From feedback_submission at filetta.cshl.edu  Tue Aug  1 12:19:19 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Tue, 1 Aug 2006 12:19:19 -0400
Subject: Feedback on POC
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From feedback_submission at filetta.cshl.edu  Wed Aug  2 06:33:31 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Wed, 2 Aug 2006 06:33:31 -0400
Subject: Feedback on POC
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From feedback_submission at filetta.cshl.edu  Wed Aug  2 19:05:57 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Wed, 2 Aug 2006 19:05:57 -0400
Subject: Feedback on POC
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From feedback_submission at filetta.cshl.edu  Wed Aug  2 21:56:52 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Wed, 2 Aug 2006 21:56:52 -0400
Subject: Feedback on POC
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From feedback_submission at filetta.cshl.edu  Thu Aug  3 07:08:52 2006
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Date: Thu, 3 Aug 2006 07:08:52 -0400
Subject: Feedback on POC
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From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:38 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:38 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73GecGi003484@filetta.cshl.org>

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

email: gwwuts at yahoo.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2004/0704.html

name: w6dzv70eev

comments: i8t929fu6dnmh3h <a href = http://www.923494.com/698125.html > y4f5dzskk6v5tubk </a> [URL=http://www.699427.com/355277.html] xvwt4xeheca3xi2i [/URL] iz36fy6t5

organization: uf837h2zf6



From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:40 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:40 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73GeeHd003524@filetta.cshl.org>

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

email: oifjag at lycos.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2005/subject.html

name: ohr0mg5epr

comments: cvg45xrts <a href = http://www.345320.com/570616.html > 16xgfe0kw2 </a> [URL=http://www.850629.com/468838.html] zprmpf0ipvb5b7 [/URL] txhlq5kc

organization: 3w0f3fyo5i



From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:39 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:39 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73GednQ003504@filetta.cshl.org>

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

email: gwwuts at yahoo.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2004/0704.html

name: w6dzv70eev

comments: i8t929fu6dnmh3h http://www.683916.com/715167.html iz36fy6t5

organization: uf837h2zf6

Clear: 



From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:39 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:39 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73GedjG003514@filetta.cshl.org>

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

email: gwwuts at yahoo.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2004/0704.html

name: w6dzv70eev

comments: i8t929fu6dnmh3h v0a4fpx0g8 iz36fy6t5

organization: uf837h2zf6

Clear: 



From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:41 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:41 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73GefDG003534@filetta.cshl.org>

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

email: oifjag at lycos.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2005/subject.html

name: ohr0mg5epr

comments: cvg45xrts [URL=http://www.850629.com/468838.html] zprmpf0ipvb5b7 [/URL] txhlq5kc

organization: 3w0f3fyo5i

Clear: 



From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:42 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:42 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73GegiJ003554@filetta.cshl.org>

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

email: oifjag at lycos.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2005/subject.html

name: ohr0mg5epr

comments: cvg45xrts cfn3bxxy txhlq5kc

organization: 3w0f3fyo5i

Clear: 



From feedback_submission at filetta.cshl.edu  Thu Aug  3 12:40:41 2006
From: feedback_submission at filetta.cshl.edu (feedback_submission at filetta.cshl.edu)
Date: Thu, 3 Aug 2006 12:40:41 -0400
Subject: Feedback on POC
Message-ID: <200608031640.k73Gef8X003544@filetta.cshl.org>

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

email: oifjag at lycos.com

send_feedback: Send your feedback

refer_to_url: http://www.plantontology.org/mailarch-dev/Apr2005/subject.html

name: ohr0mg5epr

comments: cvg45xrts http://www.633984.com/346700.html txhlq5kc

organization: 3w0f3fyo5i

Clear: 



From shuly at cshl.edu  Fri Aug  4 16:53:44 2006
From: shuly at cshl.edu (Shuly Avraham)
Date: Fri, 4 Aug 2006 16:53:44 -0400
Subject: Feedback on POC
References: <200608042037.k74Kb36d005772@filetta.cshl.org>
Message-ID: <663EE88C-3BDF-4E3D-8033-6157610893FD@cshl.edu>


>
>     *** Feedback from Plant Ontology Live Site ***
>
> refer_to_url: http://www.plantontology.org/index.html
>
> comments: THe difinition of lodicule for maize ear needs to be  
> tweaked. Currently it says:
> In a Maize ear floret, one of two or three tiny scales or flaps of  
> tissue outside the **stamens**, possibly representing reduced  
> perianth segments.
>
>
>
> name: Mary Schaeffer
>
> email: SchaefferM at missouri.edu
>
> organization:
>
> send_feedback: Send your feedback
>



From kellogge at msx.umsl.edu  Sat Aug  5 18:23:34 2006
From: kellogge at msx.umsl.edu (kellogge)
Date: Sat, 5 Aug 2006 17:23:34 -0500
Subject: Feedback on POC
In-Reply-To: <663EE88C-3BDF-4E3D-8033-6157610893FD@cshl.edu>
References: <200608042037.k74Kb36d005772@filetta.cshl.org> <663EE88C-3BDF-4E3D-8033-6157610893FD@cshl.edu>
Message-ID: <4251d0d4f04f4b5c4f55462eed9cbe7e@msx.umsl.edu>

How about "In a maize ear floret, one of two tiny scales or flaps of 
tissue outside the aborted stamens, possibly representing reduced 
perianth segments."
Toby

On Aug 4, 2006, at 3:53 PM, Shuly Avraham wrote:

>
>>
>>     *** Feedback from Plant Ontology Live Site ***
>>
>> refer_to_url: http://www.plantontology.org/index.html
>>
>> comments: THe difinition of lodicule for maize ear needs to be 
>> tweaked. Currently it says:
>> In a Maize ear floret, one of two or three tiny scales or flaps of 
>> tissue outside the **stamens**, possibly representing reduced 
>> perianth segments.
>>
>>
>>
>> name: Mary Schaeffer
>>
>> email: SchaefferM at missouri.edu
>>
>> organization:
>>
>> send_feedback: Send your feedback
>>
>
>
Elizabeth A. Kellogg
E. Desmond Lee and Family Professor of Botanical Studies
Department of Biology
University of Missouri-St. Louis
St. Louis, MO 63121
Tel: 314-516-6217; FAX: 314-516-6233
http://www.umsl.edu/services/kellogg/
This message is for the designated recipient(s) only and may contain 
privileged or confidential information.? If you received it in error, 
please notify the sender immediately and delete the original.? Thank 
you.?




From shuly at cshl.edu  Mon Aug  7 18:47:19 2006
From: shuly at cshl.edu (Shuly Avraham)
Date: Mon, 7 Aug 2006 18:47:19 -0400
Subject: Fwd: Feedback on POC
References: <200608042037.k74Kb36d005772@filetta.cshl.org>
Message-ID: <85FD1C03-21B2-464E-9502-59A5BBB43564@cshl.edu>



Begin forwarded message:

> From: feedback_submission at filetta.cshl.edu
> Date: August 4, 2006 4:37:03 PM EDT
> To: Shuly Avraham <shuly at cshl.edu>
> Subject: Feedback on POC
>
>     *** Feedback from Plant Ontology Live Site ***
>
> refer_to_url: http://www.plantontology.org/index.html
>
> comments: THe difinition of lodicule for maize ear needs to be  
> tweaked. Currently it says:
> In a Maize ear floret, one of two or three tiny scales or flaps of  
> tissue outside the **stamens**, possibly representing reduced  
> perianth segments.
>
>
>
> name: Mary Schaeffer
>
> email: SchaefferM at missouri.edu
>
> organization:
>
> send_feedback: Send your feedback
>

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From katica at acoma.Stanford.EDU  Fri Aug 11 14:08:49 2006
From: katica at acoma.Stanford.EDU (Katica)
Date: Fri, 11 Aug 2006 11:08:49 -0700
Subject: test KI - Aug 11, 2006
Message-ID: <44DCC7B1.1040602@acoma.stanford.edu>

just a test for the po at plantontology.org

KI



From donghui at stanford.edu  Fri Aug 11 14:20:36 2006
From: donghui at stanford.edu (Donghui Li)
Date: Fri, 11 Aug 2006 11:20:36 -0700
Subject: test2
Message-ID: <44DCCA74.9040903@stanford.edu>

test2

dh

-- 
Donghui Li, PhD

The Arabidopsis Information Resource
Carnegie Institution
260 Panama Street
Stanford CA 94305

donghui at stanford.edu



From kjbradford at ucdavis.edu  Fri Aug 11 12:00:00 2006
From: kjbradford at ucdavis.edu (KENT BRADFORD)
Date: Fri, 11 Aug 2006 09:00:00 -0700
Subject: FW: Compositae vocabulary
Message-ID: <70B0CAB623BFDA448F85DA2AFEE8BD42DC6FF7@EXCHANGE.plantsciences.ucdavis.edu>

I am trying the email that was published in Jaiswal et al (2005) in an
attempt to make contact regarding the questions below.
Kent Bradford

_____________________________________________
From: KENT BRADFORD 
Sent: Tuesday, August 01, 2006 2:10 PM
To: 'po at plantontology.org'
Subject: RE: Compositae vocabulary

I am trying again to obtain a response from the plant ontology group. 
Kent Bradford

_____________________________________________
From: KENT BRADFORD 
Sent: Monday, May 01, 2006 2:13 PM
To: 'po at plantontology.org'
Subject: RE: Compositae vocabulary

I did not get any response to the message below. Is this address listed
on the Plant Ontology website viable? 
Kent Bradford

_____________________________________________
From: KENT BRADFORD 
Sent: Tuesday, April 18, 2006 2:33 PM
To: 'po at plantontology.org'
Subject: Compositae vocabulary

To Whom It May Concern:
I am a Co-PI on the Compositae Genome Project that has been developing
EST and mapping resources for the Compositae, primarily lettuce and
sunflower but now expanding into 15 additional species
(http://cgpdb.ucdavis.edu). As part of this project, we have also
collected extensive phenotypic data on several hundred accessions in the
Compositae. We are in the process of developing a database to compile
and store this data and make it accessible via our website. In
describing our phenotypic data, we would like to be compatible with your
controlled vocabularies in choosing our terms. However, you note on your
website that these vocabularies are not yet available for the
Compositae, and we have many types of data that I do not see in the
current descriptions, (e.g., specific leaf shapes, rosettes, presence of
trichomes, inflorescence branching patterns, etc.). I would appreciate
your advice on how we should proceed in a way that will remain
consistent the goals of the plant ontology project to allow broad and
consistent searching on controlled vocabularies. Is anyone working on a
list of terms for the Compositae that we could work from? I can send a
list of the characteristics that we have recorded if it would help. 

Sincerely,
Kent Bradford

Kent J. Bradford
Professor
Department of Plant Sciences
Mail Stop 5
One Shields Ave.
University of California
Davis, CA 95616-8780
Phone: 1-530-752-6087
Fax: 1-530-754-7222
Email: kjbradford at ucdavis.edu



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From kjbradford at ucdavis.edu  Tue Aug  1 17:09:59 2006
From: kjbradford at ucdavis.edu (KENT BRADFORD)
Date: Tue, 1 Aug 2006 14:09:59 -0700
Subject: Compositae vocabulary
Message-ID: <70B0CAB623BFDA448F85DA2AFEE8BD42D1B8B2@EXCHANGE.plantsciences.ucdavis.edu>

I am trying again to obtain a response from the plant ontology group. 
Kent Bradford

_____________________________________________
From: KENT BRADFORD 
Sent: Monday, May 01, 2006 2:13 PM
To: 'po at plantontology.org'
Subject: RE: Compositae vocabulary

I did not get any response to the message below. Is this address listed
on the Plant Ontology website viable? 
Kent Bradford

_____________________________________________
From: KENT BRADFORD 
Sent: Tuesday, April 18, 2006 2:33 PM
To: 'po at plantontology.org'
Subject: Compositae vocabulary

To Whom It May Concern:
I am a Co-PI on the Compositae Genome Project that has been developing
EST and mapping resources for the Compositae, primarily lettuce and
sunflower but now expanding into 15 additional species
(http://cgpdb.ucdavis.edu). As part of this project, we have also
collected extensive phenotypic data on several hundred accessions in the
Compositae. We are in the process of developing a database to compile
and store this data and make it accessible via our website. In
describing our phenotypic data, we would like to be compatible with your
controlled vocabularies in choosing our terms. However, you note on your
website that these vocabularies are not yet available for the
Compositae, and we have many types of data that I do not see in the
current descriptions, (e.g., specific leaf shapes, rosettes, presence of
trichomes, inflorescence branching patterns, etc.). I would appreciate
your advice on how we should proceed in a way that will remain
consistent the goals of the plant ontology project to allow broad and
consistent searching on controlled vocabularies. Is anyone working on a
list of terms for the Compositae that we could work from? I can send a
list of the characteristics that we have recorded if it would help. 

Sincerely,
Kent Bradford

Kent J. Bradford
Professor
Department of Plant Sciences
Mail Stop 5
One Shields Ave.
University of California
Davis, CA 95616-8780
Phone: 1-530-752-6087
Fax: 1-530-754-7222
Email: kjbradford at ucdavis.edu



-------------- next part --------------
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From katica at acoma.Stanford.EDU  Fri Aug 11 19:08:15 2006
From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU)
Date: Fri, 11 Aug 2006 16:08:15 -0700 (PDT)
Subject: FW: Compositae vocabulary
In-Reply-To: <70B0CAB623BFDA448F85DA2AFEE8BD42DC6FF7@EXCHANGE.plantsciences.ucdavis.edu>
References: <70B0CAB623BFDA448F85DA2AFEE8BD42DC6FF7@EXCHANGE.plantsciences.ucdavis.edu>
Message-ID: <Pine.LNX.4.62.0608111606590.15627@aztec.stanford.edu>

Dear Kent,

I apologize for inexcusable delay in responding to your messages to 
po at plantontology.org. All your emails got caught in our spam filter. We 
will certainly try to do our best to prevent this from happening again.

As Leszek already mentioned, it would help if you could send us the list 
of the characteristics/characters that you have recorded. This would help 
us understand the scope of the request. We would work together with you on 
incorporating botanical terms specific for Compositae in the PSO. If an 
extensive changes need to be done to PO to accommodate all updates, it 
would probably take several rounds of dialogs, and may involve 
taxonomists-experts for the Compositae family.

A good way to start is to learn more about phenotypic data that you have 
and to review few examples of phenotype description, and also a list of 
controlled vocabulary terms that you would like to see in the PO.

Best regards,

Katica Ilic, POC Project Coordinator


On Fri, 11 Aug 2006, KENT BRADFORD wrote:

> I am trying the email that was published in Jaiswal et al (2005) in an
> attempt to make contact regarding the questions below.
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Tuesday, August 01, 2006 2:10 PM
> To: 'po at plantontology.org'
> Subject: RE: Compositae vocabulary
>
> I am trying again to obtain a response from the plant ontology group.
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Monday, May 01, 2006 2:13 PM
> To: 'po at plantontology.org'
> Subject: RE: Compositae vocabulary
>
> I did not get any response to the message below. Is this address listed
> on the Plant Ontology website viable?
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Tuesday, April 18, 2006 2:33 PM
> To: 'po at plantontology.org'
> Subject: Compositae vocabulary
>
> To Whom It May Concern:
> I am a Co-PI on the Compositae Genome Project that has been developing
> EST and mapping resources for the Compositae, primarily lettuce and
> sunflower but now expanding into 15 additional species
> (http://cgpdb.ucdavis.edu). As part of this project, we have also
> collected extensive phenotypic data on several hundred accessions in the
> Compositae. We are in the process of developing a database to compile
> and store this data and make it accessible via our website. In
> describing our phenotypic data, we would like to be compatible with your
> controlled vocabularies in choosing our terms. However, you note on your
> website that these vocabularies are not yet available for the
> Compositae, and we have many types of data that I do not see in the
> current descriptions, (e.g., specific leaf shapes, rosettes, presence of
> trichomes, inflorescence branching patterns, etc.). I would appreciate
> your advice on how we should proceed in a way that will remain
> consistent the goals of the plant ontology project to allow broad and
> consistent searching on controlled vocabularies. Is anyone working on a
> list of terms for the Compositae that we could work from? I can send a
> list of the characteristics that we have recorded if it would help.
>
> Sincerely,
> Kent Bradford
>
> Kent J. Bradford
> Professor
> Department of Plant Sciences
> Mail Stop 5
> One Shields Ave.
> University of California
> Davis, CA 95616-8780
> Phone: 1-530-752-6087
> Fax: 1-530-754-7222
> Email: kjbradford at ucdavis.edu
>
>
>
>

-- 
--------------------------------------------------------------------------
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  Mon Aug 14 14:16:49 2006
From: katica at acoma.Stanford.EDU (Katica)
Date: Mon, 14 Aug 2006 11:16:49 -0700
Subject: FW: Compositae vocabulary
In-Reply-To: <70B0CAB623BFDA448F85DA2AFEE8BD42DC70CB@EXCHANGE.plantsciences.ucdavis.edu>
References: <70B0CAB623BFDA448F85DA2AFEE8BD42DC70CB@EXCHANGE.plantsciences.ucdavis.edu>
Message-ID: <44E0BE11.1020603@acoma.stanford.edu>

Hi Kent,

1. Thanks for the list of terms. After brief look, I noticed that most 
terms are attributes of plant parts (i.e., entities or terms in the 
Plant Structure Ontology, abbreviated as PSO). However, PSO doesn?t 
include attributes or experimental conditions. Attribute (and value) 
terms are part of the Phenotype and Attribute ontology, PATO (URL: 
http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value). This 
ontology is generic and is meant to be sufficient for phenotype 
description across kingdoms. It is currently maintained by curators from 
M. Ashburner?s group, contact person is George Gkoutos, 
e-mail:g.gkoutos at imperial.ac.uk.

2. There are some Compositeae terms on your list that we don?t have in 
PSO yet, I?ll pass the list to the curator at Gramene (Pankaj Jaiswal). 
After August 31, someone from their group will coordinate the Plant 
Ontology project.

3. Also, POC ontology developers will discuss terms that I marked with 
red font in the attached document on our August phone conference.

4. A couple of terms on your list are already in the PSO (phyllary, 
PO:0009045, and leaf margin, PO:0020128).

5. Terms that include stages based on days after germination, flowering 
or similar, are intentionally excluded from PO. Best you can do is to 
replace them with terms (stages) in PO based on morphological features 
of the organ/plant at a particular time point depicted by counting days.

6. Regarding phenotype descriptions, TAIR, Gramene and MaizeGDB use PSO 
terms and free text description for describing mutant phenotypes. At 
TAIR, we have had a pilot project to test the description of phenotypes 
using several ontologies (PO, GO, PATO and perhaps some others). Also, 
NASC has already started using PATO (although it is not on their web 
site yet either). I can perhaps get some example from them too.

Here is an example from TAIR pilot project, an early attempt to use PATO 
terms (although they were not entered with term IDs, as some terms are 
not yet added in PATO.
Note, this is not yet displayed on TAIR web site, and is just a first 
trial. Also, please note that this is a description from published 
literature.

AN EXAMPLE of a description of mutant phenotype at TAIR, using Entity, 
Attribute and Value model (EAV):

grmplasm CS6130, allele abi3-4, locus AT3G24650, pub ref ID 5348,

Description: Abscisic acid resistant, strong allele, reduced sensitivity 
to ABA inhibition of germination, germination of seeds only slightly 
inhibited by 1mM ABA; normal plant growth; seeds fail to degrade 
chlorophyll during maturation keeping seeds green until mature.

Controlled vocabulary description:
Seed coat (PO:0009088) entity: color (attribute):green (value)
Seed maturation stage (PO:0007632): altered
Acquisition of desiccation tolerance (GO:0048700): reduced


Hope this helps. I'll get back to you after discussing this issue with 
the POC ontology group.

Best regards,

Katica

KENT BRADFORD wrote:
> Katica:
> 
> Thank you for your reply. I miss messages myself these days due to spam
> filters. 
> 
> I have worked on our character lists today, and have developed a draft
> of how we might enter our data under your PO terms. The attached
> spreadsheet has a page with all of the phenotypic characters we have (or
> expect to have) data for, and the second sheet is a rough effort by me
> to slot those characters under your existing terms, or indicate where it
> appears that new terms may be needed. Some terms can also be cross
> listed under other terms, and I have not tried to do that as yet. Am I
> on the right track with this? Thanks for your assistance.
> 
> Kent Bradford
> 
> -----Original Message-----
> From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] 
> Sent: Friday, August 11, 2006 4:08 PM
> To: po-dev at plantontology.org; KENT BRADFORD
> Subject: Re: FW: Compositae vocabulary
> 
> Dear Kent,
> 
> I apologize for inexcusable delay in responding to your messages to 
> po at plantontology.org. All your emails got caught in our spam filter. We 
> will certainly try to do our best to prevent this from happening again.
> 
> As Leszek already mentioned, it would help if you could send us the list
> 
> of the characteristics/characters that you have recorded. This would
> help 
> us understand the scope of the request. We would work together with you
> on 
> incorporating botanical terms specific for Compositae in the PSO. If an 
> extensive changes need to be done to PO to accommodate all updates, it 
> would probably take several rounds of dialogs, and may involve 
> taxonomists-experts for the Compositae family.
> 
> A good way to start is to learn more about phenotypic data that you have
> 
> and to review few examples of phenotype description, and also a list of 
> controlled vocabulary terms that you would like to see in the PO.
> 
> Best regards,
> 
> Katica Ilic, POC Project Coordinator
> 
> 
> On Fri, 11 Aug 2006, KENT BRADFORD wrote:
> 
>> I am trying the email that was published in Jaiswal et al (2005) in an
>> attempt to make contact regarding the questions below.
>> Kent Bradford
>>
>> _____________________________________________
>> From: KENT BRADFORD
>> Sent: Tuesday, August 01, 2006 2:10 PM
>> To: 'po at plantontology.org'
>> Subject: RE: Compositae vocabulary
>>
>> I am trying again to obtain a response from the plant ontology group.
>> Kent Bradford
>>
>> _____________________________________________
>> From: KENT BRADFORD
>> Sent: Monday, May 01, 2006 2:13 PM
>> To: 'po at plantontology.org'
>> Subject: RE: Compositae vocabulary
>>
>> I did not get any response to the message below. Is this address
> listed
>> on the Plant Ontology website viable?
>> Kent Bradford
>>
>> _____________________________________________
>> From: KENT BRADFORD
>> Sent: Tuesday, April 18, 2006 2:33 PM
>> To: 'po at plantontology.org'
>> Subject: Compositae vocabulary
>>
>> To Whom It May Concern:
>> I am a Co-PI on the Compositae Genome Project that has been developing
>> EST and mapping resources for the Compositae, primarily lettuce and
>> sunflower but now expanding into 15 additional species
>> (http://cgpdb.ucdavis.edu). As part of this project, we have also
>> collected extensive phenotypic data on several hundred accessions in
> the
>> Compositae. We are in the process of developing a database to compile
>> and store this data and make it accessible via our website. In
>> describing our phenotypic data, we would like to be compatible with
> your
>> controlled vocabularies in choosing our terms. However, you note on
> your
>> website that these vocabularies are not yet available for the
>> Compositae, and we have many types of data that I do not see in the
>> current descriptions, (e.g., specific leaf shapes, rosettes, presence
> of
>> trichomes, inflorescence branching patterns, etc.). I would appreciate
>> your advice on how we should proceed in a way that will remain
>> consistent the goals of the plant ontology project to allow broad and
>> consistent searching on controlled vocabularies. Is anyone working on
> a
>> list of terms for the Compositae that we could work from? I can send a
>> list of the characteristics that we have recorded if it would help.
>>
>> Sincerely,
>> Kent Bradford
>>
>> Kent J. Bradford
>> Professor
>> Department of Plant Sciences
>> Mail Stop 5
>> One Shields Ave.
>> University of California
>> Davis, CA 95616-8780
>> Phone: 1-530-752-6087
>> Fax: 1-530-754-7222
>> Email: kjbradford at ucdavis.edu
>>
>>
>>
>>
> 

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From lincoln.stein at gmail.com  Sat Aug 12 17:17:05 2006
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Sat, 12 Aug 2006 17:17:05 -0400
Subject: Compositae vocabulary
In-Reply-To: <70B0CAB623BFDA448F85DA2AFEE8BD42D1B8B2@EXCHANGE.plantsciences.ucdavis.edu>
References: <70B0CAB623BFDA448F85DA2AFEE8BD42D1B8B2@EXCHANGE.plantsciences.ucdavis.edu>
Message-ID: <6dce9a0b0608121417x39d4eb8ah322b234cefae53c4@mail.gmail.com>

Hello Kent,

We would be very happy to accept a list of terms for the Compositae. We will
need the name of each term, a brief definition of the term (following the
format in the existing ontology), and an indication of where in the ontology
the term should be placed.

Best,

Lincoln

On 8/1/06, KENT BRADFORD <kjbradford at ucdavis.edu> wrote:
>
>  I am trying again to obtain a response from the plant ontology group.
>
> Kent Bradford
>
> _____________________________________________
> ***From:* KENT BRADFORD
> ***Sent:* Monday, May 01, 2006 2:13 PM
> ***To:* 'po at plantontology.org'
> ***Subject:* RE: Compositae vocabulary
>
> I did not get any response to the message below. Is this address listed on
> the Plant Ontology website viable?
>
> Kent Bradford
>
> _____________________________________________
> ***From:* KENT BRADFORD
> ***Sent:* Tuesday, April 18, 2006 2:33 PM
> ***To:* 'po at plantontology.org'
> ***Subject:* Compositae vocabulary
>
> To Whom It May Concern:
>
> I am a Co-PI on the Compositae Genome Project that has been developing EST
> and mapping resources for the Compositae, primarily lettuce and sunflower
> but now expanding into 15 additional species (***http://cgpdb.ucdavis.edu*<http://cgpdb.ucdavis.edu>).
> As part of this project, we have also collected extensive phenotypic data
> on several hundred accessions in the Compositae. We are in the process of
> developing a database to compile and store this data and make it accessible
> via our website. In describing our phenotypic data, we would like to be
> compatible with your controlled vocabularies in choosing our terms. However,
> you note on your website that these vocabularies are not yet available for
> the Compositae, and we have many types of data that I do not see in the
> current descriptions, (e.g., specific leaf shapes, rosettes, presence of
> trichomes, inflorescence branching patterns, etc.). I would appreciate your
> advice on how we should proceed in a way that will remain consistent the
> goals of the plant ontology project to allow broad and consistent
> searching on controlled vocabularies. Is anyone working on a list of terms
> for the Compositae that we could work from? I can send a list of the
> characteristics that we have recorded if it would help.
>
> Sincerely,
>
> Kent Bradford
>
> Kent J. Bradford
>
> Professor
>
> Department of Plant Sciences
>
> Mail Stop 5
>
> One Shields Ave.
>
> University of California
>
> Davis, CA 95616-8780
>
> Phone: 1-530-752-6087
>
> Fax: 1-530-754-7222
>
> Email: kjbradford at ucdavis.edu
>
>


-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu
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From lincoln.stein at gmail.com  Sat Aug 12 17:17:05 2006
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Sat, 12 Aug 2006 17:17:05 -0400
Subject: Compositae vocabulary
In-Reply-To: <70B0CAB623BFDA448F85DA2AFEE8BD42D1B8B2@EXCHANGE.plantsciences.ucdavis.edu>
References: <70B0CAB623BFDA448F85DA2AFEE8BD42D1B8B2@EXCHANGE.plantsciences.ucdavis.edu>
Message-ID: <6dce9a0b0608121417x39d4eb8ah322b234cefae53c4@mail.gmail.com>

Hello Kent,

We would be very happy to accept a list of terms for the Compositae. We will
need the name of each term, a brief definition of the term (following the
format in the existing ontology), and an indication of where in the ontology
the term should be placed.

Best,

Lincoln

On 8/1/06, KENT BRADFORD <kjbradford at ucdavis.edu> wrote:
>
>  I am trying again to obtain a response from the plant ontology group.
>
> Kent Bradford
>
> _____________________________________________
> ***From:* KENT BRADFORD
> ***Sent:* Monday, May 01, 2006 2:13 PM
> ***To:* 'po at plantontology.org'
> ***Subject:* RE: Compositae vocabulary
>
> I did not get any response to the message below. Is this address listed on
> the Plant Ontology website viable?
>
> Kent Bradford
>
> _____________________________________________
> ***From:* KENT BRADFORD
> ***Sent:* Tuesday, April 18, 2006 2:33 PM
> ***To:* 'po at plantontology.org'
> ***Subject:* Compositae vocabulary
>
> To Whom It May Concern:
>
> I am a Co-PI on the Compositae Genome Project that has been developing EST
> and mapping resources for the Compositae, primarily lettuce and sunflower
> but now expanding into 15 additional species (***http://cgpdb.ucdavis.edu*<http://cgpdb.ucdavis.edu>).
> As part of this project, we have also collected extensive phenotypic data
> on several hundred accessions in the Compositae. We are in the process of
> developing a database to compile and store this data and make it accessible
> via our website. In describing our phenotypic data, we would like to be
> compatible with your controlled vocabularies in choosing our terms. However,
> you note on your website that these vocabularies are not yet available for
> the Compositae, and we have many types of data that I do not see in the
> current descriptions, (e.g., specific leaf shapes, rosettes, presence of
> trichomes, inflorescence branching patterns, etc.). I would appreciate your
> advice on how we should proceed in a way that will remain consistent the
> goals of the plant ontology project to allow broad and consistent
> searching on controlled vocabularies. Is anyone working on a list of terms
> for the Compositae that we could work from? I can send a list of the
> characteristics that we have recorded if it would help.
>
> Sincerely,
>
> Kent Bradford
>
> Kent J. Bradford
>
> Professor
>
> Department of Plant Sciences
>
> Mail Stop 5
>
> One Shields Ave.
>
> University of California
>
> Davis, CA 95616-8780
>
> Phone: 1-530-752-6087
>
> Fax: 1-530-754-7222
>
> Email: kjbradford at ucdavis.edu
>
>


-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu
-------------- next part --------------
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From kjbradford at ucdavis.edu  Fri Aug 11 21:02:58 2006
From: kjbradford at ucdavis.edu (KENT BRADFORD)
Date: Fri, 11 Aug 2006 18:02:58 -0700
Subject: FW: Compositae vocabulary
In-Reply-To: <Pine.LNX.4.62.0608111606590.15627@aztec.stanford.edu>
Message-ID: <70B0CAB623BFDA448F85DA2AFEE8BD42DC70CB@EXCHANGE.plantsciences.ucdavis.edu>

Katica:

Thank you for your reply. I miss messages myself these days due to spam
filters. 

I have worked on our character lists today, and have developed a draft
of how we might enter our data under your PO terms. The attached
spreadsheet has a page with all of the phenotypic characters we have (or
expect to have) data for, and the second sheet is a rough effort by me
to slot those characters under your existing terms, or indicate where it
appears that new terms may be needed. Some terms can also be cross
listed under other terms, and I have not tried to do that as yet. Am I
on the right track with this? Thanks for your assistance.

Kent Bradford

-----Original Message-----
From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] 
Sent: Friday, August 11, 2006 4:08 PM
To: po-dev at plantontology.org; KENT BRADFORD
Subject: Re: FW: Compositae vocabulary

Dear Kent,

I apologize for inexcusable delay in responding to your messages to 
po at plantontology.org. All your emails got caught in our spam filter. We 
will certainly try to do our best to prevent this from happening again.

As Leszek already mentioned, it would help if you could send us the list

of the characteristics/characters that you have recorded. This would
help 
us understand the scope of the request. We would work together with you
on 
incorporating botanical terms specific for Compositae in the PSO. If an 
extensive changes need to be done to PO to accommodate all updates, it 
would probably take several rounds of dialogs, and may involve 
taxonomists-experts for the Compositae family.

A good way to start is to learn more about phenotypic data that you have

and to review few examples of phenotype description, and also a list of 
controlled vocabulary terms that you would like to see in the PO.

Best regards,

Katica Ilic, POC Project Coordinator


On Fri, 11 Aug 2006, KENT BRADFORD wrote:

> I am trying the email that was published in Jaiswal et al (2005) in an
> attempt to make contact regarding the questions below.
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Tuesday, August 01, 2006 2:10 PM
> To: 'po at plantontology.org'
> Subject: RE: Compositae vocabulary
>
> I am trying again to obtain a response from the plant ontology group.
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Monday, May 01, 2006 2:13 PM
> To: 'po at plantontology.org'
> Subject: RE: Compositae vocabulary
>
> I did not get any response to the message below. Is this address
listed
> on the Plant Ontology website viable?
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Tuesday, April 18, 2006 2:33 PM
> To: 'po at plantontology.org'
> Subject: Compositae vocabulary
>
> To Whom It May Concern:
> I am a Co-PI on the Compositae Genome Project that has been developing
> EST and mapping resources for the Compositae, primarily lettuce and
> sunflower but now expanding into 15 additional species
> (http://cgpdb.ucdavis.edu). As part of this project, we have also
> collected extensive phenotypic data on several hundred accessions in
the
> Compositae. We are in the process of developing a database to compile
> and store this data and make it accessible via our website. In
> describing our phenotypic data, we would like to be compatible with
your
> controlled vocabularies in choosing our terms. However, you note on
your
> website that these vocabularies are not yet available for the
> Compositae, and we have many types of data that I do not see in the
> current descriptions, (e.g., specific leaf shapes, rosettes, presence
of
> trichomes, inflorescence branching patterns, etc.). I would appreciate
> your advice on how we should proceed in a way that will remain
> consistent the goals of the plant ontology project to allow broad and
> consistent searching on controlled vocabularies. Is anyone working on
a
> list of terms for the Compositae that we could work from? I can send a
> list of the characteristics that we have recorded if it would help.
>
> Sincerely,
> Kent Bradford
>
> Kent J. Bradford
> Professor
> Department of Plant Sciences
> Mail Stop 5
> One Shields Ave.
> University of California
> Davis, CA 95616-8780
> Phone: 1-530-752-6087
> Fax: 1-530-754-7222
> Email: kjbradford at ucdavis.edu
>
>
>
>

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

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From Leszek at missouri.edu  Mon Aug 14 17:23:09 2006
From: Leszek at missouri.edu (Vincent, Leszek)
Date: Mon, 14 Aug 2006 16:23:09 -0500
Subject: FW: Compositae vocabulary
In-Reply-To: <70B0CAB623BFDA448F85DA2AFEE8BD42DC70CB@EXCHANGE.plantsciences.ucdavis.edu>
Message-ID: <2BC371D49E5C86418135172EE7C130371D279E@UM-XMAIL08.um.umsystem.edu>

Hi Kent,

Thanks for the copy of your "Compositae phenotypes" file you sent on
Fri. - the one you've also shared with Katica. Following Katica's
feedback to you earlier today, I will also work with Katica on
addressing your needs so that we can provide you with a
consistent/unified response. My contribution will probably be mostly in
the area of terminology, because of my taxonomic expertise in the family
Asteraceae/Compositae, to which you appealed in one of your several
earlier communications which was 'swallowed' by an IT gremlin. 

We'll be in touch.

Sincerely,
Leszek Vincent

*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
P. Leszek D. Vincent Ph.D., FLS
Division of Plant Sciences
215 Curtis Hall
University of Missouri-Columbia
Columbia
MO 65211-7020
USA
Ph: (573) 884-3716; Skype VoIP: phytosynergy; Fax:(573) 884-7850;
Email: Leszek at missouri.edu
Associate Curator, Dunn-Palmer Herbarium (UMO);
Research Associate, Missouri Botanical Garden (MO), USA;
Plant Systematist on The Plant Ontology Consortium - NSF award 0321666 -
www.plantontology.org
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
 

-----Original Message-----
From: owner-po-dev at plantontology.org
[mailto:owner-po-dev at plantontology.org] On Behalf Of KENT BRADFORD
Sent: Friday, August 11, 2006 8:03 PM
To: katica at acoma.Stanford.EDU; po-dev at plantontology.org
Cc: Vincent, Leszek
Subject: RE: FW: Compositae vocabulary

Katica:

Thank you for your reply. I miss messages myself these days due to spam
filters. 

I have worked on our character lists today, and have developed a draft
of how we might enter our data under your PO terms. The attached
spreadsheet has a page with all of the phenotypic characters we have (or
expect to have) data for, and the second sheet is a rough effort by me
to slot those characters under your existing terms, or indicate where it
appears that new terms may be needed. Some terms can also be cross
listed under other terms, and I have not tried to do that as yet. Am I
on the right track with this? Thanks for your assistance.

Kent Bradford

-----Original Message-----
From: katica at acoma.stanford.edu [mailto:katica at acoma.stanford.edu] 
Sent: Friday, August 11, 2006 4:08 PM
To: po-dev at plantontology.org; KENT BRADFORD
Subject: Re: FW: Compositae vocabulary

Dear Kent,

I apologize for inexcusable delay in responding to your messages to 
po at plantontology.org. All your emails got caught in our spam filter. We 
will certainly try to do our best to prevent this from happening again.

As Leszek already mentioned, it would help if you could send us the list

of the characteristics/characters that you have recorded. This would
help 
us understand the scope of the request. We would work together with you
on 
incorporating botanical terms specific for Compositae in the PSO. If an 
extensive changes need to be done to PO to accommodate all updates, it 
would probably take several rounds of dialogs, and may involve 
taxonomists-experts for the Compositae family.

A good way to start is to learn more about phenotypic data that you have

and to review few examples of phenotype description, and also a list of 
controlled vocabulary terms that you would like to see in the PO.

Best regards,

Katica Ilic, POC Project Coordinator


On Fri, 11 Aug 2006, KENT BRADFORD wrote:

> I am trying the email that was published in Jaiswal et al (2005) in an
> attempt to make contact regarding the questions below.
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Tuesday, August 01, 2006 2:10 PM
> To: 'po at plantontology.org'
> Subject: RE: Compositae vocabulary
>
> I am trying again to obtain a response from the plant ontology group.
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Monday, May 01, 2006 2:13 PM
> To: 'po at plantontology.org'
> Subject: RE: Compositae vocabulary
>
> I did not get any response to the message below. Is this address
listed
> on the Plant Ontology website viable?
> Kent Bradford
>
> _____________________________________________
> From: KENT BRADFORD
> Sent: Tuesday, April 18, 2006 2:33 PM
> To: 'po at plantontology.org'
> Subject: Compositae vocabulary
>
> To Whom It May Concern:
> I am a Co-PI on the Compositae Genome Project that has been developing
> EST and mapping resources for the Compositae, primarily lettuce and
> sunflower but now expanding into 15 additional species
> (http://cgpdb.ucdavis.edu). As part of this project, we have also
> collected extensive phenotypic data on several hundred accessions in
the
> Compositae. We are in the process of developing a database to compile
> and store this data and make it accessible via our website. In
> describing our phenotypic data, we would like to be compatible with
your
> controlled vocabularies in choosing our terms. However, you note on
your
> website that these vocabularies are not yet available for the
> Compositae, and we have many types of data that I do not see in the
> current descriptions, (e.g., specific leaf shapes, rosettes, presence
of
> trichomes, inflorescence branching patterns, etc.). I would appreciate
> your advice on how we should proceed in a way that will remain
> consistent the goals of the plant ontology project to allow broad and
> consistent searching on controlled vocabularies. Is anyone working on
a
> list of terms for the Compositae that we could work from? I can send a
> list of the characteristics that we have recorded if it would help.
>
> Sincerely,
> Kent Bradford
>
> Kent J. Bradford
> Professor
> Department of Plant Sciences
> Mail Stop 5
> One Shields Ave.
> University of California
> Davis, CA 95616-8780
> Phone: 1-530-752-6087
> Fax: 1-530-754-7222
> Email: kjbradford at ucdavis.edu
>
>
>
>

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




From pj37 at cornell.edu  Thu Aug 17 11:36:01 2006
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 17 Aug 2006 11:36:01 -0400
Subject: genes for grazing / harvesting wheat
In-Reply-To: <200608170241.k7H2fHnv002436@greengenes.cit.cornell.edu>
References: <200608170241.k7H2fHnv002436@greengenes.cit.cornell.edu>
Message-ID: <44E48CE1.5060300@cornell.edu>

Hi Liuling and Dave,

According to the scales developed for Triticeae by Zadoks and Haun in 
early 1970's  [Haun, J.R. 1973. Visual quantification of wheat 
development. Agron. J. 65: 116-119.] and [Zadoks, J.C., T.T. Chang, and 
C.F. Konzak. 1974. A decimal code for growth stages of cereals. Weed 
Res. 14: 415-421.] and those mentioned on the site at 
http://www.usask.ca/agriculture/plantsci/winter_cereals/Winter_wheat/CHAPT10/cvchpt10.php 
the actual reproductive stage (the very initiation and differentiation 
of the inflorescence starts way too early. Spikelet development on the 
microscopic head is usually completed by the time the first node is 0.4 
inches (1 cm) above the soil surface. The terminal spikelet is produced 
at about Zadoks stage 31. A rapid loss of younger, poorly developed 
tillers also normally starts at this stage 
(http://www.usask.ca/agriculture/plantsci/winter_cereals/Winter_wheat/CHAPT10/cvchpt10.php#stem).

Probably the stage you are looking for the hollow stem is somewhat in 
the range of Zadoks 15-18, Zadoks 34-36. These stages are overlapping. 
This needs confirmation.

  The booting stage is very late in that sense because by that time the 
boot is already swollen, the inflorescence is well developed and ready 
to exsert out for heading stage. Therefore you will have to determine 
the stages for a couple of the standard cultivars and germplasms in a 
couple of growth conditions to see the variability. As far as I know 
after this evaluation you will be able to predict the desired stage by 
taking into account the genotype and environmental effects. You will 
find similar studies by

McMaster GS, Wilhelm WW, Frank AB (2005) Developmental sequences for 
simulating crop phenology for water-limiting conditions. Australian 
Journal of Agricultural Research 56: 1277-1288

Skiw PEJ, Jame YW, Kryzanowski L (2001) Phenological development of 
spring barley in a short-season growing area. Agron. J 93: 370-379

In all due respect you can use either of the Zadoks, Feekes or Haun 
scales as well to map your stages.

Considering the Zadok scale 31 the corresponding stage defined by Plant 
Ontology is SE.01 one node or internode visible [PO:0007091]
http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0007091

For other Zadok scale search the Plant Ontology for terms using 'Zadok'. 
The scale is listed as a synonym where ever applicable. e.g.
http://www.plantontology.org/amigo/go.cgi?session_id=7417b1155827789&page=2&view=query&search_constraint=terms&depth=&query=zadok&action=query


Please let me know if you need more help. I will be happy to hear you 
feedback.

Pankaj
[Plant Ontology]

PS: The mail is copied to plant ontology mailing list at 
po-dev at plantontology.org

Dave Matthews wrote:

> Hi Liuling,
> 
> Thanks for this information!  This is the most unusual use of wheat I'd
> ever heard of.  Grazing from November thru February, then growing for grain.
> 
> Hi Mark,
> 
> I'm sure you know about this use.  And you know a lot about phenology things
> like dormancy and probably vernalization.  Any thoughts?  (You did say you
> owe me a favor.  8)
> 
> 
> I'm especially curious about the "hollow stem" stage.  Google
> (http://www.google.com/search?q=wheat+hollow+stem) says this is a
> crucial thing for grazing/grain purposes in Oklahoma and Texas.  I don't know
> how the hollow stem relates to the initiation of reproduction.  Evidently
> this means there are stems produced in the vegetative stage but they aren't
> hollow.  
> 
> We're trying to organize the growth stages of cereals into a coherent
> database, the Plant Ontology.  This database has nothing about hollow stem
> in it yet.  The closest thing (I think) is "booting"
> http://www.gramene.org/db/ontology/search_term?id=GRO:0007090
> 
> 
> Hi Pankaj,
> 
> Can you please look into whether this is significantly different and if so
> how to include in the PO?
> 
> regards,
> - Dave
> 
> 
> 
> Date: Wed, 16 Aug 2006 19:18:25 -0500
> From: "Yan, Liuling" <liuling.yan at okstate.edu>
> 
> Hi Dave,
> 
> Please find my answers followed your questions. Just try to satisfy your 
> curiosity. Also please provide your suggestions if you have. Thank you.
> 
> ________________________________
> 
> From: Dave Matthews [mailto:matthews at greengenes.cit.cornell.edu]
> Sent: Tue 8/15/2006 8:22 PM
> To: Yan, Liuling
> Subject: re: Post for a PhD
> 
> Hi Liuling,
> 
> 
>>This advertisement says,
>>
>>  Wheat cultivars in the southern Great Plains are used for dual purpose
>>  production of forage and grain, which require a longer vegetative phase for
>>  grazing of livestock.
>>
>>Interesting.  I'd never heard of this.  When is the grazing?  Winter and
>>early spring? 
> 
> 
> We usually start to plant seeds from September, or as early as possible, 
> in order to have more vegetative tissues before winter, but it cannot be 
> earlier than September because of lack of rainfall.  Cattles are brought 
> to wheat field from November when plants have a lot of tissues to feed 
> the cattles. The cattles will be taken away from the field just before 
> 1st of March.
> 
> 
>>When is the reproductive phase desired to begin?
>>Is the reproductive phase called "booting"?  (Yes I've still got a lot to
>>learn about wheat.)
> 
> 
> A cretirion for the wheat development is that the first hollow stem 
> don't elongate before 1st of March; otherwise the cattles could eat the 
> wheat heads. Based on this cretirion, I am thinking that we should 
> select strong winter varieties that have more vernalization requiremnt 
> and do not entry "the reproductive phase" (or the first hollow stem 
> never elongate before 1st March). In other word, such varieties would 
> have a longer vegetative phase and produce more biomass for the cattles. 
> 
> 
> One of the objectives in my project will be to map genes that control 
> vernalization duration. Two parental lines (Jagger and 2174) for the CAP 
> population in Oklahoma have shown different vernalization requirements: 
> three weeks of vernalization significantly accelerating apex development 
> transition for Jagger and significant vernalization effects could be 
> observed only after six weeks of vernalization treatment for 2174.
> 
> Best regards
> 
> Liuling
> 
> 


-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683



From pj37 at cornell.edu  Mon Aug 21 11:36:05 2006
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 21 Aug 2006 11:36:05 -0400
Subject: [Fwd: RE: genes for grazing / harvesting wheat]
Message-ID: <44E9D2E5.3040601@cornell.edu>

This a forwarded message from Yan Liuling with reference to a previous 
enquiry on hollow stem stage in winter wheat.

-Pankaj

-------- Original Message --------
Subject: 	RE: genes for grazing / harvesting wheat
Date: 	Sat, 19 Aug 2006 22:09:54 -0500
From: 	Yan, Liuling <liuling.yan at okstate.edu>
To: 	Pankaj Jaiswal <pj37 at cornell.edu>, Dave Matthews
<matthews at greengenes.cit.cornell.edu>
References: 	<200608170241.k7H2fHnv002436 at greengenes.cit.cornell.edu>
<44E48CE1.5060300 at cornell.edu>



Hi Pankaj (cc: Dave),

Thank you very much for so much information and elaboration on it. When
we talk about vernalization, we always use heading time or flowering
time as outcome of vernalization. But in this particular case I need to
use the elongation stage of the first hollow stem as a creterion . In
practice, all winter varieties have a similar flowering time, no matter
how much vernalization they require, but they have signifcant
differences in reaching the elongation stage of the first hollow stem
particularly in a warm winter season. Therefore differences in earlier
developmental stages should explain vernalization effects much better
than heading or flowering itme. In Oklahoma, when the lenght of the
first hollow stem is longer than 2cM, the stem is considered detectable,
which is a signal that cattles need to take away from the field.
Compared with Zadoks scale it should be 31. This is what I can explain
right now.

Thank you again and have a nice weekend.

Liuling


------------------------------------------------------------------------
From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
Sent: Thu 8/17/2006 10:36 AM
To: Dave Matthews; Yan, Liuling
Cc: Mark Sorrells; POC-dev
Subject: Re: genes for grazing / harvesting wheat

Hi Liuling and Dave,

According to the scales developed for Triticeae by Zadoks and Haun in
early 1970's  [Haun, J.R. 1973. Visual quantification of wheat
development. Agron. J. 65: 116-119.] and [Zadoks, J.C., T.T. Chang, and
C.F. Konzak. 1974. A decimal code for growth stages of cereals. Weed
Res. 14: 415-421.] and those mentioned on the site at
http://www.usask.ca/agriculture/plantsci/winter_cereals/Winter_wheat/CHAPT10/cvchpt10.php
the actual reproductive stage (the very initiation and differentiation
of the inflorescence starts way too early. Spikelet development on the
microscopic head is usually completed by the time the first node is 0.4
inches (1 cm) above the soil surface. The terminal spikelet is produced
at about Zadoks stage 31. A rapid loss of younger, poorly developed
tillers also normally starts at this stage
(http://www.usask.ca/agriculture/plantsci/winter_cereals/Winter_wheat/CHAPT10/cvchpt10.php#stem).

Probably the stage you are looking for the hollow stem is somewhat in
the range of Zadoks 15-18, Zadoks 34-36. These stages are overlapping.
This needs confirmation.

   The booting stage is very late in that sense because by that time the
boot is already swollen, the inflorescence is well developed and ready
to exsert out for heading stage. Therefore you will have to determine
the stages for a couple of the standard cultivars and germplasms in a
couple of growth conditions to see the variability. As far as I know
after this evaluation you will be able to predict the desired stage by
taking into account the genotype and environmental effects. You will
find similar studies by

McMaster GS, Wilhelm WW, Frank AB (2005) Developmental sequences for
simulating crop phenology for water-limiting conditions. Australian
Journal of Agricultural Research 56: 1277-1288

Skiw PEJ, Jame YW, Kryzanowski L (2001) Phenological development of
spring barley in a short-season growing area. Agron. J 93: 370-379

In all due respect you can use either of the Zadoks, Feekes or Haun
scales as well to map your stages.

Considering the Zadok scale 31 the corresponding stage defined by Plant
Ontology is SE.01 one node or internode visible [PO:0007091]
http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0007091 

<http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0007091>

For other Zadok scale search the Plant Ontology for terms using 'Zadok'.
The scale is listed as a synonym where ever applicable. e.g.
http://www.plantontology.org/amigo/go.cgi?session_id=7417b1155827789&page=2&view=query&search_constraint=terms&depth=&query=zadok&action=query 

<http://www.plantontology.org/amigo/go.cgi?session_id=7417b1155827789&page=2&view=query&search_constraint=terms&depth=&query=zadok&action=query>


Please let me know if you need more help. I will be happy to hear you
feedback.

Pankaj
[Plant Ontology]




From katica at acoma.Stanford.EDU  Fri Aug 25 20:37:45 2006
From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU)
Date: Fri, 25 Aug 2006 17:37:45 -0700 (PDT)
Subject: new ontolgy updates are in the cvs, anatomy.obo rev 1.29, temporal.obo
 1.28
In-Reply-To: <Pine.LNX.4.62.0608251322290.17837@aztec.stanford.edu>
References: <DA729DE4-322A-11DB-81F3-000393911D12@cshl.edu>
 <Pine.LNX.4.62.0608241713520.3330@aztec.stanford.edu>
 <Pine.LNX.4.62.0608241824440.3330@aztec.stanford.edu>
 <Pine.LNX.4.62.0608251322290.17837@aztec.stanford.edu>
Message-ID: <Pine.LNX.4.62.0608251729200.20025@aztec.stanford.edu>

Hi,

New ontology updates are in the POC cvs, the following changes have ben 
made:

po_temporal.obo file
- Renamed term 'A zygote' to 'A zygotic stage'

po_anatomy.obo file

1. Obsoleted following 13 subcellular terms and added a comment for 
each, referring to the corresponding GO subcellular term. Also, deleted 
old comments for some of terms (only one comment can be added)

PO:0020014 columella	GO:0043674
PO:0020009 ectexine	GO:0043669
PO:0020010 endexine	GO:0043671
PO:0020008 exine	GO:0043668
PO:0020016 foot layer	GO:0043670
PO:0020017 intine	GO:0043678
PO:0020011 nexine	GO:0043672
PO:0020059 pollen wall	GO:0043667
PO:0020015 sculpture element GO:0043675
PO:0020012 sexine	GO:0043673
PO:0020013 tectum	GO:0043676
PO:0020018 germination pore	GO:0043677
PO:0000024 filiform apparatus	GO:0043680

2. added new terms under initial cell, and also under root meristem:

'root initial cell' PO:0000059, synonym: root stem cell
def: Cell in the root apical meristem that by division gives rise to two 
cells one of which remains in the meristem, the other is added produces 
different root cells.

'root cortex-endodermis initial cell' PO:0000060, synonym: root 
cortex-endodermis stem cell
def: Cell that produces root cortex and endodermis. In direct contact with 
quiescent center.

'lateral root-cap-epidermal initial' PO:0000061, synonym: lateral root 
cap-epidermal stem cell
Def: Cell that produces lateral root-cap cells and root epidermis.

3. Added four new terms under 'shoot' node:

'bud' PO:0000055; def: Undeveloped shoot

'floral bud'  PO:0000056, def: Bud that develops into a flower.

'inflorescence bud' PO:0000057, def: Bud that develops into an 
inflorescence.

'vegetative bud' PO:0000058, def: Bud that develops into a long or short 
shoot.

4. new term added: petal vascular system, PO:0000054. def: Vascular system 
of the petal.

5. Added 'meiocyte' as a synonym of the term 'sporocyte'.

Best regards,

Katica

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



From katica at acoma.Stanford.EDU  Fri Aug 25 20:51:28 2006
From: katica at acoma.Stanford.EDU (katica at acoma.Stanford.EDU)
Date: Fri, 25 Aug 2006 17:51:28 -0700 (PDT)
Subject: Feedback on POC
In-Reply-To: <200607271817.k6RIHBSV001790@filetta.cshl.org>
References: <200607271817.k6RIHBSV001790@filetta.cshl.org>
Message-ID: <Pine.LNX.4.62.0608251747070.20025@aztec.stanford.edu>


Hi Juliette,

I updated Plant Structure Ontology earlier today, adding terms you 
requested in July:

'root initial cell' PO:0000059, synonym: root stem cell

'root cortex-endodermis initial cell' PO:0000060, synonym: root 
cortex-endodermis stem cell

'lateral root-cap-epidermal initial' PO:0000061, synonym: lateral root 
cap-epidermal stem cell

It will take a week or so to see these updates on the POC web site.

Let us know if there are other terms you would like to see in the PO.

Best regards,

Katica



On Thu, 27 Jul 2006 feedback_submission at filetta.cshl.edu wrote:

>    *** Feedback from Plant Ontology Live Site ***
>
> refer_to_url: http://www.plantontology.org/index.html
>
> comments: Hello,
>
> I asked this question earlier but I might have mistaken your answer for spam. I am looking for terms describing the endodermis/cortex initial and its daughter cells, are there any, if not will you make some?
>
> Thank you,
>
> Juliette
>
> name: Juliette Colinas
>
> email: jhc16 at duke.edu
>
> organization: Duke University/ Benfey lab
>
> send_feedback: Send your feedback
>

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