From K.McNally at cgiar.org  Mon Nov  4 04:22:00 2002
From: K.McNally at cgiar.org (McNally, Kenneth)
Date: Mon, 04 Nov 2002 01:22:00 -0800
Subject: Error on cmap/viewer connect
Message-ID: <3EA5C75212CDD511B74100508BE0957601217BF0@mail.irri.cgiar.org>

To whom it may concern,

FYI at http://www.gramene.org/cmap/viewer

Error
Can't connect to database: ORA-12545: Connect failed because target host or
object does not exist (DBD ERROR: OCIServerAttach) 

What's up?  It was working last week.

Thanks,

Ken McNally
GRC, IRRI


From kclark at stein.cshl.org  Mon Nov  4 13:56:19 2002
From: kclark at stein.cshl.org (Ken Y. Clark)
Date: Mon, 4 Nov 2002 13:56:19 -0500 (EST)
Subject: Error on cmap/viewer connect
In-Reply-To: <3EA5C75212CDD511B74100508BE0957601217BF0@mail.irri.cgiar.org>
Message-ID: <Pine.LNX.4.44.0211041355110.7866-100000@formaggio.cshl.org>

On Mon, 4 Nov 2002, McNally, Kenneth wrote:

> To whom it may concern,
> 
> FYI at http://www.gramene.org/cmap/viewer
> 
> Error
> Can't connect to database: ORA-12545: Connect failed because target host or
> object does not exist (DBD ERROR: OCIServerAttach) 
> 
> What's up?  It was working last week.
> 
> Thanks,
> 
> Ken McNally
> GRC, IRRI

Ken,

It must have been a momentary glitch.  Everything's been working
today, and it seems fine now.  Perhaps our DBA shut down Oracle for a
moment?  

ky



From pj37 at cornell.edu  Mon Nov 11 14:49:42 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 11 Nov 2002 14:49:42 -0500
Subject: Feedback Submission from the Live Site
References: <200211090300.WAA27417@stein.cshl.org>
Message-ID: <3DD009D6.DD9E8521@cornell.edu>

Dear Sudad,

Following is the process how you should find the information on alpha amylase in
Gramene using rice a the anchor or start point.

1	Go to http://www.gramene.org/plant_ontology/
2	search for "amylase inhibitor" 
3 	it tells you that this term has one gene product associated with it from
Rice. 
Example is:  Alpha-amylase/subtilisin inhibitor
4 click on the term "Alpha-amylase/subtilisin inhibitor" and you will see the
detailed information on this protein from rice. 
5	then GO to the section on "Similarity to Other Proteins" and click on
"Grasses". This will take you to GenBank's Blink to find homologs in grass
family of plants. (I believe there was none from Wheat).
6	The next option is to go back to the protein page See#4
7	Go to the section on "Prosite" under "Protein Features" and click on links
from "Other Members of this Family "PS00283 ; SOYBEAN_KUNITZ  "
8	On a subsequent page you will see two proteins sharing this Prosite domain. Of
these you have already looked at one of them (from #4). So this time look at the
other one "Bifunctional alpha-amylase/subtilisin inhibitor" 
>From the detailed information page of this second protein you will find "Genome
Browser GRMP00000015199" section. 
9	from genome browser section you will be taken to the Rice genome view which
will tell you the Genome Location of this gene (on Chr 4).
10	 from there you enter the genome viewer. Check in the region of 73kB there is
this gene for "Bifunctional alpha-amylase/subtilisin inhibitor" and below it
will be a track for Triticum TIGR gene index and triticum dbEST. 
11	On these tracks you will find the sequences from Wheat that should encode for
the "alpha amylase" in wheat.
12	On the other hand You can get hold of some Alpha amylase sequence (nucleotide
sequence) and do a blastn at http://www.gramene.org/gramene/searches/blast using
different data sets. Of them couple are for Wheat.

Cheers

Pankaj
www.gramene.org

feedback_submission at brie.cshl.org wrote:
> 
>     *** Feedback from the Live Site ***
> 
> refer_to_url: http://www.gramene.org/perl/pub_search?word=wheat&table=1
> 
> comments: Dear sir,
> Pls.provid us any information in wheat alpha-amylase
> inhibitors.
> 
> Thank you in advance
> 
> name: Sudad  k. AL-Taweel
> 
> email: al-taweel at uruklink.net
> 
> organization: colleg of agricultural
> 
> send_feedback: Send your feedback

--


From rhee at acoma.Stanford.EDU  Wed Nov 13 19:32:49 2002
From: rhee at acoma.Stanford.EDU (Sue Rhee)
Date: Wed, 13 Nov 2002 16:32:49 -0800 (PST)
Subject: 'Plant Ontology' on Gramene
Message-ID: <Pine.GSO.4.44.0211131624170.17631-100000@acoma.Stanford.EDU>

Hi, folks,

I noticed recently that on your Ontology section of Gramene displays
'Plant Ontology' as browsable and searchable.

http://gramene.org/plant_ontology/

However, it looks like these ontologies are really Gramene's anatomy and
developmental stages ontologies, with Gramene IDs, which is good.

However, We at TAIR feel that we as POC haven't come to enough consensus
on the agreed-upon 'Plant Ontologies' terms and structure for anatomy and
developmental stages yet and would like to request that you change the
word 'Plant Ontology' to something more specific to Gramene. I think it's
a bit confusing the way it is. The places I'm referring to is:

1. The check box for 'Plant Ontology' in the DB search area

2. In the 'Current Ontologies' section, rather than 'Plant OntologyTM
(PO)' I think it should say 'Gramene Ontology' or something to that
effect.

Let me know if this is a problem. Perhaps we can talk more about reviving
the discussions on the PO anatomy and developmental stages at the SOFG and
Phene meetings...

Cheers,
Sue
-----------------------------------------------------------------------------
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 w.haiyan at warkaa.net  Wed Nov 13 03:13:56 2002
From: w.haiyan at warkaa.net (haiyan)
Date: Wed, 13 Nov 2002 11:13:56 +0300
Subject: asking for information (IRAQ)
Message-ID: <000301c28b04$5ad60260$7c0a040a@hayan>


      I am a postgraduated student from the university of Al-Mustansireah - Baghdad . My field work is 
" the production of salt tolerance plantlets of rice using tissue culture technique ". 
     I would appreciate receiving from you any reprints concerning and related to my subject and adresses or web site of any useful scientific place or person can help . 
I am waiting for your answer as soon as possible .

Thank you for your courtesy .



Sincerely yours
Arwa Abdul-Kareem Tawfiq

-------------- next part --------------
An HTML attachment was scrubbed...
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From sushantask at yahoo.co.in  Sat Nov 16 00:31:20 2002
From: sushantask at yahoo.co.in (=?iso-8859-1?q?sushanta=20saha?=)
Date: Sat, 16 Nov 2002 05:31:20 +0000 (GMT)
Subject: Reprint Request
Message-ID: <20021116053120.50390.qmail@web8005.mail.in.yahoo.com>

Dear Dr.

Warm Greetings. Would you please help me by sending
below mentioned reprint articles and of similar
titles.


Wang, B.Q. and S.W. Lu 1983. Inheritance of the
esterase isozyme Est-3 locus in rice. Acta Genet.
Sinica 10(6):459-464 (in Chinese with English
summary).


Yi, Q.H., S.Y. Shi and J.R. Jiang 1984. Analysis of
the esterase isozymes in three lines and F\1\ in Oryza
sativa and prediction of heterosis. Acta Bot. Sinica
26(5):506-512 (in Chinese with English summary).

Zhu, Y.G. nad W.J. Chen 1983. Preliminary study on the
genetics of esterase isozymes in hybrid rice. Sci.
Agric. Sinica (5):21-26 (in Chinese with English
summary).

Thank You
Sincerely
Sushanta

=====
Sushanta Kumar Saha
Research Scholar
National Facility for Marine Cyanobacteria
Bharathidasan University
Tiruchirappalli - 620 024, INDIA
E-mail: sushanta at bdu.ernet.in
Visit us at www.bdu.ernet.in/micro/

________________________________________________________________________
Missed your favourite TV serial last night? Try the new, Yahoo! TV.
       visit http://in.tv.yahoo.com


From ware at cshl.edu  Thu Nov 14 17:47:26 2002
From: ware at cshl.edu (Ware, Doreen)
Date: Thu, 14 Nov 2002 17:47:26 -0500
Subject: 'Plant Ontology' on Gramene
Message-ID: <39FDE54A4920D411AE0C0090274602F201C67F7B@exch01.cshl.org>

Pankaj, Lincoln and Susan,

We have been support the POC website which TAIR has been using.  We have
been using the terms plant ontology in our publications.  I do not want to
change this on our website.

Pankaj,
Can you confirm how long the TAIR curators have been aware the ontologies
have been up on our site.

Doreen

Doreen Ware
Cold Spring Harbor Laboratory
1 Bungtown Rd.
Cold Spring Harbor, NY 11724
Phone: (516) 367-6979
Fax:  (516) 367-8389
E-mail: ware at cshl.org

-----Original Message-----
From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
Sent: Wednesday, November 13, 2002 7:33 PM
To: gramene at gramene.org
Cc: Tanya Berardini; Leonore Reiser; arc at acoma.Stanford.EDU
Subject: 'Plant Ontology' on Gramene

Hi, folks,

I noticed recently that on your Ontology section of Gramene displays
'Plant Ontology' as browsable and searchable.

http://gramene.org/plant_ontology/

However, it looks like these ontologies are really Gramene's anatomy and
developmental stages ontologies, with Gramene IDs, which is good.

However, We at TAIR feel that we as POC haven't come to enough consensus
on the agreed-upon 'Plant Ontologies' terms and structure for anatomy and
developmental stages yet and would like to request that you change the
word 'Plant Ontology' to something more specific to Gramene. I think it's
a bit confusing the way it is. The places I'm referring to is:

1. The check box for 'Plant Ontology' in the DB search area

2. In the 'Current Ontologies' section, rather than 'Plant OntologyTM
(PO)' I think it should say 'Gramene Ontology' or something to that
effect.

Let me know if this is a problem. Perhaps we can talk more about reviving
the discussions on the PO anatomy and developmental stages at the SOFG and
Phene meetings...

Cheers,
Sue
----------------------------------------------------------------------------
-
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 jeffery.shen at ccmail.nevada.edu  Sat Nov 16 14:29:46 2002
From: jeffery.shen at ccmail.nevada.edu (jeffery.shen at ccmail.nevada.edu)
Date: Sat, 16 Nov 2002 11:29:46 -0800
Subject: condition for growing rice plants
Message-ID: <OFCB1CE1AE.B2137423-ON88256C73.006A7BE4@nevada.edu>

Dear Grameners,

We just started working on rice and would like advices from you regarding
the following:

1) the conditions for growing indica or japonica rice: temperature, light
intensity, light/dark cycles, soil types (if you grow rice in America,
would you let me know the company and the catalog for the soil you
purchase?).

2) a protocol for large scale RNA prep from rice seeds. We have tried
different protocols such as LiCl method, Qiagene kit etc, but the RNA
quality varies from time to time.  You have published several papers for
ABA responses in rice.  I would appreciate it very much if you can send us
a protocol for RNA prep from rice embryos and aleurone cells.


Thank you very much for your help.




Jeff Shen
Assistant Professor
Department of Biological Sciences
Mailstop 4004
University of Nevada
4505 Maryland Pkwy
Las Vegas, NV89154
Tel: (702) 895-4704
Fax: (702) 895-3956
jeffery_shen at ccmail.nevada.edu
www.unlv.edu/faculty/jeffshen





From jn66 at cornell.edu  Mon Nov 18 09:27:27 2002
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Mon, 18 Nov 2002 09:27:27 -0500
Subject: Reprint Request
References: <20021116053120.50390.qmail@web8005.mail.in.yahoo.com>
Message-ID: <3DD8F8CF.DD5C8358@cornell.edu>

Dear Mr. Sushanta Saha:

Thank you for your message. Unfortunately we are not able to give you those
reprints due to copyright issue. Please contact with the original authors
for those papers. You can try to contact with the corresponding author, or
first author if necessary. Please let's know if you have further questions.

Junjian Ni
Curator in Gramene

sushanta saha wrote:

> Dear Dr.
>
> Warm Greetings. Would you please help me by sending
> below mentioned reprint articles and of similar
> titles.
>
> Wang, B.Q. and S.W. Lu 1983. Inheritance of the
> esterase isozyme Est-3 locus in rice. Acta Genet.
> Sinica 10(6):459-464 (in Chinese with English
> summary).
>
> Yi, Q.H., S.Y. Shi and J.R. Jiang 1984. Analysis of
> the esterase isozymes in three lines and F\1\ in Oryza
> sativa and prediction of heterosis. Acta Bot. Sinica
> 26(5):506-512 (in Chinese with English summary).
>
> Zhu, Y.G. nad W.J. Chen 1983. Preliminary study on the
> genetics of esterase isozymes in hybrid rice. Sci.
> Agric. Sinica (5):21-26 (in Chinese with English
> summary).
>
> Thank You
> Sincerely
> Sushanta
>
> =====
> Sushanta Kumar Saha
> Research Scholar
> National Facility for Marine Cyanobacteria
> Bharathidasan University
> Tiruchirappalli - 620 024, INDIA
> E-mail: sushanta at bdu.ernet.in
> Visit us at www.bdu.ernet.in/micro/
>
> ________________________________________________________________________
> Missed your favourite TV serial last night? Try the new, Yahoo! TV.
>        visit http://in.tv.yahoo.com



From pj37 at cornell.edu  Mon Nov 18 12:49:44 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 18 Nov 2002 12:49:44 -0500
Subject: 'Plant Ontology' on Gramene
References: <Pine.GSO.4.44.0211131624170.17631-100000@acoma.Stanford.EDU>
Message-ID: <3DD92838.7A0D2721@cornell.edu>

Hi Everyone,

Is it possible for me to get some idea (in rough figures), on how much
integration of the TAIR antomy has been done in the TAIR datasets. This will
help me before, I start revisions on PO files. In gramene, we have already
curated about 400 mutants, 50 unigene libraries and couple of hundred of
proteins using the anatomy terms listed on our website.

I will appreciate your feedback.

Cheers
Pankaj

Sue Rhee wrote:
> 
> Hi, folks,
> 
> I noticed recently that on your Ontology section of Gramene displays
> 'Plant Ontology' as browsable and searchable.
> 
> http://gramene.org/plant_ontology/
> 
> However, it looks like these ontologies are really Gramene's anatomy and
> developmental stages ontologies, with Gramene IDs, which is good.
> 
> However, We at TAIR feel that we as POC haven't come to enough consensus
> on the agreed-upon 'Plant Ontologies' terms and structure for anatomy and
> developmental stages yet and would like to request that you change the
> word 'Plant Ontology' to something more specific to Gramene. I think it's
> a bit confusing the way it is. The places I'm referring to is:
> 
> 1. The check box for 'Plant Ontology' in the DB search area
> 
> 2. In the 'Current Ontologies' section, rather than 'Plant OntologyTM
> (PO)' I think it should say 'Gramene Ontology' or something to that
> effect.
> 
> Let me know if this is a problem. Perhaps we can talk more about reviving
> the discussions on the PO anatomy and developmental stages at the SOFG and
> Phene meetings...
> 
> Cheers,
> Sue
> -----------------------------------------------------------------------------
> 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   
******************************************


From tberardi at acoma.Stanford.EDU  Mon Nov 18 13:01:31 2002
From: tberardi at acoma.Stanford.EDU (Tanya Berardini)
Date: Mon, 18 Nov 2002 10:01:31 -0800 (PST)
Subject: 'Plant Ontology' on Gramene
In-Reply-To: <3DD92838.7A0D2721@cornell.edu>
Message-ID: <Pine.GSO.4.44.0211180957490.6767-100000@acoma.Stanford.EDU>

Hi Pankaj,

At TAIR, we have 214 gene product annotations to the TAIR anatomical terms
and 13 to the developmental growth stage terms.  You should be able to
meet up with Sue at the SOFG meeting and discuss this in more detail.

Cheers,

Tanya


On Mon, 18 Nov 2002, Pankaj Jaiswal wrote:

> Hi Everyone,
>
> Is it possible for me to get some idea (in rough figures), on how much
> integration of the TAIR antomy has been done in the TAIR datasets. This will
> help me before, I start revisions on PO files. In gramene, we have already
> curated about 400 mutants, 50 unigene libraries and couple of hundred of
> proteins using the anatomy terms listed on our website.
>
> I will appreciate your feedback.
>
> Cheers
> Pankaj
>
> Sue Rhee wrote:
> >
> > Hi, folks,
> >
> > I noticed recently that on your Ontology section of Gramene displays
> > 'Plant Ontology' as browsable and searchable.
> >
> > http://gramene.org/plant_ontology/
> >
> > However, it looks like these ontologies are really Gramene's anatomy and
> > developmental stages ontologies, with Gramene IDs, which is good.
> >
> > However, We at TAIR feel that we as POC haven't come to enough consensus
> > on the agreed-upon 'Plant Ontologies' terms and structure for anatomy and
> > developmental stages yet and would like to request that you change the
> > word 'Plant Ontology' to something more specific to Gramene. I think it's
> > a bit confusing the way it is. The places I'm referring to is:
> >
> > 1. The check box for 'Plant Ontology' in the DB search area
> >
> > 2. In the 'Current Ontologies' section, rather than 'Plant OntologyTM
> > (PO)' I think it should say 'Gramene Ontology' or something to that
> > effect.
> >
> > Let me know if this is a problem. Perhaps we can talk more about reviving
> > the discussions on the PO anatomy and developmental stages at the SOFG and
> > Phene meetings...
> >
> > Cheers,
> > Sue
> > -----------------------------------------------------------------------------
> > 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
> ******************************************
>

-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Mon Nov 18 13:15:20 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 18 Nov 2002 13:15:20 -0500
Subject: 'Plant Ontology' on Gramene
References: <Pine.GSO.4.44.0211180957490.6767-100000@acoma.Stanford.EDU>
Message-ID: <3DD92E38.F8A5F86E@cornell.edu>

Hi Tanya,

Thank you for the figures. This will help. Unfortunately, I am not attending the
SOFG meeting. 
Lincoln will be meeting Sue to discuss more on this at SOFG and I will meet with
her soon at TIGR meeting in December.

Pankaj

Tanya Berardini wrote:
> 
> Hi Pankaj,
> 
> At TAIR, we have 214 gene product annotations to the TAIR anatomical terms
> and 13 to the developmental growth stage terms.  You should be able to
> meet up with Sue at the SOFG meeting and discuss this in more detail.
> 
> Cheers,
> 
> Tanya
> 
> On Mon, 18 Nov 2002, Pankaj Jaiswal wrote:
> 
> > Hi Everyone,
> >
> > Is it possible for me to get some idea (in rough figures), on how much
> > integration of the TAIR antomy has been done in the TAIR datasets. This will
> > help me before, I start revisions on PO files. In gramene, we have already
> > curated about 400 mutants, 50 unigene libraries and couple of hundred of
> > proteins using the anatomy terms listed on our website.
> >
> > I will appreciate your feedback.
> >
> > Cheers
> > Pankaj
> >
> > Sue Rhee wrote:
> > >
> > > Hi, folks,
> > >
> > > I noticed recently that on your Ontology section of Gramene displays
> > > 'Plant Ontology' as browsable and searchable.
> > >
> > > http://gramene.org/plant_ontology/
> > >
> > > However, it looks like these ontologies are really Gramene's anatomy and
> > > developmental stages ontologies, with Gramene IDs, which is good.
> > >
> > > However, We at TAIR feel that we as POC haven't come to enough consensus
> > > on the agreed-upon 'Plant Ontologies' terms and structure for anatomy and
> > > developmental stages yet and would like to request that you change the
> > > word 'Plant Ontology' to something more specific to Gramene. I think it's
> > > a bit confusing the way it is. The places I'm referring to is:
> > >
> > > 1. The check box for 'Plant Ontology' in the DB search area
> > >
> > > 2. In the 'Current Ontologies' section, rather than 'Plant OntologyTM
> > > (PO)' I think it should say 'Gramene Ontology' or something to that
> > > effect.
> > >
> > > Let me know if this is a problem. Perhaps we can talk more about reviving
> > > the discussions on the PO anatomy and developmental stages at the SOFG and
> > > Phene meetings...
> > >
> > > Cheers,
> > > Sue
> > > -----------------------------------------------------------------------------
> > > 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
> > ******************************************
> >
> 
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------

-- 

******************************************
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 kksabu at rediffmail.com  Wed Nov 20 01:13:47 2002
From: kksabu at rediffmail.com (Sabu)
Date: 20 Nov 2002 06:13:47 -0000
Subject: AB-QTL mapping
Message-ID: <20021120061347.23275.qmail@webmail31.rediffmail.com>

An embedded and charset-unspecified text was scrubbed...
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URL: <http://brie4.cshl.edu/pipermail/gramene/attachments/20021120/87dafe37/attachment.ksh>

From tberardi at acoma.Stanford.EDU  Thu Nov 21 12:35:50 2002
From: tberardi at acoma.Stanford.EDU (Tanya Berardini)
Date: Thu, 21 Nov 2002 09:35:50 -0800 (PST)
Subject: simple question
In-Reply-To: <3DDC9389.1090900@pmtg.u-bordeaux2.fr>
Message-ID: <Pine.GSO.4.44.0211210922310.21117-100000@acoma.Stanford.EDU>

Dear Aurelien,

I see now where the problem arose.  When you download the Ontology.tgz
file from Gramene from the site you describe, this includes the three GO
ontologies as well as the plant anatomy and developmental stages
ontologies.  The GO ontologies should be identical with those you can
download from GO consortium site. In this case, it appears that the files
have gone out of sync.

As Midori mentioned in her prior email, the GO term hemoglobin GO:0005833
has been renamed 'hemoglobin complex' with the same GO id in order to
better reflect the fact that this is a component term.  This should be
reflected in the next update that Gramene does to its database. (Correct
me if I'm wrong, Gramene folks.)

Hope this clarifies matters.

Regards,

Tanya


On Thu, 21 Nov 2002, abarre wrote:

> I know that plant have hemoglobin (like the leghemoglobin). My trouble
> was to see this term in the plant ontology and not in the
> gene ontology !
> I use the latest release of the Plant Ontologie, download on
> www.gramene.org.
> (ftp://ftp.gramene.org/pub/gramene/gramene_database)
>
>
>   **
>
> Hemoglobin in Plant Ontology :
> id=5382
> accession = 0005833
>
> * 0003673 : * Gene_Ontology
> <javascript:popup('info.php?info_type=1&term_id=1&nom=Gene_Ontology',(screen.width*0.7),(screen.height*0.7))>
>
> ===== * 0005575 : * cellular_component
> <javascript:popup('info.php?info_type=1&term_id=5135&nom=cellular_component',(screen.width*0.7),(screen.height*0.7))>
>
> ======= * 0005623 : * cell
> <javascript:popup('info.php?info_type=1&term_id=5136&nom=cell',(screen.width*0.7),(screen.height*0.7))>
>
> ========   * 0005622 : * intracellular
> <javascript:popup('info.php?info_type=1&term_id=5180&nom=intracellular',(screen.width*0.7),(screen.height*0.7))>
>
> =========== * 0005737 : * cytoplasm
> <javascript:popup('info.php?info_type=1&term_id=5268&nom=cytoplasm',(screen.width*0.7),(screen.height*0.7))>
>
> ============ * 0005829 : * cytosol
> <javascript:popup('info.php?info_type=1&term_id=5362&nom=cytosol',(screen.width*0.7),(screen.height*0.7))>
>
> ============== * 0005833 : * hemoglobin
> <javascript:popup('info.php?info_type=1&term_id=5382&nom=hemoglobin',(screen.width*0.7),(screen.height*0.7))>
>
>
>
>
> thanks for your answer !
>
>
> Tanya Berardini wrote:
>
> >Dear Aurelien,
> >
> >TAIR is part of the consortium that has been developing the Plant
> >Ontologies (anatomy and developmental stages).  Which plant ontology are
> >you using that contains the term hemoglobin, what is the term ID and from
> >where did you download the ontology? Your answers to these questions will
> >help me to track down the source of your problem.
> >
> >By the way, plants do have hemoglobin genes.  See :
> >
> >1:  Hunt PW, Watts RA, Trevaskis B, Llewelyn DJ, Burnell J, Dennis ES,
> >Peacock WJ. Related Articles, Links
> >
> >Expression and evolution of functionally distinct haemoglobin genes in
> >plants.
> >Plant Mol Biol. 2001 Nov;47(5):677-92.
> >PMID: 11725952 [PubMed - indexed for MEDLINE]
> >
> >2:  Watts RA, Hunt PW, Hvitved AN, Hargrove MS, Peacock WJ, Dennis ES.
> >Related Articles, Links
> >
> >A hemoglobin from plants homologous to truncated hemoglobins of
> >microorganisms.
> >Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10119-24.
> >PMID: 11526234 [PubMed - indexed for MEDLINE]
> >
> >3:  Trevaskis B, Watts RA, Andersson CR, Llewellyn DJ, Hargrove MS, Olson
> >JS, Dennis ES, Peacock WJ. Related Articles, Links
> >
> >Two hemoglobin genes in Arabidopsis thaliana: the evolutionary origins of
> >leghemoglobins.
> >Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):12230-4.
> >PMID: 9342391 [PubMed - indexed for MEDLINE]
> >
> >(among others)
> >
> >
> >Regards,
> >
> >Tanya Berardini
> >
> >On Wed, 20 Nov 2002, abarre wrote:
> >
> >
> >
> >>Hi,
> >>
> >>I was looking for the terl present in Plnat Ontology and not in Gene
> >>Ontology.
> >>Among the list, there's "hemoglobin". For me the hemoglobin is not a
> >>specific term of plant !!!!
> >>
> >>This term is really absent in latest release of Gene Ontology but was
> >>present in the precedent (as cellular component, GO:0005833) !
> >>Something change in blood composition ? I thought it had become OBSOLETE
> >>in this case !
> >>
> >>
> >>
> >>
> >>
> >
> >-------------------------------------------------------------------------------
> >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
> >-------------------------------------------------------------------------------
> >
> >
> >
>
>
>

-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------




From FCheung at tigr.org  Wed Nov 20 17:44:53 2002
From: FCheung at tigr.org (Cheung, Foo)
Date: Wed, 20 Nov 2002 17:44:53 -0500
Subject: Plant promoter prediction software
Message-ID: <BF416591A731D411A883009027B11E9703859B86@mailserver.tigr.org>

Hello


I was wondering whether anyone knew of any plant promoter prediction
software that is available?


Many thanks in advance
kind regards
Foo


From jingyu at dnalandmarks.ca  Thu Nov 21 15:00:27 2002
From: jingyu at dnalandmarks.ca (jingyu at dnalandmarks.ca)
Date: Thu, 21 Nov 2002 15:00:27 -0500
Subject: Plant promoter prediction software
Message-ID: <OF861283BD.1238AE3D-ON85256C78.006BE4AF@dnalandmarks.ca>

Softberry - www.softberry.com/berry.phtml?topic=promoter&prg=TSSP
Genomatix - www.genomatix.de/software_services/software/products.html
Promoter Prediction Server - www.cbs.dtu.dk/services/Promoter/

Jing



                                                                                          
                    "Cheung, Foo"                                                         
                    <FCheung at tigr.org       To:     "'gramene at gramene.org'"               
                    >                        <gramene at gramene.org>                        
                    Sent by:                cc:                                           
                    owner-gramene at bri       Subject:     Plant promoter prediction        
                    e.cshl.org               software                                     
                                                                                          
                                                                                          
                    11/20/2002 05:44                                                      
                    PM                                                                    
                    Please respond to                                                     
                    gramene; Please                                                       
                    respond to                                                            
                    "Cheung, Foo"                                                         
                                                                                          
                                                                                          




Hello


I was wondering whether anyone knew of any plant promoter prediction
software that is available?


Many thanks in advance
kind regards
Foo





From pj37 at cornell.edu  Thu Nov 21 16:58:36 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 21 Nov 2002 16:58:36 -0500
Subject: simple question
References: <Pine.GSO.4.44.0211210922310.21117-100000@acoma.Stanford.EDU>
Message-ID: <3DDD570C.E69A9DBB@cornell.edu>

Hi Tanya,

Thank you for addressing Aurelien's concerns. Your assumption was right. The
Gramene database file at ftp://ftp.gramene.org/pub/gramene/gramene_database has
a zipped archive of the three ontologies and its associations, leading to the
confusion on GO occurring to dear Aurelien. 

For everybody's information, Gramene does the updates every three months only
and the next one is scheduled for December'2002. For up to date GO database and
files I would recommend the users to fetch it from GO itself.

Regards,

Pankaj  

Tanya Berardini wrote:
> 
> Dear Aurelien,
> 
> I see now where the problem arose.  When you download the Ontology.tgz
> file from Gramene from the site you describe, this includes the three GO
> ontologies as well as the plant anatomy and developmental stages
> ontologies.  The GO ontologies should be identical with those you can
> download from GO consortium site. In this case, it appears that the files
> have gone out of sync.
> 
> As Midori mentioned in her prior email, the GO term hemoglobin GO:0005833
> has been renamed 'hemoglobin complex' with the same GO id in order to
> better reflect the fact that this is a component term.  This should be
> reflected in the next update that Gramene does to its database. (Correct
> me if I'm wrong, Gramene folks.)
> 
> Hope this clarifies matters.
> 
> Regards,
> 
> Tanya
> 
> On Thu, 21 Nov 2002, abarre wrote:
> 
> > I know that plant have hemoglobin (like the leghemoglobin). My trouble
> > was to see this term in the plant ontology and not in the
> > gene ontology !
> > I use the latest release of the Plant Ontologie, download on
> > www.gramene.org.
> > (ftp://ftp.gramene.org/pub/gramene/gramene_database)
> >
> >
> >   **
> >
> > Hemoglobin in Plant Ontology :
> > id=5382
> > accession = 0005833
> >
> > * 0003673 : * Gene_Ontology
> > <javascript:popup('info.php?info_type=1&term_id=1&nom=Gene_Ontology',(screen.width*0.7),(screen.height*0.7))>
> >
> > ===== * 0005575 : * cellular_component
> > <javascript:popup('info.php?info_type=1&term_id=5135&nom=cellular_component',(screen.width*0.7),(screen.height*0.7))>
> >
> > ======= * 0005623 : * cell
> > <javascript:popup('info.php?info_type=1&term_id=5136&nom=cell',(screen.width*0.7),(screen.height*0.7))>
> >
> > ========   * 0005622 : * intracellular
> > <javascript:popup('info.php?info_type=1&term_id=5180&nom=intracellular',(screen.width*0.7),(screen.height*0.7))>
> >
> > =========== * 0005737 : * cytoplasm
> > <javascript:popup('info.php?info_type=1&term_id=5268&nom=cytoplasm',(screen.width*0.7),(screen.height*0.7))>
> >
> > ============ * 0005829 : * cytosol
> > <javascript:popup('info.php?info_type=1&term_id=5362&nom=cytosol',(screen.width*0.7),(screen.height*0.7))>
> >
> > ============== * 0005833 : * hemoglobin
> > <javascript:popup('info.php?info_type=1&term_id=5382&nom=hemoglobin',(screen.width*0.7),(screen.height*0.7))>
> >
> >
> >
> >
> > thanks for your answer !
> >
> >
> > Tanya Berardini wrote:
> >
> > >Dear Aurelien,
> > >
> > >TAIR is part of the consortium that has been developing the Plant
> > >Ontologies (anatomy and developmental stages).  Which plant ontology are
> > >you using that contains the term hemoglobin, what is the term ID and from
> > >where did you download the ontology? Your answers to these questions will
> > >help me to track down the source of your problem.
> > >
> > >By the way, plants do have hemoglobin genes.  See :
> > >
> > >1:  Hunt PW, Watts RA, Trevaskis B, Llewelyn DJ, Burnell J, Dennis ES,
> > >Peacock WJ. Related Articles, Links
> > >
> > >Expression and evolution of functionally distinct haemoglobin genes in
> > >plants.
> > >Plant Mol Biol. 2001 Nov;47(5):677-92.
> > >PMID: 11725952 [PubMed - indexed for MEDLINE]
> > >
> > >2:  Watts RA, Hunt PW, Hvitved AN, Hargrove MS, Peacock WJ, Dennis ES.
> > >Related Articles, Links
> > >
> > >A hemoglobin from plants homologous to truncated hemoglobins of
> > >microorganisms.
> > >Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10119-24.
> > >PMID: 11526234 [PubMed - indexed for MEDLINE]
> > >
> > >3:  Trevaskis B, Watts RA, Andersson CR, Llewellyn DJ, Hargrove MS, Olson
> > >JS, Dennis ES, Peacock WJ. Related Articles, Links
> > >
> > >Two hemoglobin genes in Arabidopsis thaliana: the evolutionary origins of
> > >leghemoglobins.
> > >Proc Natl Acad Sci U S A. 1997 Oct 28;94(22):12230-4.
> > >PMID: 9342391 [PubMed - indexed for MEDLINE]
> > >
> > >(among others)
> > >
> > >
> > >Regards,
> > >
> > >Tanya Berardini
> > >
> > >On Wed, 20 Nov 2002, abarre wrote:
> > >
> > >
> > >
> > >>Hi,
> > >>
> > >>I was looking for the terl present in Plnat Ontology and not in Gene
> > >>Ontology.
> > >>Among the list, there's "hemoglobin". For me the hemoglobin is not a
> > >>specific term of plant !!!!
> > >>
> > >>This term is really absent in latest release of Gene Ontology but was
> > >>present in the precedent (as cellular component, GO:0005833) !
> > >>Something change in blood composition ? I thought it had become OBSOLETE
> > >>in this case !
> > >>
> > >>
> > >>
> > >>
> > >>
> > >
> > >-------------------------------------------------------------------------------
> > >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
> > >-------------------------------------------------------------------------------
> > >
> > >
> > >
> >
> >
> >
> 
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------

-- 

******************************************
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 kksabu at rediffmail.com  Tue Nov 26 21:37:54 2002
From: kksabu at rediffmail.com (Sabu)
Date: 27 Nov 2002 02:37:54 -0000
Subject: Plant Breeding Nomenclature
Message-ID: <20021127023754.3448.qmail@mailweb33.rediffmail.com>

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From kuldeep35 at yahoo.com  Thu Nov 28 23:41:52 2002
From: kuldeep35 at yahoo.com (Kuldeep Singh)
Date: Thu, 28 Nov 2002 20:41:52 -0800 (PST)
Subject: Plant Breeding Nomenclature
In-Reply-To: <20021127023754.3448.qmail@mailweb33.rediffmail.com>
Message-ID: <20021129044152.81397.qmail@web40711.mail.yahoo.com>

Dear Dr Sabu
It should be BC1F1 and BC1S1
with regards
Kuldeep
--- Sabu <kksabu at rediffmail.com> wrote:
> Hi!
> 
> I just wonder which nomenclature is correct for the first 
> backcross progenies, BC1 or BC1F1. Also when one selfed the 
> backcross progeny like BC1 x BC1, then the resultant ones would be 
> BC1F1 or BC1S1?
> 
> Thanks
> Sabu
> 
> 
> KK Sabu PhD
> Post Doctoral Fellow
> Plant Genetics and Biotechnology
> School of Environmental and Natural Resource Sciences
> Faculty of Science and Technology
> National University of Malaysia
> 43600 Bangi, Selangor
> Tel: 603-89215870, Fax: 603-89253357
> kksabu at yahoo.com


__________________________________________________
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From srm4 at cornell.edu  Wed Nov 27 15:11:03 2002
From: srm4 at cornell.edu (Susan McCouch)
Date: Wed, 27 Nov 2002 16:11:03 -0400
Subject: Plant Breeding Nomenclature
In-Reply-To: <20021127023754.3448.qmail@mailweb33.rediffmail.com>
References: <20021127023754.3448.qmail@mailweb33.rediffmail.com>
Message-ID: <p05100301ba0ad512ab13@[128.253.184.76]>

Hi Sabu,

I see that Dr. Junjian Ni has already replied to your question.  I 
would like to add one thing:  the term S1 is used for outcrossing 
species where you have to artificially create a self.  The first 
generation of selfing in an outcrossing species is called an S1, but 
the same generation in a naturally inbreeding species is called an 
F2.  Thus, S1 is equivalent to F2 in terms of the generation, but we 
rarely use the S designation in rice, and the F designation is rarely 
used in something like maize.

I hope that helps.

Regards, Susan McCouch


>Hi!
>
>I just wonder which nomenclature is correct for the first backcross 
>progenies, BC1 or BC1F1. Also when one selfed the backcross progeny 
>like BC1 x BC1, then the resultant ones would be BC1F1 or BC1S1?
>
>Thanks
>Sabu
>
>
>KK Sabu PhD
>Post Doctoral Fellow
>Plant Genetics and Biotechnology
>School of Environmental and Natural Resource Sciences
>Faculty of Science and Technology
>National University of Malaysia
>43600 Bangi, Selangor
>Tel: 603-89215870, Fax: 603-89253357
>kksabu at yahoo.com


-- 
******************************************
Susan McCouch
Dept of Plant Breeding
418 Bradfield Hall
Cornell University
Ithaca, NY  14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu

******************************************


From jn66 at cornell.edu  Wed Nov 27 12:15:15 2002
From: jn66 at cornell.edu (Jun Jian Ni)
Date: Wed, 27 Nov 2002 12:15:15 -0500
Subject: (no subject)
Message-ID: <3DE4FDA3.C198211B@cornell.edu>

Hi Dr. Sabu,

Thank you for your message.

I would like to say it is interesting and also confusing question. Based

on my understanding and the confirmation with one of my friend who has
worked in rice breeding field for many years, it should be like as
follows:

BC1 is equal to BC1F1. BC2F1 = BC2, etc.  BC1 selfs (BC1 X BC1)
resulting BC1F2. BC2 selfs to produce BC2F2. I made a diagram using
Powerpoint for
your reference (See attached file).

As I know, there are different systems used by other researchers. I
think it will be helpful to use figure or free text for detail
explanation while using those names.

I hope this info helpful for you.

Junjian Ni
Curator in Gramene
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From pdveg at up.nic.in  Sat Nov 16 12:33:49 2002
From: pdveg at up.nic.in (pdveg)
Date: Sat, 16 Nov 2002 23:03:49 +0530
Subject: Plant Breeding Nomenclature
Message-ID: <002e01c28d96$6002c400$1d00005a@pdvr.up.nic.in>


-----Original Message-----
From: Sabu <kksabu at rediffmail.com>
To: gramene at gramene.org <gramene at gramene.org>
Cc: jn66 at cornell.edu <jn66 at cornell.edu>; D.BRAR at cgiar.org <D.BRAR at cgiar.org>
Date: Wednesday, November 27, 2002 10:15 PM
Subject: Plant Breeding Nomenclature


>Hi!
>
>I just wonder which nomenclature is correct for the first
>backcross progenies, BC1 or BC1F1.

BC1F1 is more frequently used and in my openion rightly so.

Also when one selfed the backcross progeny like BC1 x BC1, then the
resultant ones would be BC1F1 or BC1S1?


As u r selfing BC1F1, in my perception it should be BC1F2

Sanjeet Kumar
Scientist (genetics)
Indian Institute of Vegetable Research
Varanasi-221 005
India
Thanks
>Sabu
>
>
>KK Sabu PhD
>Post Doctoral Fellow
>Plant Genetics and Biotechnology
>School of Environmental and Natural Resource Sciences
>Faculty of Science and Technology
>National University of Malaysia
>43600 Bangi, Selangor
>Tel: 603-89215870, Fax: 603-89253357
>kksabu at yahoo.com



