From pj37 at cornell.edu  Fri Sep  8 10:53:44 2006
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 08 Sep 2006 10:53:44 -0400
Subject: Fwd: Feedback on POC
In-Reply-To: <85FD1C03-21B2-464E-9502-59A5BBB43564@cshl.edu>
References: <200608042037.k74Kb36d005772@filetta.cshl.org> <85FD1C03-21B2-464E-9502-59A5BBB43564@cshl.edu>
Message-ID: <450183F8.4080003@cornell.edu>

The definition of "lodicule of ear floret PO:0006382" was updated, based 
on Mary's suggestions. The new definition is as follows. It will be 
updated in the website browser at next monthly release.

New definition:
In a Maize ear floret, one of two or three tiny scales or flaps of 
tissue, possibly representing reduced perianth segments."

Pankaj



Shuly Avraham wrote:

> 
> 
> Begin forwarded message:
> 
>> From: feedback_submission at filetta.cshl.edu 
>> <mailto:feedback_submission at filetta.cshl.edu>
>> Date: August 4, 2006 4:37:03 PM EDT
>> To: Shuly Avraham <shuly at cshl.edu <mailto: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 <mailto:SchaefferM at missouri.edu>
>>
>> organization: 
>>
>> send_feedback: Send your feedback
>>
> 


-- 
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 shuly at cshl.edu  Mon Sep 11 18:33:31 2006
From: shuly at cshl.edu (Shuly Avraham)
Date: Mon, 11 Sep 2006 18:33:31 -0400
Subject: Fwd: Feedback on POC
Message-ID: <8D4214C7-41E5-11DB-8DC0-000393911D12@cshl.edu>



Begin forwarded message:

> From: feedback_submission at filetta.cshl.edu
> Date: September 11, 2006 6:30:56 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: Three terms, petal, sepal, stamen primordium visible in 
> Growh stages are mispelled, primordum is missing 'i'.
>
> name: Katica Ilic
>
> email: katica at acoma.stanford.edu
>
> organization: TAIR
>
> send_feedback: Send your feedback
>
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From kellogge at msx.umsl.edu  Tue Sep 12 10:51:13 2006
From: kellogge at msx.umsl.edu (kellogge)
Date: Tue, 12 Sep 2006 09:51:13 -0500
Subject: [Fwd: RE: genes for grazing / harvesting wheat]
In-Reply-To: <44E9D2E5.3040601@cornell.edu>
References: <44E9D2E5.3040601@cornell.edu>
Message-ID: <2ccd3f24a63018cfeed76901b86eac77@msx.umsl.edu>

Liuling is correct that the stage does fit well into any of the PO  
development categories.  The pooid grasses develop in a way that is  
rather different from that of other grasses, in that the meristem is  
kept just about at ground level for quite a while.  As Pankaj notes,  
this is probably about SE.00 or SE.01, in terms of stem elongation, but  
has no counterpart under "reproductive growth" because the  
inflorescence is certainly not visible except by really careful  
dissection.
Toby

On Aug 21, 2006, at 10:36 AM, Pankaj Jaiswal wrote:

> 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&qu 
> ery=PO:0007091
> <http://www.plantontology.org/amigo/go.cgi? 
> view=details&show_associations=terms&search_constraint=terms&depth=0&qu 
> ery=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&de 
> pth=&query=zadok&action=query
> <http://www.plantontology.org/amigo/go.cgi? 
> session_id=7417b1155827789&page=2&view=query&search_constraint=terms&de 
> pth=&query=zadok&action=query>
>
>
> Please let me know if you need more help. I will be happy to hear you
> feedback.
>
> Pankaj
> [Plant Ontology]
>
>
>
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/



From pj37 at cornell.edu  Fri Sep 15 13:54:37 2006
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 15 Sep 2006 13:54:37 -0400
Subject: Fwd: Feedback on POC [primordium spelling]
In-Reply-To: <8D4214C7-41E5-11DB-8DC0-000393911D12@cshl.edu>
References: <8D4214C7-41E5-11DB-8DC0-000393911D12@cshl.edu>
Message-ID: <450AE8DD.7060409@cornell.edu>

Fixed the spelling of  petal, sepal, stamen primordium. Primordium was 
misspelled.

The new version 1.30 of po_temporal.obo is available via CVS. The same 
will be updated in the ontology browser in the upcoming database release.

Pankaj

> Begin forwarded message:
> 
>     From: feedback_submission at filetta.cshl.edu
>     Date: September 11, 2006 6:30:56 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: Three terms, petal, sepal, stamen primordium visible in
>     Growh stages are mispelled, primordum is missing 'i'.
> 
>     name: Katica Ilic
> 
>     email: katica at acoma.stanford.edu
> 
>     organization: TAIR
> 
>     send_feedback: Send your feedback
> 



From shuly at cshl.edu  Tue Sep 26 08:53:06 2006
From: shuly at cshl.edu (Shuly Avraham)
Date: Tue, 26 Sep 2006 08:53:06 -0400
Subject: Fwd: Feedback on POC
Message-ID: <F465E7D8-4D5D-11DB-9B2F-000393911D12@cshl.edu>



Begin forwarded message:

> From: feedback_submission at filetta.cshl.edu
> Date: September 26, 2006 8:03:08 AM 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: Dear PO team,
>
>
> First of all I would like to thank you for excellent plant resource. I 
> found it useful and decided to have it in the house. Unfortunately I 
> had problem to connect gene products (symbols) from the table 
> ?gene_products? to ncbi pubmed paper ids, it should come from the 
> table ?dbxref?? The same as in the final result of your entries and a 
> category called ?Gene Product Associations to Term and its Children? 
> column ?Reference?. Please note that I am using the provided on the 
> web site MySql dump and I am using all the provided tables and 
> provided corresponding data.
>
> Thank you in advance, and wish you favorable working day
> GG
>
>
> name: georgi georgiev
>
> email: ggeca at bas.bg
>
> organization: bulgarian academy of science
>
> send_feedback: Send your feedback
>
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From shuly at cshl.edu  Tue Sep 26 09:08:29 2006
From: shuly at cshl.edu (Shuly Avraham)
Date: Tue, 26 Sep 2006 09:08:29 -0400
Subject: Feedback on POC
In-Reply-To: <200609261203.k8QC38Jb002138@filetta.cshl.org>
References: <200609261203.k8QC38Jb002138@filetta.cshl.org>
Message-ID: <1AC1900A-4D60-11DB-9B2F-000393911D12@cshl.edu>

Dear Georgi,

Thank you for your feedback.

The references and dbxref URLs are not coming from the database, but  
from the software source code (this is the way it was originally  
implemented by the GO)
When you're using AmiGO to connect to the database, the module  
NameMunger.pm holds the URL for each database. We have customized the  
module for the PO purpose. If you would like I can send you our version  
of the code.

So, for the dbxrefs URLs, we are using these for each datasource symbol:

'tair'=>'TAIR',
'tair_id' => 'TAIR',
'gr' => 'Gramene',
'maizegdb' => 'MaizeGDB',
'nasc' => 'NASC',

"gro"=>"http://www.gramene.org/db/ontology/search_term?id=GRO:$acc_no",
"tair"=>"http://arabidopsis.org/servlets/TairObject? 
accession=Keyword:$acc_no",
"maizegdb"=>"http://www.maizegdb.org/cgi-bin/termrefs.cgi?id=$acc_no",
  "nasc"=>"http://arabidopsis.info/StockInfo?NASC_id=$acc_no",
   
"go"=>"http://www.godatabase.org/cgi-bin/amigo/go.cgi? 
view=details&search_constraint=terms&depth=0&query=$acc_no"

For the associations URLs:

  "gr"=>"http://www.gramene.org/db/genes/search_gene?acc=$acc_no",
"maizegdb"=>"http://www.maizegdb.org/cgi-bin/id_search.cgi?id=$acc_no",
"tair"=>"http://arabidopsis.org/servlets/TairObject?accession=$acc_no",
"nasc"=>"http://arabidopsis.info/StockInfo?NASC_id=$acc_no",

For the references URLs

"gr"=>"http://www.gramene.org/perl/pub_search?ref_id=$acc_no",
"gr_ref"=>"http://www.gramene.org/perl/pub_search?ref_id=$acc_no",
"tair"=>"http://arabidopsis.org/servlets/TairObject?accession=$acc_no",
"nasc"=>"http://arabidopsis.info/StockInfo?NASC_id=$acc_no",
"maizegdb"=>"http://www.maizegdb.org/cgi-bin/id_search.cgi?id=$acc_no",

I hope this helps.

Shuly.

On Sep 26, 2006, at 8:03 AM, feedback_submission at filetta.cshl.edu wrote:

>     *** Feedback from Plant Ontology Live Site ***
>
> refer_to_url: http://www.plantontology.org/index.html
>
> comments: Dear PO team,
>
>
> First of all I would like to thank you for excellent plant resource. I  
> found it useful and decided to have it in the house. Unfortunately I  
> had problem to connect gene products (symbols) from the table  
> ?gene_products? to ncbi pubmed paper ids, it should come from the  
> table ?dbxref?? The same as in the final result of your entries and a  
> category called ?Gene Product Associations to Term and its Children?  
> column ?Reference?. Please note that I am using the provided on the  
> web site MySql dump and I am using all the provided tables and  
> provided corresponding data.
>
> Thank you in advance, and wish you favorable working day
> GG
>
>
> name: georgi georgiev
>
> email: ggeca at bas.bg
>
> organization: bulgarian academy of science
>
> send_feedback: Send your feedback
>