32)
Message-ID: <200409151701.i8FH16Uq019760@brie4.cshl.org>

to po-dev subscribers: This is another test messsage, please ignore it.
 
Dear Hartmut,

Thank you for your interest in plant ontologies.

Katica

> ---------- Forwarded message ----------
> Date: Wed, 15 Sep 2004 12:42:26 -0400
> From: feedback_submission at brie4.plantontology.org
> Reply-To: po-dev at plantontology.org,
feedback_submission at brie4.plantontology.org
> To: po <po-dev at plantontology.org>
> Subject: Feedback Submission from Plant Ontology Live Site
> 
>     *** Feedback from Plant Ontology Live Site ***
> 
> refer_to_url: http://www.plantontology.org/index.html
> 
> comments: this is test please ignore
> 
> name: Hartmut Foerster
> 
> email: hartmut at acoma.stanford.edu
> 
> organization: Carnegie Institution
> 
> send_feedback: Send your feedback
> 
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: 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  Wed Sep 15 13:12:22 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 15 Sep 2004 13:12:22 -0400
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
In-Reply-To: <BD6CACEF.E50C%PolaccoM@missouri.edu>
References: <BD6CACEF.E50C%PolaccoM@missouri.edu>
Message-ID: <414877F6.4090602@cornell.edu>



Mary Polacco wrote:

> 
> A.  there are a few terms where the mapping was not precise; I have checked
> with Leszek, and would like to propose that we consider adding new terms for
> these cases.
> 
> MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
> **preferred would be mapping to non-existent term: basal axillary shoot

I was discussing this issue with Toby from Garmene's QTL curation 
perspective earlier. We came up with the following structure

axillary branch
     instance - cauline axillary branch
     instance - basal axillary branch - synonym tiller

cauline axillary branch
Definition:an axillary branch that forms  above ground level, and on an 
elongated internode

basal axillary branch
Definition:an axillary  branch that forms at ground level, generally 
from a non-elongating  internode

Let me know if it works for you.

> 
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
> ** pollen is a parent term for male gametophyte
> 
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
> **strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
> but is considered that way in usage.
> 
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
> MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
> **while stem is the major component of maize stalk, it also is composed of
> leaf sheath
> 
We are using the term "stalk" at two places as synonyms
  PO:0009047 : stem
  PO:0006341 : primary shoot

I think this term "stalk" is used in a loose sense, though cited quite 
often in the literature. So do you think that it is a valid case of 
creating a new term

shoot  PO:0009006
--p--stalk (new)
----p--stem PO:0009047
----p--leaf sheath  PO:0020104

The term stalk by your suggestion is very much a grass specific term, 
where as stem PO:0009047 is generic. This could create problems with TPR 
violation.






> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
> **mid rib includes more tissue that just the mid vein, but at this time I am
> only mapping to mid vein
> 

Can we have a definition from MaizeGDB.


Thanks
Pankaj



From Gauri.Salokhe at fao.org  Wed Sep 15 13:14:21 2004
From: Gauri.Salokhe at fao.org (Salokhe, Gauri (GILW))
Date: Wed, 15 Sep 2004 19:14:21 +0200
Subject: No subject
Message-ID: <83A0A35C4606234EA2FE8664956D0D70023FAD53@giexch1.fao.org>

unsubscribe
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From katica at acoma.Stanford.EDU  Wed Sep 15 13:37:00 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Wed, 15 Sep 2004 10:37:00 -0700 (PDT)
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
In-Reply-To: <BD6CACEF.E50C%PolaccoM@missouri.edu>
Message-ID: <Pine.GSO.4.44.0409151019590.12401-100000@acoma.Stanford.EDU>


Mary,
Thanks for the info, we can talk more about terms in MaizeGDB and
Leszek's maize ontology in Eugene next week.

Please see my comments below:


On Tue, 14 Sep 2004, Mary Polacco wrote:

> Katica,
>
> Let me know if this format is OK. I am open to any suggestions on anything
> else here.
>
> I will send on soon the ones where we have no annotation yet in MaizeGDB.
> Where there was an (in sensu), I used the PO ID for the appropriate match in
> maize and picking the sensu ones as appropriate. The accessions listed in
> the mapping file are being placed into MaizeGDB to be used for providing
> AMIGO with the gene associations.
>
> Some notes.
>
> A.  there are a few terms where the mapping was not precise; I have checked
> with Leszek, and would like to propose that we consider adding new terms for
> these cases.
>
> MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
> **preferred would be mapping to non-existent term: basal axillary shoot
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
> ** pollen is a parent term for male gametophyte\

This is fine, pollen is synonym of male gametophyte in PO. However, since
there is anther sensu Zea, there should be male gametophyte sensu Zea too
(I hate to say this, but that's a reality), and this term should be mapped
to it. There might be other terms in MaizeDGB that can be mapped to
existing sensu terms, instead to generic terms.

 >
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
> **strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
> but is considered that way in usage.

Leaf cuticle is in fact part_of leaf epidermis, and it's one of those
terms that are borderline, since strictly speaking, it is subcellular
structure, a layeron the outer wall of (leaf) epidermal cell.
Is there anything annotated to this term for maize?

> > MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
> MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
> **while stem is the major component of maize stalk, it also is composed of
> leaf sheath

I don't know about this one, I wouldn't map these two (even considering
the definitions for both), but the best is to ask Toby.

>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
> **mid rib includes more tissue that just the mid vein, but at this time I am
> only mapping to mid vein

I think this might be OK
>
>
> B. I changed a several terms in MaizeGDB to be equivalent to those in PO:
>  culm node to node
>  sheath to leaf sheath
>  leaf blade to leaf lamina
>   etc
>
>
> C. in addition to Part A above, some terms in MaizeGDB should remain
> different, but be 'synonymized' with the PO term:
>  MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>  MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>  MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
>
> -mary
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
> MaizeGDB: 79057 shoot apical meristem > PO: shoot apical meristem ;
> PO:0020148
>
> MaizeGDB: 64470 node > PO: node ; PO:0020141
>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
>
> MaizeGDB: 1861 leaf > PO: leaf ; PO:0009025
>
> MaizeGDB: 24738 leaf apex > PO: leaf apex ; PO:0020137
>
> MaizeGDB: 24736 auricle > PO: auricle ; PO:0020106
>
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 104000 leaf epidermis > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 131140 guard cell > PO: guard cell ; PO:0000293
>
> MaizeGDB: 64473 ligule > PO: ligule ; PO:0020105
>
> MaizeGDB: 13810 leaf sheath > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 894644 leaf base > PO: leaf base ; PO:0020040
>
> MaizeGDB: 24740 leaf lamina > PO: leaf lamina ; PO:0020039
>
> MaizeGDB: 65488 leaf margin > PO: leaf margin ; PO:0020128
>
> MaizeGDB: 11056 coleoptile > PO: coleoptile ; PO:0020033
>
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
>
> MaizeGDB: 58047 stalk > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 60674 stem > PO: stem ; PO:0009047
>
>
>
> MaizeGDB: 106160 shoot > PO: shoot ; PO:0009006
>
> MaizeGDB: 24734 root > PO: root ; PO:0009005
>
> MaizeGDB: 106152 primary root > PO: primary root ; PO:0020127
>
> MaizeGDB: 40516 root cap > PO: root cap ; PO:0020123
>
> MaizeGDB: 894753 nodal root > PO: nodal root ; PO:0003005
>
> MaizeGDB: 100045 root hair > PO: root hair ; PO:0000256
>
>
>
> MaizeGDB: 100180 inflorescence > PO: inflorescence ; PO:0009049
>
> MaizeGDB: 64471 glume > PO: glume ; PO:0009039
>
>
>
> MaizeGDB: 24979 ear > PO: ear ; PO:0020136
>
> MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>
> MaizeGDB: 13807 pericarp > PO: pericarp ; PO:0009084
>
> MaizeGDB: 1860 aleurone > PO: aleurone layer ; PO:000536
>
> MaizeGDB: 11053 plumule > PO: plumule ; PO:0020032
>
> MaizeGDB: 894610 cotyledon > PO: cotyledon ; PO:0020030
>
> MaizeGDB: 11087 embryo > PO: embryo ; PO:0009009
>
> MaizeGDB: 86197 embryo axis > PO: embryo axis ; PO:0019018
>
> MaizeGDB: 15814 endosperm > PO: endosperm ; PO:0009089
>
> MaizeGDB: 11042 scutellum > PO: scutellum ; PO:0020110
>
> MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>
> MaizeGDB: 167982 glume of ear spikelet > PO: glume of ear spikelet ;
> PO:0006367
>
> MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
> MaizeGDB: 64631 female gametophyte > PO: female gametophyte ; PO:0020092
>
> MaizeGDB: 24753 silk > PO: silk ; PO:0006488
>
>
>
> MaizeGDB: 24990 tassel > PO: tassel ; PO:0020126
>
> MaizeGDB: 64630 male gametophyte > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 24749 anther > PO: anther ; PO:0006473
>
> MaizeGDB: 24746 glume of tassel spikelet > PO: glume of tassel spikelet ;
> PO:0006368
>
> MaizeGDB: 167379 central spike of tassel > PO: central spike of tassel ;
> PO:0006324
>
>
>
>
>
>

--------------------------------------------------------------------------
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  Wed Sep 15 13:49:38 2004
From: katica at acoma.Stanford.EDU (Katica Ilic)
Date: Wed, 15 Sep 2004 10:49:38 -0700 (PDT)
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
In-Reply-To: <BD6CACEF.E50C%PolaccoM@missouri.edu>
Message-ID: <Pine.GSO.4.44.0409151043340.13317-100000@acoma.Stanford.EDU>

Mary,

I forgot to add comments on the very last part (C)

On Tue, 14 Sep 2004, Mary Polacco wrote:

>
> C. in addition to Part A above, some terms in MaizeGDB should remain
> different, but be 'synonymized' with the PO term:

They already are all synonyms of PO terms.

>  MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001

Kernel is synonym of fruit, so this mapping is fine.


>  MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505

This too

>  MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337

This one too, so all the annotations to husk in MAizeGDB are going to show
up under inflorescence bract of the ear, when you do a query in PO AmiGO.


Katica

>
> -mary
>
> ++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
>
>
> MaizeGDB: 79057 shoot apical meristem > PO: shoot apical meristem ;
> PO:0020148
>
> MaizeGDB: 64470 node > PO: node ; PO:0020141
>
> MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
>
> MaizeGDB: 1861 leaf > PO: leaf ; PO:0009025
>
> MaizeGDB: 24738 leaf apex > PO: leaf apex ; PO:0020137
>
> MaizeGDB: 24736 auricle > PO: auricle ; PO:0020106
>
> MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 104000 leaf epidermis > PO: leaf epidermis ; PO:0006016
>
> MaizeGDB: 131140 guard cell > PO: guard cell ; PO:0000293
>
> MaizeGDB: 64473 ligule > PO: ligule ; PO:0020105
>
> MaizeGDB: 13810 leaf sheath > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 894644 leaf base > PO: leaf base ; PO:0020040
>
> MaizeGDB: 24740 leaf lamina > PO: leaf lamina ; PO:0020039
>
> MaizeGDB: 65488 leaf margin > PO: leaf margin ; PO:0020128
>
> MaizeGDB: 11056 coleoptile > PO: coleoptile ; PO:0020033
>
> MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
>
> MaizeGDB: 58047 stalk > PO: leaf sheath ; PO:0020104
>
> MaizeGDB: 60674 stem > PO: stem ; PO:0009047
>
>
>
> MaizeGDB: 106160 shoot > PO: shoot ; PO:0009006
>
> MaizeGDB: 24734 root > PO: root ; PO:0009005
>
> MaizeGDB: 106152 primary root > PO: primary root ; PO:0020127
>
> MaizeGDB: 40516 root cap > PO: root cap ; PO:0020123
>
> MaizeGDB: 894753 nodal root > PO: nodal root ; PO:0003005
>
> MaizeGDB: 100045 root hair > PO: root hair ; PO:0000256
>
>
>
> MaizeGDB: 100180 inflorescence > PO: inflorescence ; PO:0009049
>
> MaizeGDB: 64471 glume > PO: glume ; PO:0009039
>
>
>
> MaizeGDB: 24979 ear > PO: ear ; PO:0020136
>
> MaizeGDB: 11089 kernel > PO: fruit ; PO:0009001
>
> MaizeGDB: 13807 pericarp > PO: pericarp ; PO:0009084
>
> MaizeGDB: 1860 aleurone > PO: aleurone layer ; PO:000536
>
> MaizeGDB: 11053 plumule > PO: plumule ; PO:0020032
>
> MaizeGDB: 894610 cotyledon > PO: cotyledon ; PO:0020030
>
> MaizeGDB: 11087 embryo > PO: embryo ; PO:0009009
>
> MaizeGDB: 86197 embryo axis > PO: embryo axis ; PO:0019018
>
> MaizeGDB: 15814 endosperm > PO: endosperm ; PO:0009089
>
> MaizeGDB: 11042 scutellum > PO: scutellum ; PO:0020110
>
> MaizeGDB: 24759 cob > PO: central spike of ear ; PO:0006505
>
> MaizeGDB: 167982 glume of ear spikelet > PO: glume of ear spikelet ;
> PO:0006367
>
> MaizeGDB: 24742 husk > PO: infloresence bract of ear ; PO:0006337
>
> MaizeGDB: 64631 female gametophyte > PO: female gametophyte ; PO:0020092
>
> MaizeGDB: 24753 silk > PO: silk ; PO:0006488
>
>
>
> MaizeGDB: 24990 tassel > PO: tassel ; PO:0020126
>
> MaizeGDB: 64630 male gametophyte > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
>
> MaizeGDB: 24749 anther > PO: anther ; PO:0006473
>
> MaizeGDB: 24746 glume of tassel spikelet > PO: glume of tassel spikelet ;
> PO:0006368
>
> MaizeGDB: 167379 central spike of tassel > PO: central spike of tassel ;
> PO:0006324
>
>
>
>
>
>

--------------------------------------------------------------------------
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 peter.stevens at mobot.org  Thu Sep 16 07:38:21 2004
From: peter.stevens at mobot.org (Peter Stevens)
Date: Thu, 16 Sep 2004 07:38:21 -0400
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
In-Reply-To: <414877F6.4090602@cornell.edu>
References: <BD6CACEF.E50C%PolaccoM@missouri.edu>
 <414877F6.4090602@cornell.edu>
Message-ID: <f0433013dbd6f2b085a05@[172.16.16.127]>

>Actually, the definition will have to be

cauline a. b.
An axillary branch that forms above ground level, whether or not on 
an elongated internode

Or I suppose one could remove the second half of the definition...

P.

>Mary Polacco wrote:
>
>>
>>A.  there are a few terms where the mapping was not precise; I have checked
>>with Leszek, and would like to propose that we consider adding new terms for
>>these cases.
>>
>>MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
>>**preferred would be mapping to non-existent term: basal axillary shoot
>
>I was discussing this issue with Toby from Garmene's QTL curation 
>perspective earlier. We came up with the following structure
>
>axillary branch
>     instance - cauline axillary branch
>     instance - basal axillary branch - synonym tiller
>
>cauline axillary branch
>Definition:an axillary branch that forms  above ground level, and on 
>an elongated internode
>
>basal axillary branch
>Definition:an axillary  branch that forms at ground level, generally 
>from a non-elongating  internode
>
>Let me know if it works for you.
>
>>
>>MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
>>** pollen is a parent term for male gametophyte
>>
>>MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016
>>**strictly speaking, leaf cuticle is not a 'cellular' anatomical feature,
>>but is considered that way in usage.
>>
>>MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
>>MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104
>>**while stem is the major component of maize stalk, it also is composed of
>>leaf sheath
>>
>We are using the term "stalk" at two places as synonyms
>  PO:0009047 : stem
>  PO:0006341 : primary shoot
>
>I think this term "stalk" is used in a loose sense, though cited 
>quite often in the literature. So do you think that it is a valid 
>case of creating a new term
>
>shoot  PO:0009006
>--p--stalk (new)
>----p--stem PO:0009047
>----p--leaf sheath  PO:0020104
>
>The term stalk by your suggestion is very much a grass specific 
>term, where as stem PO:0009047 is generic. This could create 
>problems with TPR violation.
>
>
>
>
>
>>MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139
>>**mid rib includes more tissue that just the mid vein, but at this time I am
>>only mapping to mid vein
>>
>
>Can we have a definition from MaizeGDB.
>
>
>Thanks
>Pankaj



From pj37 at cornell.edu  Thu Sep 16 10:47:50 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 16 Sep 2004 10:47:50 -0400
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
In-Reply-To: <f0433013dbd6f2b085a05@[172.16.16.127]>
References: <BD6CACEF.E50C%PolaccoM@missouri.edu> <414877F6.4090602@cornell.edu> <f0433013dbd6f2b085a05@[172.16.16.127]>
Message-ID: <4149A796.2040804@cornell.edu>



Peter Stevens wrote:

>> Actually, the definition will have to be
> 
> 
> cauline a. b.
> An axillary branch that forms above ground level, whether or not on an 
> elongated internode
> 

This will work for us. We wanted to have this statement because cauline 
  axillary branches are also found on basal axillary branches.


Ref. It's one of Toby's paper
PNAS , 2004, 101, pp.9045-9050
<http://dev.gramene.org/perl/pub_search?ref_id=8261>

Same situation occurrs in rice though they just call it 
primary/secondary/tertiary tillers.
e.g. Scanned from a IRRI publication on breeders handbook.
http://ascus.plbr.cornell.edu/~pankaj/images/grains%20007.jpg


-Pankaj

> Or I suppose one could remove the second half of the definition...
> 
> P.
> 
>> Mary Polacco wrote:
>>
>>>
>>> A.  there are a few terms where the mapping was not precise; I have 
>>> checked
>>> with Leszek, and would like to propose that we consider adding new 
>>> terms for
>>> these cases.
>>>
>>> MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343
>>> **preferred would be mapping to non-existent term: basal axillary shoot
>>
>>
>> I was discussing this issue with Toby from Garmene's QTL curation 
>> perspective earlier. We came up with the following structure
>>
>> axillary branch
>>     instance - cauline axillary branch
>>     instance - basal axillary branch - synonym tiller
>>
>> cauline axillary branch
>> Definition:an axillary branch that forms  above ground level, and on 
>> an elongated internode
>>
>> basal axillary branch
>> Definition:an axillary  branch that forms at ground level, generally 
>> from a non-elongating  internode
>>
>> Let me know if it works for you.
>>
>



From Leszek at missouri.edu  Thu Sep 16 11:40:48 2004
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Thu, 16 Sep 2004 10:40:48 -0500
Subject: Mapping file for maize terms WITH annotation in MaizeGDB
Message-ID: <BA876152E8653240BE8572E897083EE73C4AC4@UM-EMAIL09.um.umsystem.edu>

Peter - I don't understand your inclusion of the 2nd half of the
definition ("whether or 
> not on an elongated internode") - Developmentally - when would a
cauline branch ever form/arise from an elongated internode or just an
internode?? Surely such development is restricted/associated with the
node.

The 1st half of the definition would be fine, albeit very brief.

- Leszek

> -----Original Message-----
> From: owner-po-dev at brie4.cshl.org 
> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Peter Stevens
> Sent: Thursday, September 16, 2004 6:38 AM
> To: po-dev at plantontology.org; Pankaj Jaiswal
> Subject: Re: Mapping file for maize terms WITH annotation in MaizeGDB
> 
> >Actually, the definition will have to be
> 
> cauline a. b.
> An axillary branch that forms above ground level, whether or 
> not on an elongated internode
> 
> Or I suppose one could remove the second half of the definition...
> 
> P.
> 
> >Mary Polacco wrote:
> >
> >>
> >>A.  there are a few terms where the mapping was not precise; I have 
> >>checked with Leszek, and would like to propose that we 
> consider adding 
> >>new terms for these cases.
> >>
> >>MaizeGDB: 106161 tillers > PO: axillary shoot ; PO:0006343 
> **preferred 
> >>would be mapping to non-existent term: basal axillary shoot
> >
> >I was discussing this issue with Toby from Garmene's QTL curation 
> >perspective earlier. We came up with the following structure
> >
> >axillary branch
> >     instance - cauline axillary branch
> >     instance - basal axillary branch - synonym tiller
> >
> >cauline axillary branch
> >Definition:an axillary branch that forms  above ground 
> level, and on an 
> >elongated internode
> >
> >basal axillary branch
> >Definition:an axillary  branch that forms at ground level, generally 
> >from a non-elongating  internode
> >
> >Let me know if it works for you.
> >
> >>
> >>MaizeGDB: 15809 pollen > PO: male gametophyte ; PO:0020091
> >>** pollen is a parent term for male gametophyte
> >>
> >>MaizeGDB: 45980 leaf cuticle > PO: leaf epidermis ; PO:0006016 
> >>**strictly speaking, leaf cuticle is not a 'cellular' anatomical 
> >>feature, but is considered that way in usage.
> >>
> >>MaizeGDB: 58047 stalk > PO: stem ; PO:0009047
> >>MaizeGDB: 58047 stalk >> PO: leaf sheath ; PO:0020104 
> **while stem is 
> >>the major component of maize stalk, it also is composed of 
> leaf sheath
> >>
> >We are using the term "stalk" at two places as synonyms
> >  PO:0009047 : stem
> >  PO:0006341 : primary shoot
> >
> >I think this term "stalk" is used in a loose sense, though 
> cited quite 
> >often in the literature. So do you think that it is a valid case of 
> >creating a new term
> >
> >shoot  PO:0009006
> >--p--stalk (new)
> >----p--stem PO:0009047
> >----p--leaf sheath  PO:0020104
> >
> >The term stalk by your suggestion is very much a grass 
> specific term, 
> >where as stem PO:0009047 is generic. This could create problems with 
> >TPR violation.
> >
> >
> >
> >
> >
> >>MaizeGDB: 64474 mid rib > PO: mid vein ; PO:0020139 **mid 
> rib includes 
> >>more tissue that just the mid vein, but at this time I am 
> only mapping 
> >>to mid vein
> >>
> >
> >Can we have a definition from MaizeGDB.
> >
> >
> >Thanks
> >Pankaj
> 
> 



From pj37 at cornell.edu  Fri Sep 17 13:29:34 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 17 Sep 2004 13:29:34 -0400
Subject: new anatomy.definition file version (1.31) in CVS
Message-ID: <414B1EFE.4040203@cornell.edu>

Hi Everyone,

I just now committed a new version 1.31 of the anatomy.definition file 
in the CVS.

Here is the log message

1-added word OBSOLETE to the PO:0006067 definition.
2-modified the text "obsolete" in definitions to upper case "DEFINITION"
in order to allow AmiGO to detect correctly that obsolete terms are to 
be displayed in gray color.

Perhaps #2 should be case insensitive. I am going to suggest Chris 
Mungal at GO database for making the changes in the AmiGO scripts.

Thanks
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
************************




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Subject: Feedback on POC
Message-ID: <200409172015.i8HKFtXd017951@brie4.cshl.org>

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

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

comments: I am testing for Katica. Please ignore this message.

name: Suparna

email: smundodi at acoma.stanford.edu

organization: 

send_feedback: Send your feedback



From jitterbug at plantontology.org  Fri Sep 17 16:29:12 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Fri, 17 Sep 2004 16:29:12 -0400
Subject: Test soybean question Suparna - Feedback on POC (fwd) (PR#34)
Message-ID: <200409172029.i8HKTCUq018328@brie4.cshl.org>

Jitterbug test:
Friday 1:28 pm

Test Friday Sept 17, 1:24 pm
 
Subject line 53 ch
 
my reply to Suparna
 
We are almost there!
 
Katica
 
> ---------- Forwarded message ----------
> Date: Fri, 17 Sep 2004 16:15:55 -0400
> From: feedback_submission at brie4.plantontology.org
> Reply-To: po-dev at plantontology.org,
feedback_submission at brie4.plantontology.org
> 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: I am testing for Katica. Please ignore this message.
> 
> name: Suparna
> 
> email: smundodi at acoma.stanford.edu
> 
> organization:
> 
> send_feedback: Send your feedback
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: 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 smundodi at acoma.Stanford.EDU  Fri Sep 17 16:39:43 2004
From: smundodi at acoma.Stanford.EDU (Suparna Mundodi)
Date: Fri, 17 Sep 2004 13:39:43 -0700 (PDT)
Subject: Test soybean question Suparna - Feedback on POC (fwd) (PR#34)
In-Reply-To: <200409172029.i8HKTCUq018328@brie4.cshl.org>
Message-ID: <Pine.GSO.4.44.0409171339320.6630-100000@acoma.Stanford.EDU>

I hate you,.........

Supi


On Fri, 17 Sep 2004, Katica Ilic wrote:

> Jitterbug test:
> Friday 1:28 pm
>
> Test Friday Sept 17, 1:24 pm
>
> Subject line 53 ch
>
> my reply to Suparna
>
> We are almost there!
>
> Katica
>
> > ---------- Forwarded message ----------
> > Date: Fri, 17 Sep 2004 16:15:55 -0400
> > From: feedback_submission at brie4.plantontology.org
> > Reply-To: po-dev at plantontology.org,
> feedback_submission at brie4.plantontology.org
> > 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: I am testing for Katica. Please ignore this message.
> >
> > name: Suparna
> >
> > email: smundodi at acoma.stanford.edu
> >
> > organization:
> >
> > send_feedback: Send your feedback
> >
> >
> Katica Ilic, TAIR Curator,	     E-mail: 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.
>

****************************************************************************
Suparna Mundodi, Ph.D.			email:smundodi at acoma.stanford.edu
The Arabidopsis Information Resources	Fax:650-325-6857
Carnegie Institution of Washington	URL:http://arabidopsis.org/
Department of Plant Biology             phone:650-325-1521 x342
260 Panama St.
Stanford, CA 94305
****************************************************************************




From jitterbug at plantontology.org  Fri Sep 17 16:46:16 2004
From: jitterbug at plantontology.org (Katica Ilic)
Date: Fri, 17 Sep 2004 16:46:16 -0400
Subject: Test soybean question Suparna - Feedback on POC (fwd) (PR#34)
Message-ID: <200409172046.i8HKkGUq018841@brie4.cshl.org>

Jitterbug test:
Friday 1:28 pm

Test Friday Sept 17, 1:24 pm
 
Subject line 53 ch
 
my reply to Suparna
 
We are almost there!
 
Katica
 
> ---------- Forwarded message ----------
> Date: Fri, 17 Sep 2004 16:15:55 -0400
> From: feedback_submission at brie4.plantontology.org
> Reply-To: po-dev at plantontology.org,
feedback_submission at brie4.plantontology.org
> 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: I am testing for Katica. Please ignore this message.
> 
> name: Suparna
> 
> email: smundodi at acoma.stanford.edu
> 
> organization:
> 
> send_feedback: Send your feedback
> 
> 
Katica Ilic, TAIR Curator,	     E-mail: 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 smundodi at acoma.Stanford.EDU  Fri Sep 17 17:01:04 2004
From: smundodi at acoma.Stanford.EDU (Suparna Mundodi)
Date: Fri, 17 Sep 2004 14:01:04 -0700 (PDT)
Subject: Test soybean question Suparna - Feedback on POC (fwd) (PR#34)
In-Reply-To: <200409172048.i8HKmoUq018869@brie4.cshl.org>
Message-ID: <Pine.GSO.4.44.0409171400480.6630-100000@acoma.Stanford.EDU>

OK, hate you more....

Supi


On Fri, 17 Sep 2004, Katica Ilic wrote:

> Supi,
>
> Heyyy, That can't be true!!!
>
> this is the last one (today)
>
> Katica
>
> > I hate you,.........
> >
> > Supi
> >
> >
> > On Fri, 17 Sep 2004, Katica Ilic wrote:
> >
> >> Jitterbug test:
> >> Friday 1:28 pm
> >>
> >> Test Friday Sept 17, 1:24 pm
> >>
> >> Subject line 53 ch
> >>
> >> my reply to Suparna
> >>
> >> We are almost there!
> >>
> >> Katica
> >>
> >> > ---------- Forwarded message ----------
> >> > Date: Fri, 17 Sep 2004 16:15:55 -0400
> >> > From: feedback_submission at brie4.plantontology.org
> >> > Reply-To: po-dev at plantontology.org,
> >> feedback_submission at brie4.plantontology.org
> >> > 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: I am testing for Katica. Please ignore this message.
> >> >
> >> > name: Suparna
> >> >
> >> > email: smundodi at acoma.stanford.edu
> >> >
> >> > organization:
> >> >
> >> > send_feedback: Send your feedback
> >> >
> >> >
> >> Katica Ilic, TAIR Curator,	     E-mail: 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.
> >>
> >
> > ****************************************************************************
> > Suparna Mundodi, Ph.D.			email:smundodi at acoma.stanford.edu
> > The Arabidopsis Information Resources	Fax:650-325-6857
> > Carnegie Institution of Washington	URL:http://arabidopsis.org/
> > Department of Plant Biology             phone:650-325-1521 x342
> > 260 Panama St.
> > Stanford, CA 94305
> > ****************************************************************************
> >
> >
> >
> Katica Ilic, TAIR Curator,	     E-mail: 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.
>

****************************************************************************
Suparna Mundodi, Ph.D.			email:smundodi at acoma.stanford.edu
The Arabidopsis Information Resources	Fax:650-325-6857
Carnegie Institution of Washington	URL:http://arabidopsis.org/
Department of Plant Biology             phone:650-325-1521 x342
260 Panama St.
Stanford, CA 94305
****************************************************************************




From smundodi at acoma.Stanford.EDU  Fri Sep 17 17:36:49 2004
From: smundodi at acoma.Stanford.EDU (Suparna Mundodi)
Date: Fri, 17 Sep 2004 14:36:49 -0700 (PDT)
Subject: Test soybean question Suparna - Feedback on POC (fwd) (PR#34)
In-Reply-To: <200409172110.i8HLAKUq019376@brie4.cshl.org>
Message-ID: <Pine.GSO.4.44.0409171436330.6630-100000@acoma.Stanford.EDU>

I got this email twoce as well.

Supi

On Fri, 17 Sep 2004, Katica Ilic wrote:

> Supi,
>
> Heyyy, That can't be true!!!
>
> this is the last one (today)
>
> Katica
>
> > I hate you,.........
> >
> > Supi
> >
> >
> > On Fri, 17 Sep 2004, Katica Ilic wrote:
> >
> >> Jitterbug test:
> >> Friday 1:28 pm
> >>
> >> Test Friday Sept 17, 1:24 pm
> >>
> >> Subject line 53 ch
> >>
> >> my reply to Suparna
> >>
> >> We are almost there!
> >>
> >> Katica
> >>
> >> > ---------- Forwarded message ----------
> >> > Date: Fri, 17 Sep 2004 16:15:55 -0400
> >> > From: feedback_submission at brie4.plantontology.org
> >> > Reply-To: po-dev at plantontology.org,
> >> feedback_submission at brie4.plantontology.org
> >> > 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: I am testing for Katica. Please ignore this message.
> >> >
> >> > name: Suparna
> >> >
> >> > email: smundodi at acoma.stanford.edu
> >> >
> >> > organization:
> >> >
> >> > send_feedback: Send your feedback
> >> >
> >> >
> >> Katica Ilic, TAIR Curator,	     E-mail: 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.
> >>
> >
> > ****************************************************************************
> > Suparna Mundodi, Ph.D.			email:smundodi at acoma.stanford.edu
> > The Arabidopsis Information Resources	Fax:650-325-6857
> > Carnegie Institution of Washington	URL:http://arabidopsis.org/
> > Department of Plant Biology             phone:650-325-1521 x342
> > 260 Panama St.
> > Stanford, CA 94305
> > ****************************************************************************
> >
> >
> >
> Katica Ilic, TAIR Curator,	     E-mail: 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.
>

****************************************************************************
Suparna Mundodi, Ph.D.			email:smundodi at acoma.stanford.edu
The Arabidopsis Information Resources	Fax:650-325-6857
Carnegie Institution of Washington	URL:http://arabidopsis.org/
Department of Plant Biology             phone:650-325-1521 x342
260 Panama St.
Stanford, CA 94305
****************************************************************************




From shuly at cshl.edu  Sat Sep 18 01:25:38 2004
From: shuly at cshl.edu (Shuly)
Date: Sat, 18 Sep 2004 01:25:38 -0400
Subject: ontology updates on POC site
Message-ID: <414BC6D2.40401@cshl.org>

Dear Everyone,

The ontology browser on the plant ontology web site at
http://amigo.plantontology.org/go.cgi is now pointing to the latest
versions of the ontology files available from cvs.

CVS files:
anatomy.ontology ver 1.29
anatomy.definition  ver 1.31


Many thanks

Shuly.



From feedback_submission at brie4.plantontology.org  Sat Sep 18 17:50:13 2004
From: feedback_submission at brie4.plantontology.org (feedback_submission at brie4.plantontology.org)
Date: Sat, 18 Sep 2004 17:50:13 -0400
Subject: Feedback on POC
Message-ID: <200409182150.i8ILoD8M030337@brie4.cshl.org>

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

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

comments: test jitterbug Sep 18

name: shuly

email: shuly_avraham at hotmail.com

organization: home

send_feedback: Send your feedback



From jitterbug at plantontology.org  Sat Sep 18 18:03:45 2004
From: jitterbug at plantontology.org (Shuly Avraham)
Date: Sat, 18 Sep 2004 18:03:45 -0400
Subject: [Fwd: Feedback on POC] (PR#35)
Message-ID: <200409182203.i8IM3jUq030555@brie4.cshl.org>

Reply to shuly_avraham at hotmail.com via jitterbug 
(check if forwarder to po-dev).


From shuly_avraham at hotmail.com  Sat Sep 18 18:09:26 2004
From: shuly_avraham at hotmail.com (Shuly Avraham)
Date: Sat, 18 Sep 2004 22:09:26 +0000
Subject: [Fwd: Feedback on POC] (PR#35)
Message-ID: <BAY2-F6PGtNRLdm5cgt0002dbe1@hotmail.com>


this is a reply from shuly_avraham at hotmail.com to jitterbug
(only 'reply' not 'reply to all')

&gt;From: Shuly Avraham &lt;jitterbug at plantontology.org&gt;
&gt;To: shuly_avraham at hotmail.com
&gt;CC: po-dev at plantontology.org
&gt;Subject: Re: [Fwd: Feedback on POC] (PR#35)
&gt;Date: Sat, 18 Sep 2004 18:03:45 -0400
&gt;
&gt;Reply to shuly_avraham at hotmail.com via jitterbug
&gt;(check if forwarder to po-dev).

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today - it's FREE! 
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/



From jitterbug at plantontology.org  Sat Sep 18 18:15:34 2004
From: jitterbug at plantontology.org (Shuly Avraham)
Date: Sat, 18 Sep 2004 18:15:34 -0400
Subject: [Fwd: Feedback on POC] (PR#35)
Message-ID: <200409182215.i8IMFYUq030657@brie4.cshl.org>

This is the second reply from jitterbug to shuly_avraham at hotmail.com


From shuly_avraham at hotmail.com  Sat Sep 18 18:28:58 2004
From: shuly_avraham at hotmail.com (Shuly Avraham)
Date: Sat, 18 Sep 2004 22:28:58 +0000
Subject: [Fwd: Feedback on POC] (PR#35)
Message-ID: <BAY2-F37Jz2GrIn2WMl000300f6@hotmail.com>


second followup from hotmail to jitterbug, and cc po-dev -
using 'reply to all'

&gt;From: Shuly Avraham &lt;jitterbug at plantontology.org&gt;
&gt;To: shuly_avraham at hotmail.com
&gt;CC: po-dev at plantontology.org
&gt;Subject: Re: [Fwd: Feedback on POC] (PR#35)
&gt;Date: Sat, 18 Sep 2004 18:15:34 -0400
&gt;
&gt;This is the second reply from jitterbug to shuly_avraham at hotmail.com

_________________________________________________________________
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From shuly_avraham at hotmail.com  Sat Sep 18 18:28:58 2004
From: shuly_avraham at hotmail.com (Shuly Avraham)
Date: Sat, 18 Sep 2004 22:28:58 +0000
Subject: [Fwd: Feedback on POC] (PR#35)
Message-ID: <BAY2-F37Jz2GrIn2WMl000300f6@hotmail.com>


second followup from hotmail to jitterbug, and cc po-dev -
using 'reply to all'

&gt;From: Shuly Avraham &lt;jitterbug at plantontology.org&gt;
&gt;To: shuly_avraham at hotmail.com
&gt;CC: po-dev at plantontology.org
&gt;Subject: Re: [Fwd: Feedback on POC] (PR#35)
&gt;Date: Sat, 18 Sep 2004 18:15:34 -0400
&gt;
&gt;This is the second reply from jitterbug to shuly_avraham at hotmail.com

_________________________________________________________________
Is your PC infected? Get a FREE online computer virus scan from McAfee? 
Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963



From jclark at ebi.ac.uk  Wed Sep 22 07:49:45 2004
From: jclark at ebi.ac.uk (J Clark)
Date: Wed, 22 Sep 2004 12:49:45 +0100
Subject: plants in GO
Message-ID: <415166D9.5040402@ebi.ac.uk>

Hi,

Is anybody in the plant ontology community able to comment 
on the terms I've made up to cover plant gametophyte 
development in the gene ontology? I'd really appreciate any 
feedback that people could give me. Feedback sent as a reply 
to this e-mail would be excellent if people do not have a 
sourceforge username.

[ 1003916 ] female gametophyte development
https://sourceforge.net/tracker/index.php?func=detail&aid=1003916&group_id=36855&atid=440764

Thanks,

Jen



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



From pj37 at cornell.edu  Wed Sep 22 14:44:17 2004
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Wed, 22 Sep 2004 14:44:17 -0400
Subject: plants in GO
In-Reply-To: <415166D9.5040402@ebi.ac.uk>
References: <415166D9.5040402@ebi.ac.uk>
Message-ID: <4151C801.6060409@cornell.edu>

Just a had quick look and here are the suggestion

development sexual reproduction needs rephrasing or we don't need this 
term. Sexual reproduction is good enough. About the regulation terms, do 
we really need them at this time. My suggestion is that first we should 
organize the top level structure and then look for adding regulation terms.


female gamete generation (sensu Magnoliophyta)
	I am not sure if this is the statement in definition 'as in, but not 
restricted to, the flowering plants (Magnoliophyta, 
ncbi_taxonomy_id:3398)." makes sense". In the term we are using sensu 
and in definition we are saying not restricted to...?
Also I would consider it as the same as megagametogenesis.

We should list the following at same level because they are more or less 
governed by the temporal nature of the processes and often one process 
precedes/overlaps the other. So first it is the ovule that 
develops-->megaspores-->embryosac(female gametophyte/megagametohyte)

Sexual reproduction
-i-sexual reproduction (sensu Magnoliophyta)
--i--female reproductive organ development  (sensu Magnoliophyta)
---p--ovule development
---p--megagametophyte development
------p--megagametogenesis
------p--megasporogenesis
------p-- megagametophyte maturation


for ovule development I would restrict it to  the inclusion and 
development of the
p-antiraphe
p-chalaza
p-integument
p-micropyle
p-nucellus
      p-megasporocyte
p-raphe

Since megaspore develops from megasporocyte, then the process enters 
megasporogenesis
Megasporogenesis
-p-- megasporocyte differentiation
-p-- megasporocyte meiosis
---p--megasporocyte meiosis-division 1
---p--megasporocyte meiosis-division 2
---p--megaspore maturation, syn: functional megaspore formation  (this 
also includes degeneration of other 3 megaspores depending on teh type 
of embryosac)

Then comes the megagametogenesis

megagametogenesis
-p--megaspore mitotic division 1
-p--megaspore mitotic division 2
-p--megaspore mitotic division 3

Followed by (the instances are not ordered in temporal way)
  megagametophyte maturation
--p--cellularization of megagametophyte
--p--differentiation of the antipodal cell
--p--egg apparatus differentiation
--p--female gametophyte central cell differentiation
--p--megagametophyte nuclear migration
--p--synergid cell differentiation

I am not sure about megagametophyte nuclear division, the definition 
appears to have some parts from microspore dev.


All these suggestion are based on the most popular monosporic 8-nucleate 
polygonum type and could change based on the type of embryosac.

Some ref
http://www.unizh.ch/botinst/Cyto_Website/schneitzLab/OvuleDevelopment/outlook.html
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=161260&rendertype=abstract
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=160483&action=stream&blobtype=pdf

J Clark wrote:

> Hi,
> 
> Is anybody in the plant ontology community able to comment on the terms 
> I've made up to cover plant gametophyte development in the gene 
> ontology? I'd really appreciate any feedback that people could give me. 
> Feedback sent as a reply to this e-mail would be excellent if people do 
> not have a sourceforge username.
> 
> [ 1003916 ] female gametophyte development
> https://sourceforge.net/tracker/index.php?func=detail&aid=1003916&group_id=36855&atid=440764 
> 
> 
> Thanks,
> 
> Jen
> 
> 
> 

-- 
************************
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 cain at cshl.edu  Fri Sep 24 10:58:31 2004
From: cain at cshl.edu (Scott Cain)
Date: Fri, 24 Sep 2004 10:58:31 -0400
Subject: loading plant ontology into chado
Message-ID: <1096037911.2252.12.camel@localhost.localdomain>

Hello all,

I wanted to add the plant ontology to chado config file so that it is on
the list of "easy to install" ontologies when someone installs chado.
However, PO is not as easy as SO, where there is a single ontology file
and a singe definition file, so I was wondering if someone would like to
give me any pointers for how and what to load, and if necessary, in what
order.

Thanks much,
Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



From shuly at cshl.edu  Sat Sep 25 12:29:31 2004
From: shuly at cshl.edu (Shuly)
Date: Sat, 25 Sep 2004 12:29:31 -0400
Subject: loading plant ontology into chado
In-Reply-To: <1096037911.2252.12.camel@localhost.localdomain>
References: <1096037911.2252.12.camel@localhost.localdomain>
Message-ID: <41559CEB.8020103@cshl.org>

Hi Scott,

Are you looking at the Poc ontologies cvs ?
If that so - all you need are those 2 files:

Ontologies:
Poc/anatomy/anatomy.ontology

Definitions
Poc/definitions/anatomy.definition

Shuly.

Scott Cain wrote:

>Hello all,
>
>I wanted to add the plant ontology to chado config file so that it is on
>the list of "easy to install" ontologies when someone installs chado.
>However, PO is not as easy as SO, where there is a single ontology file
>and a singe definition file, so I was wondering if someone would like to
>give me any pointers for how and what to load, and if necessary, in what
>order.
>
>Thanks much,
>Scott
>
>  
>



From cain at cshl.edu  Sun Sep 26 19:15:54 2004
From: cain at cshl.edu (Scott Cain)
Date: Sun, 26 Sep 2004 19:15:54 -0400
Subject: loading plant ontology into chado
In-Reply-To: <41559CEB.8020103@cshl.org>
References: <1096037911.2252.12.camel@localhost.localdomain>
	 <41559CEB.8020103@cshl.org>
Message-ID: <1096240554.1978.5.camel@localhost.localdomain>

Thanks Shuly,

There were just so many files, it wasn't clear to me which I needed.

Scott


On Sat, 2004-09-25 at 12:29, Shuly wrote:
> Hi Scott,
> 
> Are you looking at the Poc ontologies cvs ?
> If that so - all you need are those 2 files:
> 
> Ontologies:
> Poc/anatomy/anatomy.ontology
> 
> Definitions
> Poc/definitions/anatomy.definition
> 
> Shuly.
> 
> Scott Cain wrote:
> 
> >Hello all,
> >
> >I wanted to add the plant ontology to chado config file so that it is on
> >the list of "easy to install" ontologies when someone installs chado.
> >However, PO is not as easy as SO, where there is a single ontology file
> >and a singe definition file, so I was wondering if someone would like to
> >give me any pointers for how and what to load, and if necessary, in what
> >order.
> >
> >Thanks much,
> >Scott
> >
> >  
> >
-- 
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Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory