From pj37 at cornell.edu  Thu Aug  1 15:11:51 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 01 Aug 2002 15:11:51 -0400
Subject: Important Plant Journals into PubMed--Attached
References: <Pine.GSO.4.44.0207310935040.24591-100000@acoma.Stanford.EDU>
Message-ID: <3D4987F7.9A33223C@cornell.edu>

Hi Sue,

Just now checked for the journals I suggested and figured out that

Journal name	In Gramene	In PubMed

Molecular plant-microbe interactions	33	33
Genes and Genetic Systems 	23	10
Bioscience, Biotechnology and Biochemistry 	73	65
Indian Journal of Experimental Biology	33	4 
Japanese Journal of Genetics	78	9
J Science in China Series C Life Sciences	21	1
Hereditas	8	8

are actually in PubMed but not all the back issues, though the new ones are in.
That's why you see the difference in numbers from what's in Gramene Vs in PubMed 


Some of the journals are listed in Pubmed but they do not carry all the
references. They have been listed in PubMed just because they came in as Xrefs
to some other paper.

Such as 

Jour. name 	total Pubmed records

Japanese Journal of Crop Science  1 
Photosynthetica  2
Journal of Plant Nutrition  16
Aust J Plant Physiol	4
Can J Bot	18
Crop Sci	83
JOURNAL OF PLANT PHYSIOLOGY	44
Photosynth Res	7
Physiological and molecular plant pathology	15
Phytopathology	185
Plant Cell Environ	86
Plant Soil	3
Plant Cell Rep	6
Plant Growth Regul	11
Plant Mol Biol Rep	01
Plant Physiol Biochem	23


I used http://locatorplus.gov/ to search for the journals that are in NLM and
PubMed. The last two columns in excel sheet show what's there in Gramene Vs the
corresponding in PubMed.

The updated list (excel) is attached.

Thanks
Pankaj


Sue Rhee wrote:
> 
> Pankaj
> 
> Thanks for the list. For the additional journals you added, I need more
> information. 1. Are they in the NLM database? (search through Journal
> Browser, http://www.ncbi.nlm.nih.gov:80/entrez/jrbrowser.cgi). 2. For
> those that are in the NLM database, how many rice articles PubMed
> currently contains. It looks like some of the journals you added are
> already handled by PubMed.
> 
> Cheers,
> Sue
> 
> rice genetics newsletter
> japanese journal of breeding
> breeding science
> plant breeding
> International Rice Research Notes
> Photosynthetica
> Journal of Plant Nutrition
> Plant Pathology
> Euphytica
> Journal of Bioscience and Bioengineering
> Memoirs of the Faculty of Agriculture, Hokkaido University
> Genes and Genetic Systems
> Zeitschrift fuer Naturforschung
> Japanese Journal of Crop Science
> Chinese Journal of Rice Science
> Biochemical Genetics
> Biologia Plantarum Prague
> Bioscience, Biotechnology and Biochemistry
> CRRN, Chinese Rice Research Newsletter
> Hereditas Landskrona
> Hereditas
> Indian Journal of Agricultural Sciences
> Indian Journal of Biochemistry and Biophysics
> Indian Journal of Experimental Biology
> Indian Journal of Genetics and Plant Breeding
> Indian Journal of Plant Physiology
> International Rice Research Newsletter
> Japanese Journal of Genetics
> JARQ, Japan Agricultural Research Quarterly
> Molecular plant-microbe interactions :  MPMI
> Oryza
> Pakistan Journal of Agricultural Research
> Science in China Series C Life Sciences
> 
> On Wed, 31 Jul 2002, Pankaj Jaiswal wrote:
> 
> > Dear Sue,
> >
> > We have gone through the list of journals you provided. Based on it and one from
> > PubMed, we have added a few more to the list (marked in red) and updated the
> > numbers from Gramene. I hope this will help in mobolizing the PubMed to cover a
> > variety of plant journals.
> >
> > The updated list is attached both in excel and tab delimited file format
> >
> > Best
> > Pankaj
> >
> > Susan McCouch wrote:
> > >
> > > Sue,
> > >
> > > We will look at the list you sent and get back to you shortly with
> > > any additional journals of interest to Gramene.  It's a great idea to
> > > go forward together on this and it sure would make our jobs easier.
> > >
> > > Best,
> > > Susan
> > >
> > > >Thanks Ed!
> > > >
> > > >I think backfilling would be harder than future additions, but it seems
> > > >like this is a reasonable number of new journals to support. I hope we can
> > > >get them all in. I will wait until Friday to see if there are any
> > > >more feedback from others to send the list to NCBI.
> > > >
> > > >Cheers,
> > > >Sue
> > > >
> > > >
> > > >On Mon, 29 Jul 2002, Ed Coe wrote:
> > > >
> > > >>  Updated list attached, ...29jul02.
> > > >>  The tallies for MaizeDB sometimes extend back as far as 1900.
> > > >>  If most or all of these journals can be covered in PubMed, we will be
> > > >>  greatly aided!!!
> > > >>  Ed
> > > >>
> > > >
> 
> -----------------------------------------------------------------------------
> Sue Rhee                                rhee at acoma.stanford.edu
> The Arabidopsis Information Resource    URL: www.arabidopsis.org
> Carnegie Institution of Washington      FAX: +1-650-325-6857
> Department of Plant Biology             Tel: +1-650-325-1521 ext. 251
> 260 Panama St.
> Stanford, CA 94305
> U.S.A.
> -----------------------------------------------------------------------------

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************
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From pj37 at cornell.edu  Fri Aug  2 09:47:38 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 02 Aug 2002 09:47:38 -0400
Subject: Swissprot/Trembl Rice Proteins Database?
References: <Pine.GSO.4.44.0207311033400.8159-100000@nature.Berkeley.EDU>
Message-ID: <3D4A8D7A.541D3B60@cornell.edu>

Dear Shibo,

Gramene makes a major release every quarter. Last time we did an update was on
April 29th 2002, release 5.0 of Gramene. The new release is due and will be
available shortly. We expect to have all the publicly available  entries in the
new release, though we tend to present only those that have been annotated by
the contributor (original author of the sequence data).

Sincerely

Pankaj
www.gramene.org

Shibo Zhang wrote:
> 
> Dear Gramene,
> 
> I have a question regarding the rice protein db used in your blast page.
> 
> How often is updated? It has covered >95% rice protein sequences in public
> sector? The TIGR rice protein DB covered more than this rice DB?
> 
> Thank you in advance,
> 
> regards,
> 
> Shibo

--


From rhee at acoma.Stanford.EDU  Thu Aug  1 20:32:31 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Thu, 1 Aug 2002 17:32:31 -0700 (PDT)
Subject: Important Plant Journals into PubMed--Attached
In-Reply-To: <3D4987F7.9A33223C@cornell.edu>
Message-ID: <Pine.GSO.4.44.0208011732270.984-100000@acoma.Stanford.EDU>

Thanks,
Sue

On Thu, 1 Aug 2002, Pankaj Jaiswal wrote:

> Hi Sue,
>
> Just now checked for the journals I suggested and figured out that
>
> Journal name	In Gramene	In PubMed
>
> Molecular plant-microbe interactions	33	33
> Genes and Genetic Systems 	23	10
> Bioscience, Biotechnology and Biochemistry 	73	65
> Indian Journal of Experimental Biology	33	4
> Japanese Journal of Genetics	78	9
> J Science in China Series C Life Sciences	21	1
> Hereditas	8	8
>
> are actually in PubMed but not all the back issues, though the new ones are in.
> That's why you see the difference in numbers from what's in Gramene Vs in PubMed
>
>
> Some of the journals are listed in Pubmed but they do not carry all the
> references. They have been listed in PubMed just because they came in as Xrefs
> to some other paper.
>
> Such as
>
> Jour. name 	total Pubmed records
>
> Japanese Journal of Crop Science  1
> Photosynthetica  2
> Journal of Plant Nutrition  16
> Aust J Plant Physiol	4
> Can J Bot	18
> Crop Sci	83
> JOURNAL OF PLANT PHYSIOLOGY	44
> Photosynth Res	7
> Physiological and molecular plant pathology	15
> Phytopathology	185
> Plant Cell Environ	86
> Plant Soil	3
> Plant Cell Rep	6
> Plant Growth Regul	11
> Plant Mol Biol Rep	01
> Plant Physiol Biochem	23
>
>
> I used http://locatorplus.gov/ to search for the journals that are in NLM and
> PubMed. The last two columns in excel sheet show what's there in Gramene Vs the
> corresponding in PubMed.
>
> The updated list (excel) is attached.
>
> Thanks
> Pankaj
>
>
> Sue Rhee wrote:
> >
> > Pankaj
> >
> > Thanks for the list. For the additional journals you added, I need more
> > information. 1. Are they in the NLM database? (search through Journal
> > Browser, http://www.ncbi.nlm.nih.gov:80/entrez/jrbrowser.cgi). 2. For
> > those that are in the NLM database, how many rice articles PubMed
> > currently contains. It looks like some of the journals you added are
> > already handled by PubMed.
> >
> > Cheers,
> > Sue
> >
> > rice genetics newsletter
> > japanese journal of breeding
> > breeding science
> > plant breeding
> > International Rice Research Notes
> > Photosynthetica
> > Journal of Plant Nutrition
> > Plant Pathology
> > Euphytica
> > Journal of Bioscience and Bioengineering
> > Memoirs of the Faculty of Agriculture, Hokkaido University
> > Genes and Genetic Systems
> > Zeitschrift fuer Naturforschung
> > Japanese Journal of Crop Science
> > Chinese Journal of Rice Science
> > Biochemical Genetics
> > Biologia Plantarum Prague
> > Bioscience, Biotechnology and Biochemistry
> > CRRN, Chinese Rice Research Newsletter
> > Hereditas Landskrona
> > Hereditas
> > Indian Journal of Agricultural Sciences
> > Indian Journal of Biochemistry and Biophysics
> > Indian Journal of Experimental Biology
> > Indian Journal of Genetics and Plant Breeding
> > Indian Journal of Plant Physiology
> > International Rice Research Newsletter
> > Japanese Journal of Genetics
> > JARQ, Japan Agricultural Research Quarterly
> > Molecular plant-microbe interactions :  MPMI
> > Oryza
> > Pakistan Journal of Agricultural Research
> > Science in China Series C Life Sciences
> >
> > On Wed, 31 Jul 2002, Pankaj Jaiswal wrote:
> >
> > > Dear Sue,
> > >
> > > We have gone through the list of journals you provided. Based on it and one from
> > > PubMed, we have added a few more to the list (marked in red) and updated the
> > > numbers from Gramene. I hope this will help in mobolizing the PubMed to cover a
> > > variety of plant journals.
> > >
> > > The updated list is attached both in excel and tab delimited file format
> > >
> > > Best
> > > Pankaj
> > >
> > > Susan McCouch wrote:
> > > >
> > > > Sue,
> > > >
> > > > We will look at the list you sent and get back to you shortly with
> > > > any additional journals of interest to Gramene.  It's a great idea to
> > > > go forward together on this and it sure would make our jobs easier.
> > > >
> > > > Best,
> > > > Susan
> > > >
> > > > >Thanks Ed!
> > > > >
> > > > >I think backfilling would be harder than future additions, but it seems
> > > > >like this is a reasonable number of new journals to support. I hope we can
> > > > >get them all in. I will wait until Friday to see if there are any
> > > > >more feedback from others to send the list to NCBI.
> > > > >
> > > > >Cheers,
> > > > >Sue
> > > > >
> > > > >
> > > > >On Mon, 29 Jul 2002, Ed Coe wrote:
> > > > >
> > > > >>  Updated list attached, ...29jul02.
> > > > >>  The tallies for MaizeDB sometimes extend back as far as 1900.
> > > > >>  If most or all of these journals can be covered in PubMed, we will be
> > > > >>  greatly aided!!!
> > > > >>  Ed
> > > > >>
> > > > >
> >
> > -----------------------------------------------------------------------------
> > Sue Rhee                                rhee at acoma.stanford.edu
> > The Arabidopsis Information Resource    URL: www.arabidopsis.org
> > Carnegie Institution of Washington      FAX: +1-650-325-6857
> > Department of Plant Biology             Tel: +1-650-325-1521 ext. 251
> > 260 Panama St.
> > Stanford, CA 94305
> > U.S.A.
> > -----------------------------------------------------------------------------
>
> --
>
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org
> ******************************************

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------



From shibo at nature.Berkeley.EDU  Fri Aug  2 12:29:21 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Fri, 2 Aug 2002 09:29:21 -0700 (PDT)
Subject: Swissprot/Trembl Rice Proteins Database?
In-Reply-To: <3D4A8D7A.541D3B60@cornell.edu>
Message-ID: <Pine.GSO.4.44.0208020928090.26636-100000@nature.Berkeley.EDU>

Dear Pankaj,

Thank you very much for this info. I am looking forward to the new
release.

Shibo


On Fri, 2 Aug 2002, Pankaj Jaiswal wrote:

> Dear Shibo,
>
> Gramene makes a major release every quarter. Last time we did an update was on
> April 29th 2002, release 5.0 of Gramene. The new release is due and will be
> available shortly. We expect to have all the publicly available  entries in the
> new release, though we tend to present only those that have been annotated by
> the contributor (original author of the sequence data).
>
> Sincerely
>
> Pankaj
> www.gramene.org
>
> Shibo Zhang wrote:
> >
> > Dear Gramene,
> >
> > I have a question regarding the rice protein db used in your blast page.
> >
> > How often is updated? It has covered >95% rice protein sequences in public
> > sector? The TIGR rice protein DB covered more than this rice DB?
> >
> > Thank you in advance,
> >
> > regards,
> >
> > Shibo
>
> --
>



From shibo at nature.Berkeley.EDU  Mon Aug  5 14:57:41 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Mon, 5 Aug 2002 11:57:41 -0700 (PDT)
Subject: robot
In-Reply-To: <200208051846.OAA22000@cshl.org>
Message-ID: <Pine.GSO.4.44.0208051149430.9176-100000@nature.Berkeley.EDU>

Hi, Steven,

I am runing a file to get the protein description from the id by
html-parser.

Should I downloaded all your data to my local server?
Any suggestion is appreciated.

I am sorry if anyting from me is making trouble to your server.

regards,


Shibo


On Mon, 5 Aug 2002, Steven Schmidt wrote:

> Hi,
>
> Someone at UC Berkeley
> (on 128.32.175.81)
> is doing a search on the gramene site every 5 seconds.
> For example:
> /perl/protein_search?word=GLN2_ORYSA
> /perl/protein_search?word=TBB2_ORYSA
> /perl/protein_search?word=TBA1_ORYSA
>
> Do you have an idea who this could be?
>
> If someone wants a lot of data, we can provide it in a more efficient and
> mutually  convenient way.
>
> -Steve
>
>
> --
> Steven Schmidt
> www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977
>



From schmidt at cshl.edu  Mon Aug  5 14:46:01 2002
From: schmidt at cshl.edu (Steven Schmidt)
Date: Mon, 5 Aug 2002 14:46:01 -0400
Subject: robot
Message-ID: <200208051846.OAA22000@cshl.org>

Hi,

Someone at UC Berkeley
(on 128.32.175.81)
is doing a search on the gramene site every 5 seconds.
For example:
/perl/protein_search?word=GLN2_ORYSA 
/perl/protein_search?word=TBB2_ORYSA 
/perl/protein_search?word=TBA1_ORYSA 

Do you have an idea who this could be?

If someone wants a lot of data, we can provide it in a more efficient and
mutually  convenient way.

-Steve


-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


From zhaow at cshl.edu  Mon Aug  5 15:50:38 2002
From: zhaow at cshl.edu (Wei Zhao)
Date: Mon, 5 Aug 2002 15:50:38 -0400 (EDT)
Subject: robot
In-Reply-To: <Pine.GSO.4.44.0208051149430.9176-100000@nature.Berkeley.EDU>
Message-ID: <Pine.GSO.4.05.10208051510120.23836-100000@phage.cshl.org>


Hi Shibo,

Please find the protein description dump at
ftp://www.gramene.org/pub/gramene/protein/Gramene_Protein_Desc.txt

Please let us know if you need other data/infomation.

Thank you for your interest in Gramene,

Wei

--
Wei Zhao
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


On Mon, 5 Aug 2002, Shibo Zhang wrote:

> Hi, Steven,
> 
> I am runing a file to get the protein description from the id by
> html-parser.
> 
> Should I downloaded all your data to my local server?
> Any suggestion is appreciated.
> 
> I am sorry if anyting from me is making trouble to your server.
> 
> regards,
> 
> 
> Shibo
> 
> 
> On Mon, 5 Aug 2002, Steven Schmidt wrote:
> 
> > Hi,
> >
> > Someone at UC Berkeley
> > (on 128.32.175.81)
> > is doing a search on the gramene site every 5 seconds.
> > For example:
> > /perl/protein_search?word=GLN2_ORYSA
> > /perl/protein_search?word=TBB2_ORYSA
> > /perl/protein_search?word=TBA1_ORYSA
> >
> > Do you have an idea who this could be?
> >
> > If someone wants a lot of data, we can provide it in a more efficient and
> > mutually  convenient way.
> >
> > -Steve
> >
> >
> > --
> > Steven Schmidt
> > www.gramene.org
> > Cold Spring Harbor Laboratory
> > 516-367-6977
> >
> 
> 






From pj37 at cornell.edu  Mon Aug  5 15:20:21 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 05 Aug 2002 15:20:21 -0400
Subject: robot
References: <Pine.GSO.4.44.0208051149430.9176-100000@nature.Berkeley.EDU>
Message-ID: <3D4ECFF5.81C3D1B3@cornell.edu>

Dear Shibo,

Please let us know the exactly what you are looking for and the purpose of your
batch query of Protein Db at Gramene. I hope we would be able to help you get
the necessary info in a rather more convenient way.


Thanks
Pankaj


Shibo Zhang wrote:
> 
> Hi, Steven,
> 
> I am runing a file to get the protein description from the id by
> html-parser.
> 
> Should I downloaded all your data to my local server?
> Any suggestion is appreciated.
> 
> I am sorry if anyting from me is making trouble to your server.
> 
> regards,
> 
> Shibo
> 
> On Mon, 5 Aug 2002, Steven Schmidt wrote:
> 
> > Hi,
> >
> > Someone at UC Berkeley
> > (on 128.32.175.81)
> > is doing a search on the gramene site every 5 seconds.
> > For example:
> > /perl/protein_search?word=GLN2_ORYSA
> > /perl/protein_search?word=TBB2_ORYSA
> > /perl/protein_search?word=TBA1_ORYSA
> >
> > Do you have an idea who this could be?
> >
> > If someone wants a lot of data, we can provide it in a more efficient and
> > mutually  convenient way.
> >
> > -Steve
> >
> >
> > --
> > Steven Schmidt
> > www.gramene.org
> > Cold Spring Harbor Laboratory
> > 516-367-6977
> >


From shibo at nature.Berkeley.EDU  Mon Aug  5 15:55:55 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Mon, 5 Aug 2002 12:55:55 -0700 (PDT)
Subject: robot
In-Reply-To: <Pine.GSO.4.05.10208051510120.23836-100000@phage.cshl.org>
Message-ID: <Pine.GSO.4.44.0208051252470.9176-100000@nature.Berkeley.EDU>

Hi, Wei,

Thank you and I will download this file. However, I would like to finish
my current job, before I do that.

It should be done very soon.

Sorry for any inconvenience.


Shibo


On Mon, 5 Aug 2002, Wei Zhao wrote:

>
> Hi Shibo,
>
> Please find the protein description dump at
> ftp://www.gramene.org/pub/gramene/protein/Gramene_Protein_Desc.txt
>
> Please let us know if you need other data/infomation.
>
> Thank you for your interest in Gramene,
>
> Wei
>
> --
> Wei Zhao
> www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977
>
>
> On Mon, 5 Aug 2002, Shibo Zhang wrote:
>
> > Hi, Steven,
> >
> > I am runing a file to get the protein description from the id by
> > html-parser.
> >
> > Should I downloaded all your data to my local server?
> > Any suggestion is appreciated.
> >
> > I am sorry if anyting from me is making trouble to your server.
> >
> > regards,
> >
> >
> > Shibo
> >
> >
> > On Mon, 5 Aug 2002, Steven Schmidt wrote:
> >
> > > Hi,
> > >
> > > Someone at UC Berkeley
> > > (on 128.32.175.81)
> > > is doing a search on the gramene site every 5 seconds.
> > > For example:
> > > /perl/protein_search?word=GLN2_ORYSA
> > > /perl/protein_search?word=TBB2_ORYSA
> > > /perl/protein_search?word=TBA1_ORYSA
> > >
> > > Do you have an idea who this could be?
> > >
> > > If someone wants a lot of data, we can provide it in a more efficient and
> > > mutually  convenient way.
> > >
> > > -Steve
> > >
> > >
> > > --
> > > Steven Schmidt
> > > www.gramene.org
> > > Cold Spring Harbor Laboratory
> > > 516-367-6977
> > >
> >
> >
>
>
>
>



From shibo at nature.Berkeley.EDU  Mon Aug  5 16:49:08 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Mon, 5 Aug 2002 13:49:08 -0700 (PDT)
Subject: robot
In-Reply-To: <Pine.GSO.4.44.0208051252470.9176-100000@nature.Berkeley.EDU>
Message-ID: <Pine.GSO.4.44.0208051340020.9176-100000@nature.Berkeley.EDU>

Hi, Wei,


As I said in my last message, I will not do it again I promise. However, I
really appreciate if let me finish my current job today.

I hope I have not been blocked from your side to run my file to get the
info just for today.

Thanks in advance,


Shibo


On Mon, 5 Aug 2002, Shibo Zhang wrote:

> Hi, Wei,
>
> Thank you and I will download this file. However, I would like to finish
> my current job, before I do that.
>
> It should be done very soon.
>
> Sorry for any inconvenience.
>
>
> Shibo
>
>
> On Mon, 5 Aug 2002, Wei Zhao wrote:
>
> >
> > Hi Shibo,
> >
> > Please find the protein description dump at
> > ftp://www.gramene.org/pub/gramene/protein/Gramene_Protein_Desc.txt
> >
> > Please let us know if you need other data/infomation.
> >
> > Thank you for your interest in Gramene,
> >
> > Wei
> >
> > --
> > Wei Zhao
> > www.gramene.org
> > Cold Spring Harbor Laboratory
> > 516-367-6977
> >
> >
> > On Mon, 5 Aug 2002, Shibo Zhang wrote:
> >
> > > Hi, Steven,
> > >
> > > I am runing a file to get the protein description from the id by
> > > html-parser.
> > >
> > > Should I downloaded all your data to my local server?
> > > Any suggestion is appreciated.
> > >
> > > I am sorry if anyting from me is making trouble to your server.
> > >
> > > regards,
> > >
> > >
> > > Shibo
> > >
> > >
> > > On Mon, 5 Aug 2002, Steven Schmidt wrote:
> > >
> > > > Hi,
> > > >
> > > > Someone at UC Berkeley
> > > > (on 128.32.175.81)
> > > > is doing a search on the gramene site every 5 seconds.
> > > > For example:
> > > > /perl/protein_search?word=GLN2_ORYSA
> > > > /perl/protein_search?word=TBB2_ORYSA
> > > > /perl/protein_search?word=TBA1_ORYSA
> > > >
> > > > Do you have an idea who this could be?
> > > >
> > > > If someone wants a lot of data, we can provide it in a more efficient and
> > > > mutually  convenient way.
> > > >
> > > > -Steve
> > > >
> > > >
> > > > --
> > > > Steven Schmidt
> > > > www.gramene.org
> > > > Cold Spring Harbor Laboratory
> > > > 516-367-6977
> > > >
> > >
> > >
> >
> >
> >
> >
>
>



From shibo at nature.Berkeley.EDU  Mon Aug  5 17:07:34 2002
From: shibo at nature.Berkeley.EDU (Shibo Zhang)
Date: Mon, 5 Aug 2002 14:07:34 -0700 (PDT)
Subject: robot
In-Reply-To: <Pine.GSO.4.44.0208051340020.9176-100000@nature.Berkeley.EDU>
Message-ID: <Pine.GSO.4.44.0208051404440.9176-100000@nature.Berkeley.EDU>

Thank you very much.

I really appreciated your help.


Shibo



On Mon, 5 Aug 2002, Shibo Zhang wrote:

> Hi, Wei,
>
>
> As I said in my last message, I will not do it again I promise. However, I
> really appreciate if let me finish my current job today.
>
> I hope I have not been blocked from your side to run my file to get the
> info just for today.
>
> Thanks in advance,
>
>
> Shibo
>
>
> On Mon, 5 Aug 2002, Shibo Zhang wrote:
>
> > Hi, Wei,
> >
> > Thank you and I will download this file. However, I would like to finish
> > my current job, before I do that.
> >
> > It should be done very soon.
> >
> > Sorry for any inconvenience.
> >
> >
> > Shibo
> >
> >
> > On Mon, 5 Aug 2002, Wei Zhao wrote:
> >
> > >
> > > Hi Shibo,
> > >
> > > Please find the protein description dump at
> > > ftp://www.gramene.org/pub/gramene/protein/Gramene_Protein_Desc.txt
> > >
> > > Please let us know if you need other data/infomation.
> > >
> > > Thank you for your interest in Gramene,
> > >
> > > Wei
> > >
> > > --
> > > Wei Zhao
> > > www.gramene.org
> > > Cold Spring Harbor Laboratory
> > > 516-367-6977
> > >
> > >
> > > On Mon, 5 Aug 2002, Shibo Zhang wrote:
> > >
> > > > Hi, Steven,
> > > >
> > > > I am runing a file to get the protein description from the id by
> > > > html-parser.
> > > >
> > > > Should I downloaded all your data to my local server?
> > > > Any suggestion is appreciated.
> > > >
> > > > I am sorry if anyting from me is making trouble to your server.
> > > >
> > > > regards,
> > > >
> > > >
> > > > Shibo
> > > >
> > > >
> > > > On Mon, 5 Aug 2002, Steven Schmidt wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Someone at UC Berkeley
> > > > > (on 128.32.175.81)
> > > > > is doing a search on the gramene site every 5 seconds.
> > > > > For example:
> > > > > /perl/protein_search?word=GLN2_ORYSA
> > > > > /perl/protein_search?word=TBB2_ORYSA
> > > > > /perl/protein_search?word=TBA1_ORYSA
> > > > >
> > > > > Do you have an idea who this could be?
> > > > >
> > > > > If someone wants a lot of data, we can provide it in a more efficient and
> > > > > mutually  convenient way.
> > > > >
> > > > > -Steve
> > > > >
> > > > >
> > > > > --
> > > > > Steven Schmidt
> > > > > www.gramene.org
> > > > > Cold Spring Harbor Laboratory
> > > > > 516-367-6977
> > > > >
> > > >
> > > >
> > >
> > >
> > >
> > >
> >
> >
>
>



From schmidt at cshl.edu  Mon Aug  5 16:59:32 2002
From: schmidt at cshl.edu (Steven Schmidt)
Date: Mon, 5 Aug 2002 16:59:32 -0400
Subject: robot (fwd)
In-Reply-To: <Pine.GSO.4.05.10208051656530.4665-100000@phage.cshl.org>
References: <Pine.GSO.4.05.10208051656530.4665-100000@phage.cshl.org>
Message-ID: <200208052059.QAA08926@cshl.org>

Hi Shibo,

I blocked you because your robot contributed to problems our site was having.
We've changed some parameters and expect it to be ok now.
You're unblocked.

-Steve



On Monday 05 August 2002 16:57, Wei Zhao wrote:
> ---------- Forwarded message ----------
> Date: Mon, 5 Aug 2002 13:49:08 -0700 (PDT)
> From: Shibo Zhang <shibo at nature.Berkeley.EDU>
> To: Wei Zhao <zhaow at cshl.edu>
> Cc: gramene at gramene.org
> Subject: Re: robot
>
> Hi, Wei,
>
>
> As I said in my last message, I will not do it again I promise. However, I
> really appreciate if let me finish my current job today.
>
> I hope I have not been blocked from your side to run my file to get the
> info just for today.
>
> Thanks in advance,
>
>
> Shibo
>
> On Mon, 5 Aug 2002, Shibo Zhang wrote:
> > Hi, Wei,
> >
> > Thank you and I will download this file. However, I would like to finish
> > my current job, before I do that.
> >
> > It should be done very soon.
> >
> > Sorry for any inconvenience.
> >
> >
> > Shibo
> >
> > On Mon, 5 Aug 2002, Wei Zhao wrote:
> > > Hi Shibo,
> > >
> > > Please find the protein description dump at
> > > ftp://www.gramene.org/pub/gramene/protein/Gramene_Protein_Desc.txt
> > >
> > > Please let us know if you need other data/infomation.
> > >
> > > Thank you for your interest in Gramene,
> > >
> > > Wei
> > >
> > > --
> > > Wei Zhao
> > > www.gramene.org
> > > Cold Spring Harbor Laboratory
> > > 516-367-6977
> > >
> > > On Mon, 5 Aug 2002, Shibo Zhang wrote:
> > > > Hi, Steven,
> > > >
> > > > I am runing a file to get the protein description from the id by
> > > > html-parser.
> > > >
> > > > Should I downloaded all your data to my local server?
> > > > Any suggestion is appreciated.
> > > >
> > > > I am sorry if anyting from me is making trouble to your server.
> > > >
> > > > regards,
> > > >
> > > >
> > > > Shibo
> > > >
> > > > On Mon, 5 Aug 2002, Steven Schmidt wrote:
> > > > > Hi,
> > > > >
> > > > > Someone at UC Berkeley
> > > > > (on 128.32.175.81)
> > > > > is doing a search on the gramene site every 5 seconds.
> > > > > For example:
> > > > > /perl/protein_search?word=GLN2_ORYSA
> > > > > /perl/protein_search?word=TBB2_ORYSA
> > > > > /perl/protein_search?word=TBA1_ORYSA
> > > > >
> > > > > Do you have an idea who this could be?
> > > > >
> > > > > If someone wants a lot of data, we can provide it in a more
> > > > > efficient and mutually  convenient way.
> > > > >
> > > > > -Steve
> > > > >
> > > > >
> > > > > --
> > > > > Steven Schmidt
> > > > > www.gramene.org
> > > > > Cold Spring Harbor Laboratory
> > > > > 516-367-6977

-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


From teytelma at cshl.edu  Tue Aug 13 12:19:20 2002
From: teytelma at cshl.edu (Lenny Teytelman)
Date: Tue, 13 Aug 2002 12:19:20 -0400 (EDT)
Subject: wheat ESTs
In-Reply-To: <3D72857C@webmail.ksu.edu>
Message-ID: <Pine.GSO.4.05.10208131201210.27405-100000@phage.cshl.org>

Dear Mike,

If the EST is from dbEST, you can find whether it has been positioned on
the rice genome by searching for the accession at:
	http://www.gramene.org/perl/SeqTable
Just enter the accession into the 'Lookup' field, and if the EST was
mapped, you will get back the clones and positions of the alignments.  You
may then follow the link to view the region in the Genome Browser.

If the EST is not part of dbEST, you can do a blast search using its
sequence against the rice genome or the dbEST library.  Just select 'Rice
IRGSP Clones' or 'Triticum Aestivum ESTs' in the 'Database' drop-down
menu at:
http://www.gramene.org/gramene/searches/blast
 
Another option is to simply download the list of the ESTs and the clones
to which they align from:
ftp://brie.cshl.org/pub/gramene/insilico_data/ESTs/

The 'final_triticum_est_bacs_052202.dat.gz' file contains all of the
results for the wheat EST alignments.  The fields in the file are:
        Internal_ID
	EST_Accession
        EST_Start
        EST_Stop
        Clone_ACC
        Clone_Version
        Clone_Start
        Clone_Stop
        Percent_Identity_of_match

Regards,

Lenny

PS  The 72,000 is the total number of alignments, but some ESTs can hit
two or three times.  The actual number of distinct wheat ESTs is 49,146.
Please see
http://www.gramene.org/documentation/EST/triticum_est_rice_genome.txt
for more information on the wheat alignments.


> Dear Lenny: 
> I?m an entomologist at Kansas State University leading a group of students & 
> post docs to map genes for aphid resistance in wheat.
> 
> I read in Grain Genes recently where you have identified homologies of 72,000 
> wheat ESTs to rice BAC/PACs from a set of 167,000 ESTs examined 20 June '02.
> 
> I have no bioinformatics training, but have acquired several wheat chromosome 
> 7DS ESTs from the USDA Lab in Albany, CA.  Although none are closely linked to 
> our genes of interest, we know where they fit into an overall emerging linkage 
> map, primarily on wheat chromosome 7.
> 
> My questions for you are: how do I locate a given EST in your list, and once I 
> find one, how do I match it with a given rice BAC/PCS?    Mike Smith
> 
> 
> 

-- 
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelman at cshl.org



From Phillip.Seeberg at nav-international.com  Wed Aug 14 15:08:02 2002
From: Phillip.Seeberg at nav-international.com (Seeberg, Phillip M (Phil))
Date: Wed, 14 Aug 2002 14:08:02 -0500
Subject: http://www.gramene.org/plant_ontology/suggestions.pdf
Message-ID: <8794C8184C54D511A9A900508BAC6CCF01C04B01@CANXSPN3.can.navistar.com>

If I may be so bold, I am interested in implementing a form that does what I
think your form (at http://www.gramene.org/plant_ontology/suggestions.pdf)
does. That is, when the user presses the button (that in your case reads
"Submit Ontology") I want to have the contents of the pdf form to be emailed
to someone.
If you would be so kind, can you show me the code behind that button?



Phillip Seeberg
CSO - Sr. Staff Specialist / System Development
International Truck and Engine Corporation
4201 Winfield Road
P.O. Box 1488
Warrenville, IL 60555

Phone: (630) 753-5425
Fax: (630) 753-5838
phillip.seeberg at nav-international.com




From pj37 at cornell.edu  Thu Aug 15 10:39:37 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 15 Aug 2002 10:39:37 -0400
Subject: HELP!: GO Term Error
References: <Pine.LNX.4.10.10208150918490.19623-100000@pigeon.ebi.ac.uk>
Message-ID: <3D5BBD29.38F98720@cornell.edu>

Well I disagree with Midori !
Reason at some point in an organism's life if one looks logically, each and
every one of the gene product can be called as a nutrient reserve in some form
or the other. All the proteins can be broken down in its components for example
into  peptides ->amino acids->C/H/N/O/P/S/. This is what actually happens when
an organism undergoes a situation where it becomes its necessity to survive by
recycling its own organization units i.e. at the time of "aging". Proteins is
just one example, same is true for nucleotides and carbohydrates and lipids.

Therefore I still feel that this term "storage protein of seed" should be
brought back. Another reason that these proteins in "Monocot plants" also have
an additional function of "serine protease inhibitor". There are several
instances of such proteins as Tanya already mentioned about them in her first
mail at the start of this debate.(cited below) 

http://www.geneontology.org/email/go-arc/go-2002/2028.html

"Midori: There are many different seed storage proteins: vicilin-type 
globulin, albumin, glutenin/gliadin, C hordein, etc. "

>From my perspective 'nutrient reserve' is a very broad term and we will mislead
the community by annotating any such term.

Pankaj


Midori Harris wrote:
> 
> Hi,
> 
> We will stick with 'nutrient reserve'. "Storage protein of seed" has
> exactly the same problems as "seed storage protein": 'seed' is a
> localization and 'protein' is a gene product, not an activity.
> 
> I'll put 'nutrient reserve' in the SourceForge list so we don't forget to
> actually add it.
> 
> Midori
> 
> On Wed, 14 Aug 2002, Suparna Mundodi wrote:
> 
> > Hi Midori,
> >
> > What has happened to the "seed storage protein" term. Recently there was a
> > request from Pankaj to include the "storage protein of seed" and I think
> > he makes a valid point here. Are we going to stick with the "nutreint
> > reserve" term or "Storage protein of seed"?
> >
> > I have attached Pankaj's email below.
> >
> > Suparna
> >
> >
> >
> > Date: Tue, 13 Aug 2002 16:11:02 -0400
> > From: Pankaj Jaiswal <pj37 at cornell.edu>
> > To: Tanya Berardini <tberardi at acoma.Stanford.EDU>
> > Subject: Re: seed storage protein
> >
> > Hi Tanya,
> >
> > I really did not know about this debate. Why can't we have a term instead
> > "storage protein of seed", just to convince the concept. Doesn't matter if
> > there
> > is a compartmentalization aspect here "anatomy term=seed".  If GO can have
> > fat
> > body/lipid storage body/protein storage vacuole(!!!), then this is a valid
> > reframed term that defines a function, that its a storage protein
> > providing
> > nutritional buffer to the embryo, when it undergoes germination.
> >
> > Now the situation is how should we annotate "alpha-globulin", the function
> > is
> > seed storage protein. The other model organisms don't have this seed
> > storage
> > protein example is
> > http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/blink?pid=1783206&tax=0&org=0&pdb=0&sort=1&cut=100&all=0
> >
> > there are 75 such entries from plants but none from others. I was even
> > going to
> > ask a new term request for "alpha-globulin", which is an instance of
> > storage
> > protein of seed by functional definition.
> > _________________________
> >
> > Same way GO has different terms for "response" "susceptibility" &
> > "resistance".
> > I think resistance and susceptibility is a score/attribute  of determining
> > the
> > level of "response". The "Response" is biological in origin but the
> > "resistance"
> > / "susceptible" are phenotype terms and one needs to avoid this. We have
> > had a
> > considerable discussion on this before when Leonore was there and she
> > reframed
> > the phenotypic terms to responses, but they have reappeared.
> >
> >
> > Pankaj
> >
> >
> >
> >
> >
> > On Wed, 31 Jul 2002, Midori Harris wrote:
> >
> > > Of course I like 'nutrient reserve' -- it was my idea. ;)
> > >
> > > If no one complains (and soon) we will put 'nutrient reserve' in, with a
> > > comment that it can be used for gene products formerly annotated to any of
> > > the 'storage protein' terms.
> > >
> > > Midori
> > >
> > > On Wed, 31 Jul 2002, Suparna Mundodi wrote:
> > >
> > > > Midori: If we are making "seed storage protein" obsolete, then have we
> > > > come to a consensus on the term this is going to replace "seed storage protein"
> > > > ? I vote on the use of "nutrient reserve" and "amino acid reserve" as you
> > > > suggested earlier.
> > > >
> > > > Suparna
> > > >
> > > >
> > > > On Mon, 29
> > > > Jul 2002, Tanya Berardini wrote:
> > > >
> > > > > Thanks for the note, Harold.
> > > > >
> > > > > Midori: There are many different seed storage proteins: vicilin-type
> > > > > globulin, albumin, glutenin/gliadin, C hordein, etc.
> > > > >
> > > > > Please bring back "seed storage protein" from the dead!!!  Oddly enough,
> > > > > the other term that I added the same day GO:0009914 is still alive
> > > > > and well.
> > > > >
> > > > > Advice on what to do??
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Tanya
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Mon, 29 Jul 2002, Midori Harris wrote:
> > > > >
> > > > > > sounds like it ought to be obsolete -- gene product-y
> > > > > >
> > > > > > m
> > > > > >
> > > > > > On Mon, 29 Jul 2002, Harold Drabkin wrote:
> > > > > >
> > > > > > > Thought someone in TAIR or GRAMANE would want to know:
> > > > > > >
> > > > > > > While we were doing our nightly load of GO, we noticed that
> > > > > > >
> > > > > > > GO:0009915 (seed storage protein) exists in current our GO vocabulary from
> > > > > > > the previous load,  but it is not in
> > > > > > > the recent input file.
> > > > > > >
> > > > > > > It's not in the obsolete nodes either.
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > -------------------------------------------------------------------------------
> > > > > Tanya Berardini, Ph.D.                  tberardi at acoma.stanford.edu
> > > > > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > > > > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 325
> > > > > Department of Plant Biology             URL: http://arabidopsis.org/
> > > > > 260 Panama St.
> > > > > Stanford, CA 94305
> > > > > -------------------------------------------------------------------------------
> > > > >
> > > >
> > > > ****************************************************************************
> > > > Suparna Mundodi, Ph.D.                    email:smundodi at acoma.stanford.edu
> > > > Curator,                          Tel:650-325-1521 x342
> > > > The Arabidopsis Information Resources     Fax:650-325-6857
> > > > Carnegie Institution of Washington        URL:http://arabidopsis.org/
> > > > Department of Plant Biology
> > > > 260 Panama St.
> > > > Stanford, CA 94305
> > > > ****************************************************************************
> > > >
> > > >
> > > >
> > > >
> > >
> >
> > ****************************************************************************
> > Suparna Mundodi, Ph.D.                        email:smundodi at acoma.stanford.edu
> > Curator,                              Tel:650-325-1521 x342
> > The Arabidopsis Information Resources Fax:650-325-6857
> > Carnegie Institution of Washington    URL:http://arabidopsis.org/
> > Department of Plant Biology
> > 260 Panama St.
> > Stanford, CA 94305
> > ****************************************************************************
> >
> >
> >

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************


From pj37 at cornell.edu  Fri Aug 16 11:52:07 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 16 Aug 2002 11:52:07 -0400
Subject: HELP!: GO Term Error
References: <Pine.LNX.4.10.10208161004530.29228-100000@pigeon.ebi.ac.uk>
Message-ID: <3D5D1FA7.11B90C0B@cornell.edu>



Midori Harris wrote:
> 
> On Thu, 15 Aug 2002, Sue Rhee wrote:
> 
> > how about:
> >
> > nutrient reserve
> >  amino acid reserve
> >   amino acid reserve in seed syn: seed storage protein
> 
> we could add 'amino acid reserve' if it's useful -- opinions?
> 
> '... in seed' is still problematic -- we don't want function terms to
> include cellular component or anatomy info.
> 
> m

We also don't want to include anatomy or cellular component info into the term
though sometimes its unavoidable, unless we have a crossproduct ontology to
combine anatomy_seed "as location" to function_amino_acid_reserve "as function"
to define an explicit meaning to the new term "amino acid reserve in seed". 

For example mitochondrial H+ ATPase and Chloroplast ATPase. Both of them have
the same EC number because they carry out the same function H+ translocation
coupled to ATP asynthesis. But the way they are localized in the subcellular
compartment is different. The F1-subcomplex of mitochondria faces(present in)
the lumen where as that of chloroplast is present in the intermembrane space
between inner and outer thylakoid membranes. Going by the GO version, didn't we
bring in the explicit meaning to the term H+ATPase by intergrating the cellular
component term, even though at the sequence as well as at the function or
structure level the subunits are similar. Unfortunately the only option we have
is to use "sensu" but we cannot use this for anatomy term.

So I suggest to have either amino acid reserve in seed or seed storage protein.
I think the function is very much clear from the term and in a way also makes it
explicit.

That's my opinion, I might be wrong!

Pankaj


From midori at ebi.ac.uk  Thu Aug 15 10:56:40 2002
From: midori at ebi.ac.uk (Midori Harris)
Date: Thu, 15 Aug 2002 15:56:40 +0100 (BST)
Subject: HELP!: GO Term Error
In-Reply-To: <3D5BBD29.38F98720@cornell.edu>
Message-ID: <Pine.LNX.4.10.10208151544580.19623-100000@pigeon.ebi.ac.uk>



On Thu, 15 Aug 2002, Pankaj Jaiswal wrote:

> Well I disagree with Midori !
> Reason at some point in an organism's life if one looks logically, each and
> every one of the gene product can be called as a nutrient reserve in some form
> or the other. All the proteins can be broken down in its components for example
> into  peptides ->amino acids->C/H/N/O/P/S/.

Certainly -- but this is not an _activity_ catalyzed by the proteins (or
lipids, carbohydtates, or nucleic acids) themselves. 'Nutrient reserve' is
itself far from an ideal GO term, largely for exactly this reason. The
term is being created to accommodate those proteins that are, as far as we
know, synthesized _solely_ for the purpose of stashing amino acids.

 This is what actually happens when
> an organism undergoes a situation where it becomes its necessity to survive by
> recycling its own organization units i.e. at the time of "aging". Proteins is
> just one example, same is true for nucleotides and carbohydrates and lipids.

This is covered by GO process terms such as 'aging', 'apoptosis',
'response to starvation', etc.

> Therefore I still feel that this term "storage protein of seed" should be
> brought back.

You have not addressed either of the problems that prompted us to remove
'seed storage protein'; 'storage protein of seed' is merely a rewording
of the same thing.

> Another reason that these proteins in "Monocot plants" also have
> an additional function of "serine protease inhibitor". 

This has nothing to do with the merits (or lack thereof) of the terms
'seed storage protein', 'storage protein of seed', or 'nutrient reserve'.
These proteins can and should be annotated to the existing term 'serine
protease inhibitor' (GO:0004867).

> There are several
> instances of such proteins as Tanya already mentioned about them in her first
> mail at the start of this debate.(cited below) 
> 
> http://www.geneontology.org/email/go-arc/go-2002/2028.html
> 
> "Midori: There are many different seed storage proteins: vicilin-type 
> globulin, albumin, glutenin/gliadin, C hordein, etc. "

These are all gene products. Their activities should be represented by GO
terms, but not the proteins or protein families.

Midori




From midori at ebi.ac.uk  Fri Aug 16 05:06:53 2002
From: midori at ebi.ac.uk (Midori Harris)
Date: Fri, 16 Aug 2002 10:06:53 +0100 (BST)
Subject: HELP!: GO Term Error
In-Reply-To: <Pine.GSO.4.44.0208151129420.5246-100000@acoma.Stanford.EDU>
Message-ID: <Pine.LNX.4.10.10208161004530.29228-100000@pigeon.ebi.ac.uk>


On Thu, 15 Aug 2002, Sue Rhee wrote:

> how about:
> 
> nutrient reserve
>  amino acid reserve
>   amino acid reserve in seed syn: seed storage protein

we could add 'amino acid reserve' if it's useful -- opinions?

'... in seed' is still problematic -- we don't want function terms to
include cellular component or anatomy info.

m



From rhee at acoma.Stanford.EDU  Thu Aug 15 14:31:36 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Thu, 15 Aug 2002 11:31:36 -0700 (PDT)
Subject: HELP!: GO Term Error
In-Reply-To: <3D5BBD29.38F98720@cornell.edu>
Message-ID: <Pine.GSO.4.44.0208151129420.5246-100000@acoma.Stanford.EDU>

how about:

nutrient reserve
 amino acid reserve
  amino acid reserve in seed syn: seed storage protein

or is this something already in place?

sue

On Thu, 15 Aug 2002, Pankaj Jaiswal wrote:

> Well I disagree with Midori !
> Reason at some point in an organism's life if one looks logically, each and
> every one of the gene product can be called as a nutrient reserve in some form
> or the other. All the proteins can be broken down in its components for example
> into  peptides ->amino acids->C/H/N/O/P/S/. This is what actually happens when
> an organism undergoes a situation where it becomes its necessity to survive by
> recycling its own organization units i.e. at the time of "aging". Proteins is
> just one example, same is true for nucleotides and carbohydrates and lipids.
>
> Therefore I still feel that this term "storage protein of seed" should be
> brought back. Another reason that these proteins in "Monocot plants" also have
> an additional function of "serine protease inhibitor". There are several
> instances of such proteins as Tanya already mentioned about them in her first
> mail at the start of this debate.(cited below)
>
> http://www.geneontology.org/email/go-arc/go-2002/2028.html
>
> "Midori: There are many different seed storage proteins: vicilin-type
> globulin, albumin, glutenin/gliadin, C hordein, etc. "
>
> From my perspective 'nutrient reserve' is a very broad term and we will mislead
> the community by annotating any such term.
>
> Pankaj
>
>
> Midori Harris wrote:
> >
> > Hi,
> >
> > We will stick with 'nutrient reserve'. "Storage protein of seed" has
> > exactly the same problems as "seed storage protein": 'seed' is a
> > localization and 'protein' is a gene product, not an activity.
> >
> > I'll put 'nutrient reserve' in the SourceForge list so we don't forget to
> > actually add it.
> >
> > Midori
> >
> > On Wed, 14 Aug 2002, Suparna Mundodi wrote:
> >
> > > Hi Midori,
> > >
> > > What has happened to the "seed storage protein" term. Recently there was a
> > > request from Pankaj to include the "storage protein of seed" and I think
> > > he makes a valid point here. Are we going to stick with the "nutreint
> > > reserve" term or "Storage protein of seed"?
> > >
> > > I have attached Pankaj's email below.
> > >
> > > Suparna
> > >
> > >
> > >
> > > Date: Tue, 13 Aug 2002 16:11:02 -0400
> > > From: Pankaj Jaiswal <pj37 at cornell.edu>
> > > To: Tanya Berardini <tberardi at acoma.Stanford.EDU>
> > > Subject: Re: seed storage protein
> > >
> > > Hi Tanya,
> > >
> > > I really did not know about this debate. Why can't we have a term instead
> > > "storage protein of seed", just to convince the concept. Doesn't matter if
> > > there
> > > is a compartmentalization aspect here "anatomy term=seed".  If GO can have
> > > fat
> > > body/lipid storage body/protein storage vacuole(!!!), then this is a valid
> > > reframed term that defines a function, that its a storage protein
> > > providing
> > > nutritional buffer to the embryo, when it undergoes germination.
> > >
> > > Now the situation is how should we annotate "alpha-globulin", the function
> > > is
> > > seed storage protein. The other model organisms don't have this seed
> > > storage
> > > protein example is
> > > http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/blink?pid=1783206&tax=0&org=0&pdb=0&sort=1&cut=100&all=0
> > >
> > > there are 75 such entries from plants but none from others. I was even
> > > going to
> > > ask a new term request for "alpha-globulin", which is an instance of
> > > storage
> > > protein of seed by functional definition.
> > > _________________________
> > >
> > > Same way GO has different terms for "response" "susceptibility" &
> > > "resistance".
> > > I think resistance and susceptibility is a score/attribute  of determining
> > > the
> > > level of "response". The "Response" is biological in origin but the
> > > "resistance"
> > > / "susceptible" are phenotype terms and one needs to avoid this. We have
> > > had a
> > > considerable discussion on this before when Leonore was there and she
> > > reframed
> > > the phenotypic terms to responses, but they have reappeared.
> > >
> > >
> > > Pankaj
> > >
> > >
> > >
> > >
> > >
> > > On Wed, 31 Jul 2002, Midori Harris wrote:
> > >
> > > > Of course I like 'nutrient reserve' -- it was my idea. ;)
> > > >
> > > > If no one complains (and soon) we will put 'nutrient reserve' in, with a
> > > > comment that it can be used for gene products formerly annotated to any of
> > > > the 'storage protein' terms.
> > > >
> > > > Midori
> > > >
> > > > On Wed, 31 Jul 2002, Suparna Mundodi wrote:
> > > >
> > > > > Midori: If we are making "seed storage protein" obsolete, then have we
> > > > > come to a consensus on the term this is going to replace "seed storage protein"
> > > > > ? I vote on the use of "nutrient reserve" and "amino acid reserve" as you
> > > > > suggested earlier.
> > > > >
> > > > > Suparna
> > > > >
> > > > >
> > > > > On Mon, 29
> > > > > Jul 2002, Tanya Berardini wrote:
> > > > >
> > > > > > Thanks for the note, Harold.
> > > > > >
> > > > > > Midori: There are many different seed storage proteins: vicilin-type
> > > > > > globulin, albumin, glutenin/gliadin, C hordein, etc.
> > > > > >
> > > > > > Please bring back "seed storage protein" from the dead!!!  Oddly enough,
> > > > > > the other term that I added the same day GO:0009914 is still alive
> > > > > > and well.
> > > > > >
> > > > > > Advice on what to do??
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Tanya
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Mon, 29 Jul 2002, Midori Harris wrote:
> > > > > >
> > > > > > > sounds like it ought to be obsolete -- gene product-y
> > > > > > >
> > > > > > > m
> > > > > > >
> > > > > > > On Mon, 29 Jul 2002, Harold Drabkin wrote:
> > > > > > >
> > > > > > > > Thought someone in TAIR or GRAMANE would want to know:
> > > > > > > >
> > > > > > > > While we were doing our nightly load of GO, we noticed that
> > > > > > > >
> > > > > > > > GO:0009915 (seed storage protein) exists in current our GO vocabulary from
> > > > > > > > the previous load,  but it is not in
> > > > > > > > the recent input file.
> > > > > > > >
> > > > > > > > It's not in the obsolete nodes either.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > -------------------------------------------------------------------------------
> > > > > > Tanya Berardini, Ph.D.                  tberardi at acoma.stanford.edu
> > > > > > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > > > > > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 325
> > > > > > Department of Plant Biology             URL: http://arabidopsis.org/
> > > > > > 260 Panama St.
> > > > > > Stanford, CA 94305
> > > > > > -------------------------------------------------------------------------------
> > > > > >
> > > > >
> > > > > ****************************************************************************
> > > > > Suparna Mundodi, Ph.D.                    email:smundodi at acoma.stanford.edu
> > > > > Curator,                          Tel:650-325-1521 x342
> > > > > The Arabidopsis Information Resources     Fax:650-325-6857
> > > > > Carnegie Institution of Washington        URL:http://arabidopsis.org/
> > > > > Department of Plant Biology
> > > > > 260 Panama St.
> > > > > Stanford, CA 94305
> > > > > ****************************************************************************
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > ****************************************************************************
> > > Suparna Mundodi, Ph.D.                        email:smundodi at acoma.stanford.edu
> > > Curator,                              Tel:650-325-1521 x342
> > > The Arabidopsis Information Resources Fax:650-325-6857
> > > Carnegie Institution of Washington    URL:http://arabidopsis.org/
> > > Department of Plant Biology
> > > 260 Panama St.
> > > Stanford, CA 94305
> > > ****************************************************************************
> > >
> > >
> > >
>
> --
>
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org
> ******************************************
>

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------



From pj37 at cornell.edu  Fri Aug 16 16:24:39 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 16 Aug 2002 16:24:39 -0400
Subject: HELP!: GO Term Error
References: <Pine.LNX.4.10.10208161004530.29228-100000@pigeon.ebi.ac.uk>
Message-ID: <3D5D5F87.8EDB8D52@cornell.edu>



Midori Harris wrote:
> 
> On Thu, 15 Aug 2002, Sue Rhee wrote:
> 
> > how about:
> >
> > nutrient reserve
> >  amino acid reserve
> >   amino acid reserve in seed syn: seed storage protein
> 
> we could add 'amino acid reserve' if it's useful -- opinions?
> 
> '... in seed' is still problematic -- we don't want function terms to
> include cellular component or anatomy info.
> 
> m

Hi All,

We figured out more,  the structural component is there under GO_function with
several of the anatomical terms as part of function.

examples:
muscle myosin
non-muscle myosin
muscle thin filament tropomyosin
structural constituent of myelin sheath
anther dehiscence
structural constituent of bone

and several other instances of  
*structural constituent* 

Most of them have anatomical descriptors as part of the term.

Also there is a term for "yolk protein" under "structural molecule". This a
storage protein for the developing embryo a distant equivalent of seed storage
protein, but atleast the later term refelcts some fucntion.

Infact the term part "molecule" in "structural molecule" might be considered for
removal the same way as the term part "protein". 

Any opinions! 


I think I have made my point here and I don't want to be so critical every time.
Sorry about that.

Cheers
Pankaj


From polaccom at missouri.edu  Fri Aug 16 14:45:05 2002
From: polaccom at missouri.edu (Polacco, Mary L.)
Date: Fri, 16 Aug 2002 13:45:05 -0500
Subject: HELP!: GO Term Error
Message-ID: <927E1B4A3F8CAB48B854D808E001BD2E2FACC5@col-mailnode04.col.missouri.edu>

Both term parsimony, and GO harmony are served if we stop at amino acid reserve, with the location not being included in the function. Leaf proteins may also have a nutrient reserve role, so you wouldn't have to invent a new term
for those guys.
    -mary; curator MaizeDB

-----Original Message-----
From:	Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
Sent:	Thu 8/15/2002 1:31 PM
To:	Pankaj Jaiswal
Cc:	Midori Harris; Suparna Mundodi; Tanya Berardini; GO MAILING LIST; TAIR curators; brie
Subject:	Re: HELP!: GO Term Error

how about:

nutrient reserve
 amino acid reserve
  amino acid reserve in seed syn: seed storage protein

or is this something already in place?

sue

On Thu, 15 Aug 2002, Pankaj Jaiswal wrote:

> Well I disagree with Midori !
> Reason at some point in an organism's life if one looks logically, each and
> every one of the gene product can be called as a nutrient reserve in some form
> or the other. All the proteins can be broken down in its components for example
> into  peptides ->amino acids->C/H/N/O/P/S/. This is what actually happens when
> an organism undergoes a situation where it becomes its necessity to survive by
> recycling its own organization units i.e. at the time of "aging". Proteins is
> just one example, same is true for nucleotides and carbohydrates and lipids.
>
> Therefore I still feel that this term "storage protein of seed" should be
> brought back. Another reason that these proteins in "Monocot plants" also have
> an additional function of "serine protease inhibitor". There are several
> instances of such proteins as Tanya already mentioned about them in her first
> mail at the start of this debate.(cited below)
>
> http://www.geneontology.org/email/go-arc/go-2002/2028.html
>
> "Midori: There are many different seed storage proteins: vicilin-type
> globulin, albumin, glutenin/gliadin, C hordein, etc. "
>
> From my perspective 'nutrient reserve' is a very broad term and we will mislead
> the community by annotating any such term.
>
> Pankaj
>
>
> Midori Harris wrote:
> >
> > Hi,
> >
> > We will stick with 'nutrient reserve'. "Storage protein of seed" has
> > exactly the same problems as "seed storage protein": 'seed' is a
> > localization and 'protein' is a gene product, not an activity.
> >
> > I'll put 'nutrient reserve' in the SourceForge list so we don't forget to
> > actually add it.
> >
> > Midori
> >
> > On Wed, 14 Aug 2002, Suparna Mundodi wrote:
> >
> > > Hi Midori,
> > >
> > > What has happened to the "seed storage protein" term. Recently there was a
> > > request from Pankaj to include the "storage protein of seed" and I think
> > > he makes a valid point here. Are we going to stick with the "nutreint
> > > reserve" term or "Storage protein of seed"?
> > >
> > > I have attached Pankaj's email below.
> > >
> > > Suparna
> > >
> > >
> > >
> > > Date: Tue, 13 Aug 2002 16:11:02 -0400
> > > From: Pankaj Jaiswal <pj37 at cornell.edu>
> > > To: Tanya Berardini <tberardi at acoma.Stanford.EDU>
> > > Subject: Re: seed storage protein
> > >
> > > Hi Tanya,
> > >
> > > I really did not know about this debate. Why can't we have a term instead
> > > "storage protein of seed", just to convince the concept. Doesn't matter if
> > > there
> > > is a compartmentalization aspect here "anatomy term=seed".  If GO can have
> > > fat
> > > body/lipid storage body/protein storage vacuole(!!!), then this is a valid
> > > reframed term that defines a function, that its a storage protein
> > > providing
> > > nutritional buffer to the embryo, when it undergoes germination.
> > >
> > > Now the situation is how should we annotate "alpha-globulin", the function
> > > is
> > > seed storage protein. The other model organisms don't have this seed
> > > storage
> > > protein example is
> > > http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/blink?pid=1783206&tax=0&org=0&pdb=0&sort=1&cut=100&all=0
> > >
> > > there are 75 such entries from plants but none from others. I was even
> > > going to
> > > ask a new term request for "alpha-globulin", which is an instance of
> > > storage
> > > protein of seed by functional definition.
> > > _________________________
> > >
> > > Same way GO has different terms for "response" "susceptibility" &
> > > "resistance".
> > > I think resistance and susceptibility is a score/attribute  of determining
> > > the
> > > level of "response". The "Response" is biological in origin but the
> > > "resistance"
> > > / "susceptible" are phenotype terms and one needs to avoid this. We have
> > > had a
> > > considerable discussion on this before when Leonore was there and she
> > > reframed
> > > the phenotypic terms to responses, but they have reappeared.
> > >
> > >
> > > Pankaj
> > >
> > >
> > >
> > >
> > >
> > > On Wed, 31 Jul 2002, Midori Harris wrote:
> > >
> > > > Of course I like 'nutrient reserve' -- it was my idea. ;)
> > > >
> > > > If no one complains (and soon) we will put 'nutrient reserve' in, with a
> > > > comment that it can be used for gene products formerly annotated to any of
> > > > the 'storage protein' terms.
> > > >
> > > > Midori
> > > >
> > > > On Wed, 31 Jul 2002, Suparna Mundodi wrote:
> > > >
> > > > > Midori: If we are making "seed storage protein" obsolete, then have we
> > > > > come to a consensus on the term this is going to replace "seed storage protein"
> > > > > ? I vote on the use of "nutrient reserve" and "amino acid reserve" as you
> > > > > suggested earlier.
> > > > >
> > > > > Suparna
> > > > >
> > > > >
> > > > > On Mon, 29
> > > > > Jul 2002, Tanya Berardini wrote:
> > > > >
> > > > > > Thanks for the note, Harold.
> > > > > >
> > > > > > Midori: There are many different seed storage proteins: vicilin-type
> > > > > > globulin, albumin, glutenin/gliadin, C hordein, etc.
> > > > > >
> > > > > > Please bring back "seed storage protein" from the dead!!!  Oddly enough,
> > > > > > the other term that I added the same day GO:0009914 is still alive
> > > > > > and well.
> > > > > >
> > > > > > Advice on what to do??
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Tanya
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > On Mon, 29 Jul 2002, Midori Harris wrote:
> > > > > >
> > > > > > > sounds like it ought to be obsolete -- gene product-y
> > > > > > >
> > > > > > > m
> > > > > > >
> > > > > > > On Mon, 29 Jul 2002, Harold Drabkin wrote:
> > > > > > >
> > > > > > > > Thought someone in TAIR or GRAMANE would want to know:
> > > > > > > >
> > > > > > > > While we were doing our nightly load of GO, we noticed that
> > > > > > > >
> > > > > > > > GO:0009915 (seed storage protein) exists in current our GO vocabulary from
> > > > > > > > the previous load,  but it is not in
> > > > > > > > the recent input file.
> > > > > > > >
> > > > > > > > It's not in the obsolete nodes either.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > > -------------------------------------------------------------------------------
> > > > > > Tanya Berardini, Ph.D.                  tberardi at acoma.stanford.edu
> > > > > > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > > > > > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 325
> > > > > > Department of Plant Biology             URL: http://arabidopsis.org/
> > > > > > 260 Panama St.
> > > > > > Stanford, CA 94305
> > > > > > -------------------------------------------------------------------------------
> > > > > >
> > > > >
> > > > > ****************************************************************************
> > > > > Suparna Mundodi, Ph.D.                    email:smundodi at acoma.stanford.edu
> > > > > Curator,                          Tel:650-325-1521 x342
> > > > > The Arabidopsis Information Resources     Fax:650-325-6857
> > > > > Carnegie Institution of Washington        URL:http://arabidopsis.org/
> > > > > Department of Plant Biology
> > > > > 260 Panama St.
> > > > > Stanford, CA 94305
> > > > > ****************************************************************************
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > ****************************************************************************
> > > Suparna Mundodi, Ph.D.                        email:smundodi at acoma.stanford.edu
> > > Curator,                              Tel:650-325-1521 x342
> > > The Arabidopsis Information Resources Fax:650-325-6857
> > > Carnegie Institution of Washington    URL:http://arabidopsis.org/
> > > Department of Plant Biology
> > > 260 Panama St.
> > > Stanford, CA 94305
> > > ****************************************************************************
> > >
> > >
> > >
>
> --
>
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org
> ******************************************
>

-----------------------------------------------------------------------------
Sue Rhee                         	rhee at acoma.stanford.edu
The Arabidopsis Information Resource	URL: www.arabidopsis.org
Carnegie Institution of Washington	FAX: +1-650-325-6857
Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
260 Panama St.
Stanford, CA 94305
U.S.A.
-----------------------------------------------------------------------------




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From midori at ebi.ac.uk  Mon Aug 19 06:30:23 2002
From: midori at ebi.ac.uk (Midori Harris)
Date: Mon, 19 Aug 2002 11:30:23 +0100 (BST)
Subject: HELP!: GO Term Error
In-Reply-To: <3D5D5F87.8EDB8D52@cornell.edu>
Message-ID: <Pine.LNX.4.10.10208191120410.14854-100000@pigeon.ebi.ac.uk>

Hi Pankaj,

You do have a good point about some of the existing function terms. We
should make an effort to remove those that mention cellular component or
anatomy terms. For example, all of the 'structural constituent of ... '
terms could be merged into their parent.

The 'myosin' terms are in the cellular component ontology, and 'anther
dehiscence' is in process; all are OK.

Midori

On Fri, 16 Aug 2002, Pankaj Jaiswal wrote:

> 
> 
> Midori Harris wrote:
> > 
> > On Thu, 15 Aug 2002, Sue Rhee wrote:
> > 
> > > how about:
> > >
> > > nutrient reserve
> > >  amino acid reserve
> > >   amino acid reserve in seed syn: seed storage protein
> > 
> > we could add 'amino acid reserve' if it's useful -- opinions?
> > 
> > '... in seed' is still problematic -- we don't want function terms to
> > include cellular component or anatomy info.
> > 
> > m
> 
> Hi All,
> 
> We figured out more,  the structural component is there under GO_function with
> several of the anatomical terms as part of function.
> 
> examples:
> muscle myosin
> non-muscle myosin
> muscle thin filament tropomyosin
> structural constituent of myelin sheath
> anther dehiscence
> structural constituent of bone
> 
> and several other instances of  
> *structural constituent* 
> 
> Most of them have anatomical descriptors as part of the term.
> 
> Also there is a term for "yolk protein" under "structural molecule". This a
> storage protein for the developing embryo a distant equivalent of seed storage
> protein, but atleast the later term refelcts some fucntion.
> 
> Infact the term part "molecule" in "structural molecule" might be considered for
> removal the same way as the term part "protein". 
> 
> Any opinions! 
> 
> 
> I think I have made my point here and I don't want to be so critical every time.
> Sorry about that.
> 
> Cheers
> Pankaj
> 





From conceptoazul at easy.pacifictel.net  Fri Aug 16 17:55:16 2002
From: conceptoazul at easy.pacifictel.net (Concepto Azul)
Date: Fri, 16 Aug 2002 16:55:16 -0500
Subject: orward to Drs. M.L.P. Abenes and N. Huang, Please 
Message-ID: <5.1.0.14.0.20020816165421.00a7bad0@mail1.easynet.net.ec>

FROM: Monica Ramirez /Univ Guayaquil/ECUADOR
TO:

I wish to contact Drs. M.L.P. Abenes and N. Huang who are working on rice 
molecular markers, at the IRRI: Could you please forward the following 
message to them. Please let me know if they have an electronic address.

Thank you very much.

Sincerely yours,

Monica Ramirez
FROM: Monica Ramirez /Univ Guayaquil/ECUADOR
TO: M.L.P. Abenes and N. Huang / International Rice Research Institute, 
P.O. Box 933, Manila, Philippines
SUBJECT: Request for some reprints, Please

Dear Drs. Abenes and N. Huang,

At the University of Guayaquil, we are organizing different courses related 
to plant biotechnology, particularly a Master in "Molecular Biology and 
Biotechnology" and a training course applied to sugarcane and rice.

We are very interested in your research works. Could you please give me 
further details about the molecular markers that you have been developing 
for selection of bacterial blight resistant rice plants?

If you have published related articles, could you please send me a copy of 
them (by electronic mail, if possible).


Thank you very much.


Sincerely yours,


Monica Ramirez


Concepto Azul
PO Box 09-02-142A
Cdla Vernaza
Mz. 10, Villa 34
Guayaquil - Ecuador

Telfax: (+593) 42 284 615 / 289 247 / 28284 066
<conceptoazul at easy.pacifictel.net>
                       



From sakunthala_p at yahoo.com  Tue Aug 20 07:37:25 2002
From: sakunthala_p at yahoo.com (sakunthala perera)
Date: Tue, 20 Aug 2002 04:37:25 -0700 (PDT)
Subject: rice research information
Message-ID: <20020820113725.4106.qmail@web14609.mail.yahoo.com>


Respected Sir/ Madam,

I am a postgraduate student from the university of Peradeniya, Sri lanka. As per the curriculum i am to do a project and prepare a report.

the project that I did was "identification of polymorphism in traditional rice varieties using RAPDs"

i would be grateful to you if you could assist me in my literature survey as it is very difficult to find any article about this subject in the library

thanking you

yours sincerely

sakunthala perera

21/8, Ananda Balika Mawatha,

Pitakotte.

Sri lanka.

sakunthala_p at yahoo.com

 

 



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From Elisabeth.Gasteiger at isb-sib.ch  Thu Aug 22 04:01:05 2002
From: Elisabeth.Gasteiger at isb-sib.ch (Elisabeth Gasteiger)
Date: Thu, 22 Aug 2002 10:01:05 +0200
Subject: links from SWISS-PROT to Gramene
Message-ID: <3D649A41.7776B673@isb-sib.ch>

Hello,

as you may know we will soon introduce links from SWISS-PROT/TrEMBL
to Gramene. 
I am now trying to figure out the URL we should best be using
to link out to you from ExPASy, 
e.g. http://us.expasy.org/cgi-bin/niceprot.pl?4CL2_ORYSA
I have seen that I can search by SWISS-PROT accession number,
e.g.
http://www.gramene.org/perl/protein_search?word=P93436

However, the page we would really like to link to directly
is the one you obtain once you click on the SWISS-PROT
accession number, i.e.
http://www.gramene.org/perl/protein_search?protein_id=77704

Unfortunately, this URL only contains the ID 77704, and not
the SWISS-PROT accession number, which is the only information
we have in our links. OUr links will be of the form

DR   Gramene; O04109; -.

Would it be possible for you to provide a way of getting to the "final"
page, using the SWISS-PROT accession number in the link?
We would really like to allow our users to reach the information
in cross-referenced databases with as few clicks as possible.

Thanks in advance
Elisabeth Gasteiger
-- 
-----------------------------------------------------------------
Elisabeth Gasteiger
Swiss Institute of Bioinformatics
CMU - 1, rue Michel Servet                Tel. (+41 22) 702 58 75
CH - 1211 Geneva 4 Switzerland            Fax  (+41 22) 702 58 58
Elisabeth.Gasteiger at isb-sib.ch            http://www.expasy.org/ 
-----------------------------------------------------------------


From zhaow at cshl.edu  Fri Aug 23 17:03:52 2002
From: zhaow at cshl.edu (Wei Zhao)
Date: Fri, 23 Aug 2002 17:03:52 -0400 (EDT)
Subject: links from SWISS-PROT to Gramene
In-Reply-To: <3D649A41.7776B673@isb-sib.ch>
Message-ID: <Pine.GSO.4.05.10208231646210.24387-100000@phage.cshl.org>


Dear Elisabeth,

The "final" protein page can be linked to directly using the SWISS-PROT
accession number, which is also our primary identifier.
Here is the URL syntax:

http://www.gramene.org/perl/protein_search?acc=XXXXXX
Example 
http://www.gramene.org/perl/protein_search?acc=P93436


For more information, please see
http://www.gramene.org/documentation/linkback.html
and
ftp://www.gramene.org/pub/gramene/protein/linkback/linkback_README

We look forward to seeing links from SWISS-PROT/TrEMBL to Gramene.

Regards,

Wei


On Thu, 22 Aug 2002, Elisabeth Gasteiger wrote:

> Hello,
> 
> as you may know we will soon introduce links from SWISS-PROT/TrEMBL
> to Gramene. 
> I am now trying to figure out the URL we should best be using
> to link out to you from ExPASy, 
> e.g. http://us.expasy.org/cgi-bin/niceprot.pl?4CL2_ORYSA
> I have seen that I can search by SWISS-PROT accession number,
> e.g.
> http://www.gramene.org/perl/protein_search?word=P93436
> 
> However, the page we would really like to link to directly
> is the one you obtain once you click on the SWISS-PROT
> accession number, i.e.
> http://www.gramene.org/perl/protein_search?protein_id=77704
> 
> Unfortunately, this URL only contains the ID 77704, and not
> the SWISS-PROT accession number, which is the only information
> we have in our links. OUr links will be of the form
> 
> DR   Gramene; O04109; -.
> 
> Would it be possible for you to provide a way of getting to the "final"
> page, using the SWISS-PROT accession number in the link?
> We would really like to allow our users to reach the information
> in cross-referenced databases with as few clicks as possible.
> 
> Thanks in advance
> Elisabeth Gasteiger
> -- 
> -----------------------------------------------------------------
> Elisabeth Gasteiger
> Swiss Institute of Bioinformatics
> CMU - 1, rue Michel Servet                Tel. (+41 22) 702 58 75
> CH - 1211 Geneva 4 Switzerland            Fax  (+41 22) 702 58 58
> Elisabeth.Gasteiger at isb-sib.ch            http://www.expasy.org/ 
> -----------------------------------------------------------------
> 

-- 
Wei Zhao
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From pj37 at cornell.edu  Fri Aug 23 16:23:58 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 23 Aug 2002 16:23:58 -0400
Subject: links from SWISS-PROT to Gramene
References: <3D649A41.7776B673@isb-sib.ch>
Message-ID: <3D6699DE.E38E8072@cornell.edu>


Dear Elisabeth,

Its great to know that SPTrEMBL will be providing links to Gramene for rice
proteins.

For details on the URL syntax please refer to 
http://brie2.cshl.org:8082/documentation/linkback.html

Or please follow: Linking back to Protein Database at Gramene

Use the Protein identifier file swissprot_linkback.txt at 
ftp://www.gramene.org/pub/gramene/protein/linkback/swissprot_linkback.txt

File format is as follows: 
Accession number|SWALL or SWISSPROT ID|Gramene Primary Identifier|Secondary
Identifier 
 for example: 
P19395|UGST_ORYSA|P19395|78073 

Using the SWISSPROT accession number (which is also our primary identifier): 
http://www.gramene.org/perl/protein_search?acc=accession number 
http://www.gramene.org/perl/protein_search?acc=P19395 

Using the SWISSPROT/SWALL ID: 
http://www.gramene.org/perl/protein_search?swall=SWISSPROT ID 
http://www.gramene.org/perl/protein_search?swall=UGST_ORYSA 

Using the Gramene internal IDs (Gramene's secondary ID): 
http://www.gramene.org/perl/protein_search?protein_id=Gramene ID 
http://www.gramene.org/perl/protein_search?protein_id=78073 

Sincerely

Pankaj
www.gramene.org


Elisabeth Gasteiger wrote:
> 
> Hello,
> 
> as you may know we will soon introduce links from SWISS-PROT/TrEMBL
> to Gramene.
> I am now trying to figure out the URL we should best be using
> to link out to you from ExPASy,
> e.g. http://us.expasy.org/cgi-bin/niceprot.pl?4CL2_ORYSA
> I have seen that I can search by SWISS-PROT accession number,
> e.g.
> http://www.gramene.org/perl/protein_search?word=P93436
> 
> However, the page we would really like to link to directly
> is the one you obtain once you click on the SWISS-PROT
> accession number, i.e.
> http://www.gramene.org/perl/protein_search?protein_id=77704
> 
> Unfortunately, this URL only contains the ID 77704, and not
> the SWISS-PROT accession number, which is the only information
> we have in our links. OUr links will be of the form
> 
> DR   Gramene; O04109; -.
> 
> Would it be possible for you to provide a way of getting to the "final"
> page, using the SWISS-PROT accession number in the link?
> We would really like to allow our users to reach the information
> in cross-referenced databases with as few clicks as possible.
> 
> Thanks in advance
> Elisabeth Gasteiger
> --
> -----------------------------------------------------------------
> Elisabeth Gasteiger
> Swiss Institute of Bioinformatics
> CMU - 1, rue Michel Servet                Tel. (+41 22) 702 58 75
> CH - 1211 Geneva 4 Switzerland            Fax  (+41 22) 702 58 58
> Elisabeth.Gasteiger at isb-sib.ch            http://www.expasy.org/
> -----------------------------------------------------------------


From steven at stein.cshl.org  Fri Aug 23 17:00:01 2002
From: steven at stein.cshl.org (Steven Schmidt)
Date: Fri, 23 Aug 2002 17:00:01 -0400 (EDT)
Subject: links from SWISS-PROT to Gramene
Message-ID: <Pine.LNX.4.44.0208231657210.3899-100000@formaggio.cshl.org>

Hello Elizabeth,

You can use 
http://www.gramene.org/perl/protein_search?acc=P93436

-Steve

Elisabeth Gasteiger wrote:

>  Hello,

>  as you may know we will soon introduce links from SWISS-PROT/TrEMBL
>  to Gramene.
>  I am now trying to figure out the URL we should best be using
>  to link out to you from ExPASy,
>  e.g. http://us.expasy.org/cgi-bin/niceprot.pl?4CL2_ORYSA
>  I have seen that I can search by SWISS-PROT accession number,
>  e.g.
>  http://www.gramene.org/perl/protein_search?word=P93436

>  However, the page we would really like to link to directly
>  is the one you obtain once you click on the SWISS-PROT
>  accession number, i.e.
>  http://www.gramene.org/perl/protein_search?protein_id=77704

>  Unfortunately, this URL only contains the ID 77704, and not
>  the SWISS-PROT accession number, which is the only information
>  we have in our links. OUr links will be of the form

>  DR   Gramene; O04109; -.

>  Would it be possible for you to provide a way of getting to the "final"
>  page, using the SWISS-PROT accession number in the link?
>  We would really like to allow our users to reach the information
>  in cross-referenced databases with as few clicks as possible.

>  Thanks in advance
>  Elisabeth Gasteiger
>  --
>  -----------------------------------------------------------------
>  Elisabeth Gasteiger
>  Swiss Institute of Bioinformatics
>  CMU - 1, rue Michel Servet                Tel. (+41 22) 702 58 75
>  CH - 1211 Geneva 4 Switzerland            Fax  (+41 22) 702 58 58
>  Elisabeth.Gasteiger at isb-sib.ch           
http://www.expasy.org/
>  -----------------------------------------------------------------





-- 
Steven Schmidt
www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977



From jingyu at dnalandmarks.ca  Mon Aug 26 15:56:10 2002
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Mon, 26 Aug 2002 15:56:10 -0400
Subject: bench query from Gramene
Message-ID: <OFBECFF61F.E84E356E-ON85256C21.0067B35F@dnalandmarks.ca>

Dear Gramene curators,

I wish I could get a table that contains below information from Gramene:

1. MarkerName (only from map JRGP RFLP 2000) ,
2. MapName,
3. LinkageGroupNumber,
4. LocusName,
5. PositionOnMap,
6. GenomeView(s) - e.g. clone name(s) in contigview

For example, if for markers V32,G107:
--------------------------------------------------------
Marker  Map               LG  Locus  Position   Clone
--------------------------------------------------------
G107    "JRGP RFLP 2000"  1   G107   -1.5       AP002909
G107    "JRGP RFLP 2000"  1   G107   -1.5       AP003233
RZ543   "JRGP RFLP 2000"  1   V32     8.7       AP002909
RZ543   "JRGP RFLP 2000"  1   V32     8.7       AP003233
--------------------------------------------------------

The No. 1-5 seems can be gained from Marker Search of Gramene, but it is
_very_ slow so that I doubt whether I can really get it if through internet
- I tried for only 200 markers two hours ago and nothing hasn't shown up
yet on my screen!

And for No. 6 , I wish to bench get them. So far I only can get the info
for one marker each time by clicking on "Marker Details"...

Could you help me to obtain such info in one table?

Thanks in advance,


Jing



From makineni73 at rediffmail.com  Sat Aug 24 04:57:54 2002
From: makineni73 at rediffmail.com (venkat ma lu)
Date: 24 Aug 2002 08:57:54 -0000
Subject: request info
Message-ID: <20020824085754.21999.qmail@webmail18.rediffmail.com>

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From noelyap at ascus.plbr.cornell.edu  Tue Aug 27 13:19:06 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Tue, 27 Aug 2002 13:19:06 -0400
Subject: bench query from Gramene
In-Reply-To: <OFBECFF61F.E84E356E-ON85256C21.0067B35F@dnalandmarks.ca>
References: <OFBECFF61F.E84E356E-ON85256C21.0067B35F@dnalandmarks.ca>
Message-ID: <20020827171906.GE4890@ascus.plbr.cornell.edu>

On Mon, Aug 26, 2002 at 03:56:10PM -0400, jingyu at dnalandmarks.ca wrote:
> Dear Gramene curators,
> 
> I wish I could get a table that contains below information from Gramene:
> 
> 1. MarkerName (only from map JRGP RFLP 2000) ,
> 2. MapName,
> 3. LinkageGroupNumber,
> 4. LocusName,
> 5. PositionOnMap,
> 6. GenomeView(s) - e.g. clone name(s) in contigview
> 
> For example, if for markers V32,G107:
> --------------------------------------------------------
> Marker  Map               LG  Locus  Position   Clone
> --------------------------------------------------------
> G107    "JRGP RFLP 2000"  1   G107   -1.5       AP002909
> G107    "JRGP RFLP 2000"  1   G107   -1.5       AP003233
> RZ543   "JRGP RFLP 2000"  1   V32     8.7       AP002909
> RZ543   "JRGP RFLP 2000"  1   V32     8.7       AP003233
> --------------------------------------------------------
> 
> The No. 1-5 seems can be gained from Marker Search of Gramene, but it is
> _very_ slow so that I doubt whether I can really get it if through internet
> - I tried for only 200 markers two hours ago and nothing hasn't shown up
> yet on my screen!
> 
> And for No. 6 , I wish to bench get them. So far I only can get the info
> for one marker each time by clicking on "Marker Details"...
> 
> Could you help me to obtain such info in one table?
> 
> Thanks in advance,
> 
> 
> Jing

Jing,

I think you mean "batch" query.

You can FTP the map positions for all the genetic maps in Gramene from
this URL:

    ftp://brie.cshl.org/pub/gramene/maps

If you just want the JRPG RFLP 2000 map specifically, you just need to
click on RJ_00.dat.  See the README file for details.

As for the corresponding clone names, I don't think that there is
currently a way to do this by batch in Gramene.  I agree that it would
be a convenient feature to have.  We at Gramene are actually
discussing how this might be implemented.

I note that this same information is available on the JRGP website:

    http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html

including the associated clone names.

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From pj37 at cornell.edu  Tue Aug 27 14:16:56 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 27 Aug 2002 14:16:56 -0400
Subject: request info
References: <20020824085754.21999.qmail@webmail18.rediffmail.com>
Message-ID: <3D6BC218.909523DE@cornell.edu>

Dear Venkat,

We do not carry any such information in Gramene. Try to query other search
engines like Google/Yahoo/Excite for this.

Sincerely,

Pankaj
www.gramene.org

venkat ma lu wrote:
> 
> hello my name is jyothi(Msc,bioTechnology,Nagarjuna u'sity)
> i am searching a job in hyderabad(AP).plz help me one thing ie)
> if you now the addresses or email  of biotechnology research
> centers, plz mail me


From noelyap at ascus.plbr.cornell.edu  Tue Aug 27 15:32:07 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Tue, 27 Aug 2002 15:32:07 -0400
Subject: bench query from Gramene
In-Reply-To: <OF5F0C8E73.10086319-ON85256C22.0067B7D4@dnalandmarks.ca>
References: <OF5F0C8E73.10086319-ON85256C22.0067B7D4@dnalandmarks.ca>
Message-ID: <20020827193207.GH4890@ascus.plbr.cornell.edu>

On Tue, Aug 27, 2002 at 03:11:27PM -0400, jingyu at dnalandmarks.ca wrote:
> Yes, i can get a table include both map positions and clones from there,
> but the clone info is from rgp rather than that from gramene, which is
> different.  For example:  for  marker R3309 on chromosome 2 (position 150.5
> cM), rgp gives clone as D39309 and AU032043, but gramene gives clones as
> AP004081.

Ah yes, I didn't look closely enough.  AP004081 is a genomic BAC
sequenced by the IRGSP.  The other two are non-IRGSP sequences.

> Is there a way to query from Gramene to obtain a table includes both map
> positions and clones from gramene (such as that can possibly get from
> tablemaker if from acedb) through internet?

Upon further poking around in Gramene, I discovered this FTP directory:

    ftp://brie.cshl.org/pub/gramene/insilico_data/

I think you want the file called final_markers_contigs_020502.dat.gz
See the README file for more information.  The file doesn't have
genetic map positions, though.  I don't think there's any way (yet!) 
in Gramene to get the kind of table you're looking for.

Regards,
Noel
-- 
Immanuel V. Yap <ivy1 at cornell.edu>
Department of Plant Breeding and Biometry, Cornell University
G15 Bradfield Hall, Ithaca, NY 14853
Phone: 1-607-255-3103
http://www.gramene.org


From jingyu at dnalandmarks.ca  Tue Aug 27 15:11:27 2002
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Tue, 27 Aug 2002 15:11:27 -0400
Subject: bench query from Gramene
Message-ID: <OF5F0C8E73.10086319-ON85256C22.0067B7D4@dnalandmarks.ca>

Hi Noel,

Nice to hear from you!
Thank you for the quick reply.  But, may be I didn't clearly explain what I
want, your email doesn't really solve my problem:

> ftp://brie.cshl.org/pub/gramene/maps
> click on RJ_00.dat.  See the README file for details.

Yes, I can get data for map positions in this way, but it doesn't associate
clones.


> http://rgp.dna.affrc.go.jp/publicdata/geneticmap2000/index.html

Yes, i can get a table include both map positions and clones from there,
but the clone info is from rgp rather than that from gramene, which is
different.  For example:  for  marker R3309 on chromosome 2 (position 150.5
cM), rgp gives clone as D39309 and AU032043, but gramene gives clones as
AP004081.

Is there a way to query from Gramene to obtain a table includes both map
positions and clones from gramene (such as that can possibly get from
tablemaker if from acedb) through internet?

Thanks again, anyway.

Jing



From jingyu at dnalandmarks.ca  Tue Aug 27 16:15:55 2002
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Tue, 27 Aug 2002 16:15:55 -0400
Subject: bench query from Gramene
Message-ID: <OF702016AF.CBBF4AFA-ON85256C22.006EFC59@dnalandmarks.ca>

Noel,

>  ftp://brie.cshl.org/pub/gramene/insilico_data/
> final_markers_contigs_020502.dat.gz


This is much helpful.  Thanks.


Jing



