From pj37 at cornell.edu  Mon Apr  1 14:34:23 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Mon, 01 Apr 2002 14:34:23 -0500
Subject: Plant Ontology Relationship type ?
Message-ID: <3CA8B63F.7F176528@cornell.edu>

Dear Michael,

I have a question about the "term type". In the following example(GPO:IDs are my
internal work IDs) from a plant anatomy, there are several terms under
%androecium_type ; GPO:0200060 as its instances, however, all these terms are
actually various "TYPES of" or modifications of androecium found in various
plant genera. Same is true for instances of  %stamen_structure ; GPO:0200458,
where the terms are instances of various structural forms of  stamen.

    %flower ; GPO:0200470
     <androecium ; GPO:0200002 < floret ; GPO:0200464 < flower ; GPO:0200038
      %androecium_type ; GPO:0200060
       %apostemonous ; GPO:0200455
       %diadelphous ; GPO:0200388
       %gynandrial ; GPO:0200453 ; synonym:gynosteminal
       %monadelphous ; GPO:0200452
       %petalostemonous ; GPO:0200454
       %polyandrous ; GPO:0200465
       %polydelphous ; GPO:0200456
       %syngenesious ; GPO:0200457
      <stamen ; GPO:0200190
       <anther ; GPO:0200187
        <anther locule ; GPO:0200025 ; synonym:anther lobe
         <pollen sac ; GPO:0200026
         <tapetum ; GPO:0200152
        <pollen ; GPO:0200151 ; synonym:microspore ; synonym:pollen grain
       <anther filament ; GPO:0200189
        <filament connective ; GPO:0200188
       %stamen_structure ; GPO:0200458
        %stamen_appendicular ; GPO:0200459
        %stamen_filantherous ; GPO:0200463
        %stamen_laminar ; GPO:0200461
        %stamen_petalantherous ; GPO:0200460
        %stamen_petaloid ; GPO:0200462
      %staminodium ; GPO:0200041
       %staminal disc ; GPO:0200040

We can consider them using as attributes, however they are very specific to the
plant part anatomy. In the examples, I have tried to represent the terms as
either

      %androecium_type ; GPO:0200060
       %apostemonous ; GPO:0200455
       %diadelphous ; GPO:0200388
or

       %stamen_structure ; GPO:0200458
        %stamen_appendicular ; GPO:0200459
        %stamen_filantherous ; GPO:0200463

Can you suggest which is the best way to represent them in plant ontology.
Should I use them like       
      %androecium_type ; GPO:0200060
       %apostemonous ; GPO:0200455
       %diadelphous ; GPO:0200388

or 

      %androecium_type ; GPO:0200060
       %androecium_apostemonous ; GPO:0200455
       %androecium_diadelphous ; GPO:0200388

Second question is on relating them as instances of either %androecium_type ;
GPO:0200060  or %stamen_structure ; GPO:0200458.  If we can use a different
relationship type as "TYPEOF" androecium or stamen, then we may avoid using the
X_structure or X_type term. If you think I can do as said just now, then can you
recommend using a particular character for the "TYPEOF" relationship. It is not
a derived from relationship

    

Regards

Pankaj


******************************************
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 liuxx175 at tc.umn.edu  Mon Apr  1 12:23:38 2002
From: liuxx175 at tc.umn.edu (Sixin Liu)
Date: Mon, 1 Apr 2002 09:23:38 -0800
Subject: please update links to GrainGenes
Message-ID: <l03130300b8ce46268b13@[134.84.43.63]>

Hello,

Please update links to GrainGenes. For example, after looking up AP002541,
the ESTs linked to GrainGenes does not work any more. The new URL of
GrainGenes is http://www.graingenes.org.

Thanks,

Sixin Liu
University of Minnesota




From ma11 at gen.cam.ac.uk  Sun Apr  7 15:05:28 2002
From: ma11 at gen.cam.ac.uk (Michael Ashburner (Genetics))
Date: Sun, 7 Apr 2002 20:05:28 +0100
Subject: Plant Ontology Relationship type ?
Message-ID: <E16uHyi-0001hW-00@ma11.gen.cam.ac.uk>


Pankaj

I do not understand why you need the *-type concept at all, what is
wrong with

     <androecium ; GPO:0200002 < floret ; GPO:0200464 < flower ; GPO:0200038
      %apostemonous ; GPO:0200455
      %diadelphous ; GPO:0200388

OR
     <androecium ; GPO:0200002 < floret ; GPO:0200464 < flower ; GPO:0200038
      %apostemonous androecium ; GPO:0200455
      %diadelphous androecium ; GPO:0200388
#

      <stamen ; GPO:0200190
       %stamen_appendicular ; GPO:0200459
       %stamen_filantherous ; GPO:0200463

or

      <stamen ; GPO:0200190
       %appendicular stamen ; GPO:0200459
       %filantherous stamen ; GPO:0200463


Michael


From lazo at pw.usda.gov  Thu Apr 11 14:51:19 2002
From: lazo at pw.usda.gov (Gerard R Lazo)
Date: Thu, 11 Apr 2002 11:51:19 -0700 (PDT)
Subject: subscription to gramene-announce
Message-ID: <200204111851.g3BIpJb03570@wheat.pw.usda.gov>

Thank you!

-                                                                      -
Gerard R Lazo    / USDA-ARS-Western Regional Research Ctr \ 510.559.5640
lazo at pw.usda.gov \ 800 Buchanan St, Albany, CA 94710-1105 / 510.559.6449

> From: Steven Schmidt <schmidt at brie.cshl.org>
> Date: Thu, 11 Apr 2002 13:11:58 -0400
> MIME-Version: 1.0
> To: gramene-announce at brie.cshl.org
> Subject: subscription to gramene-announce
> Content-Transfer-Encoding: 8bit
> X-MIME-Autoconverted: from quoted-printable to 8bit by stein.cshl.org id 
NAA12766
> 
> Hi,
> You have been subscribed to the gramene-announce list.
> This list will contain announcements of new features available at 
> www.gramene.org
> 
> To unsubscribe from this list, send mail to 
> majordomo at gramene.org
> with
> unsubscribe gramene-announce
> in the BODY of the message.
> 
> To correspond with gramene developers and users, subscribe to the gramene list
> (send mail to 
> majordomo at gramene.org
> with
> subscribe gramene
> in the BODY of the message.)
> 
> For information on recent developments, look at
> http://www.gramene.org/whatsnew.html
> 
> -- 
> Steven Schmidt
> www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977
> 
> 
> 




From normanac at terra.com.mx  Sun Apr 14 02:53:25 2002
From: normanac at terra.com.mx (=?iso-8859-1?Q?Ra=FAl_Arredondo-Peter?=)
Date: Sun, 14 Apr 2002 01:53:25 -0500
Subject: Request of help.
Message-ID: <000a01c1e381$15495ba0$261ef694@hppav>

Dear Sir/Madam:

I would appreciate any help to identify the chromosomal location of the following genes: O04986, O04985, Q94FT8 and Q94FT7. From your web page apparently there is no link between the accession numbers and the bac names.

Sincerely,

Raul Arredondo-Peter

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From teytelma at stein.cshl.org  Mon Apr 15 11:55:21 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Mon, 15 Apr 2002 11:55:21 -0400 (EDT)
Subject: Request of help.
In-Reply-To: <000a01c1e381$15495ba0$261ef694@hppav>
Message-ID: <Pine.GSO.4.05.10204151138250.4259-100000@phage.cshl.org>

Dear Raul,

Please keep in mind that the rice sequencing is still in progress.  If the
clone which contains a given gene has not been sequenced yet or is in
phase 1, it will not be in the Genome Browser.

Those genes that are in the sequenced IRGSP clones will have links into
the genome browser.

Sincerely,

Lenny Teytelman

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

On Sun, 14 Apr 2002, [iso-8859-1] Ra?l Arredondo-Peter wrote:

> Dear Sir/Madam:
> 
> I would appreciate any help to identify the chromosomal location of the following genes: O04986, O04985, Q94FT8 and Q94FT7. From your web page apparently there is no link between the accession numbers and the bac names.
> 
> Sincerely,
> 
> Raul Arredondo-Peter
> 
> 




From teytelma at stein.cshl.org  Mon Apr 15 11:55:21 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Mon, 15 Apr 2002 11:55:21 -0400 (EDT)
Subject: Request of help.
In-Reply-To: <000a01c1e381$15495ba0$261ef694@hppav>
Message-ID: <Pine.GSO.4.05.10204151138250.4259-100000@phage.cshl.org>

Dear Raul,

Please keep in mind that the rice sequencing is still in progress.  If the
clone which contains a given gene has not been sequenced yet or is in
phase 1, it will not be in the Genome Browser.

Those genes that are in the sequenced IRGSP clones will have links into
the genome browser.

Sincerely,

Lenny Teytelman

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

On Sun, 14 Apr 2002, [iso-8859-1] Ra?l Arredondo-Peter wrote:

> Dear Sir/Madam:
> 
> I would appreciate any help to identify the chromosomal location of the following genes: O04986, O04985, Q94FT8 and Q94FT7. From your web page apparently there is no link between the accession numbers and the bac names.
> 
> Sincerely,
> 
> Raul Arredondo-Peter
> 
> 




From pj37 at cornell.edu  Tue Apr 16 10:17:01 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 16 Apr 2002 10:17:01 -0400
Subject: Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
References: <Pine.GSO.4.44.0204151913500.11892-100000@acoma.Stanford.EDU>
Message-ID: <3CBC325D.538554F6@cornell.edu>

Hi Leonore ,

I saw the changes you made at GOBO on GOCVS. It is like

!autogenerated-by:     DAG-Edit version 1.311
!saved-by:             lreiser
!date:                 Mon Apr 15 18:32:37 PDT 2002
!version: $Revision: 1.2 $
!editors: Leonore Reiser, Jonathan Clarke
$TAIR_ontology_of_arabidopsis ; TAIR:0000001
 %TAIR_anatomy_of_Arabidopsis ; TAIR:0000111
  %whole organism ; TAIR:0000304
   <cell type ; TAIR:0000298
    %aerenchyma cell ; TAIR:0000294
    %antipodal cell ; TAIR:0000192 < megagametophyte ; TAIR:0000188
    %atrichoblast ; TAIR:0000263 ; synonym:non-hair cell < elongation zone ;
TAIR:0000324 < root epidermis ; TAIR:0000361
    %cambial initial ; TAIR:0000295
    %central cell ; TAIR:0000194 < megagametophyte ; TAIR:0000188
     <polar nucleus ; TAIR:0000196

I am still surprised to see the identifiers that we agreed not to have, although
it does make sense to have them, since it is representing Arabidopsis. In the
past we agreed to have a PO identifier and an assigned number space similar to
GO. However, what I could recollect from the conference call and some other e
mails is that Sue (TAIR) did not want to create another accession and virtually
agreed to use the PO identifier for the terms coming from anatomy and
developmental stages. We also agreed and the same was again followed up when I
had a talk with Tanya last week, that its fine. The reason, since TAIR has
already released the arabidopsis anatomy and temporal ontology to the public
which the people might have started using them. Given the situation its wise for
us to use the terms with PO identifiers to make it generic for others to use
(attributing the PO terms, with the original TAIR ID:1111xxx as a DBXref.) and
identify it by the number space showing it was contributed by TAIR.

Following our conversations on e mail, I am adopting the same strategy, while
integrating the TAIR terms in a test release of PO.  

Here is an example of my flat file, (the example, helps me in integrating the
TAIR terms in PO since it allows me to use DAG edit tool to drag and drop the
DBXref field, that's why you see TAIR written twice once as DBXref and another
as synonym). I will clean the flat file once I am done with the complete
integration.


$Plant ontology ; PO:0006561
 %plant anatomy ; PO:0005025
  %whole organism ; PO:0000304 ; TAIR:1111304 ; synonym:TAIR\:1111304
   <cell type ; PO:0000298 ; TAIR:1111298 ; synonym:TAIR\:1111298
    %aerenchyma cell ; PO:0000294 ; TAIR:1111294 ; synonym:TAIR\:1111294
    %antipodal cell ; PO:0000192 ; TAIR:1111192 ; synonym:TAIR\:1111192 <
megagametophyte ; PO:0000188

I am in the process of compiling the integrated version and putting it up on the
web (test version) for everyone from POC to look at it. At the moment my
suggestion would be of not changing anything on our respective databases untill,
the integration is complete. I wish we would be able to integrate the PO very
soon. 

I will be happy to share my flat files, once I am satisfied with the draft
version. 

With kind regards

Pankaj


Leonore Reiser wrote:
> 
> I finally got around to changing the numberspace- I removed the leading
> zeros so now TAIR terms start from 0000001-
> 
> since I only changed the 1111 to 0000 the  last 3 digits should be the
> same.
> I have updated this in gobo on GO cvs and will update files in TAIR's ftp
> site and literature curation database tomrrow.
> 
> Leonore
> 
> On Fri, 22 Mar 2002, Vincent, Leszek wrote:
> 
> > Hi Colleagues
> >
> > Lots of good email 'dialogue' has been taking place during the past few days, predominantly regarding the questions of number space & prefix.
> >
> > Based on what's been offered here's my synthesis / proposal.
> >
> > Number Space: Allocation of groups of 5,000 numbers from within the 7 digit number space as follows:
> >
> > 0000001 - 0005000     TAIR
> > 0005001 - 0010000     GRAMENE
> > 0010001 - 0015000     IRRI
> > 0015001 - 0020000     MAIZEDB
> >
> > This would seem to provide ample number space for each group's development of ontologies. It also provides lots of room for further number space allocations to be made to new plant ontologists.
> >
> > Prefix: PO is to be used as the prefix for all the ontologies originating from the various collaborating groups of the POC. Anatomy, development, temporal etc. ontologies will all be included under the PO umbrella prefix (this parallels the GO paradigm). The same applies to Trait ontologies (TO), however it is represented.
> >
> > May I suggest that we consider acknowledging the source of the relevant CV terms by inserting our database 'acronym' and perhaps the initials of the curator in the Dbxref field adjacent to the term definition field in DAG-Edit (e.g. MAIZEDB:pldv, GRAMENE:pj, TAIR:lr etc.). This would be in addition to the relevant Dbxref info. provided for the term being defined. Leonore did this for some of the terms in her anatomy ontology & I think it provides a useful link to the origins of the term - perhaps especially important with us working in a multi-species arena. It seems like the browser would need to be tweaked so that this Dbxref field is displayed. In any case I think it is very important that the Dbxref info. for the term definition be displayed as it's an important component of the definition. So also including the database abbreviation & curator initials from this Dbxref field should be feasible. Comments on this??
> >
> > The conference call stimulated considerable thought about matters raised during the call and it has been great reading the constructive dialogue that has followed. Thanks for working to reach consensus.
> >
> > I'll copy the recent emails to Victor Ulat, Richard's DB colleague at IRRI - add his email to your list (V.ULAT at CGIAR.ORG).
> >
> > If you think I've misrepresented something please don't hesitate to point this out to me - we're learning together.
> >
> > Sincerely,
> > - Leszek
> > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > P. Leszek D. Vincent Ph.D., FLS
> > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> > University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
> > 884-3716 (Agronomy), Fax:(573) 884-7850;
> > Ph/Fax (Home): (573) 441-1228;
> > Email: Leszek at missouri.edu
> > Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> > (http://www.cafnr.missouri.edu/mmp/ and  http://www.agron.missouri.edu/)
> > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> >
> > > -----Original Message-----
> > > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > Sent: Friday, March 22, 2002 2:42 PM
> > > To: Pankaj Jaiswal
> > > Cc: Vincent, Leszek; Coe, Edward H.; Polacco, Mary L.; Curator TAIR;
> > > Leonor Reiser; Richard Bruskiewich; Tanya; Lincoln Stein;
> > > Susan McCouch;
> > > Doreen Ware; brie
> > > Subject: Re: [Fwd: FW: suggestions for 'POC' methods]
> > >
> > >
> > > Pankaj,
> > >
> > > Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> > > Ontology accessions to be used with the PO prefix. And we are
> > > also good
> > > with leaving out trait ontolgies as a part of PO for now, particularly
> > > because there may be a more general trait ontology developing
> > > and it may
> > > be more desirable to minimize the number of Accessions for
> > > the same term.
> > >
> > > If we agree on the 7 digit integer, we would like to use up
> > > 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR
> > > temporal or
> > > 0000001-0002000 and 0002001-0003000, respectively if you want
> > > a leading
> > > zero, since we already have these accessions associated to
> > > the terms we
> > > have.
> > >
> > > I'm not sure what you mean below when you say you will
> > > provide PO IDs from
> > > the database for TAIR terms and use TAIR IDs as synonyms.
> > > Since we agree
> > > on the namespace, there will be one and only one accession
> > > for the TAIR
> > > anatomy and temporal terms. We will have internal identifiers
> > > but these
> > > won't need to be used externally.
> > >
> > > > Lastly but not the least, since we are designating the
> > > number space to every
> > > > group, I am not hesitant in using the TAIR IDs as either
> > > DBXref/synonyms. Next
> > > > time when we update the DB I will provide the PO ID for the
> > > anatomy/development
> > > > term, and will use the TAIR ID as either the synonym or
> > > DBXref, if you agree.
> > > > Could you please tell me if you have already incorporated
> > > these terms/IDs in
> > > > your curation or still in the process of using them. It
> > > will help us at Gramene
> > > > in setting up the tables and browser. Even though I am
> > > suggesting all these view
> > > > points you will agree that it takes a certain amount of
> > > resources and time and
> > > > everyone of us is limited within the scope and mandate, we
> > > will try our best.
> > > >
> > > > Thanks
> > > >
> > > > Pankaj
> > > >
> > > > Sue Rhee wrote:
> > > > >
> > > > > Hi, Pankaj,
> > > > >
> > > > > I don't see that Michael is suggesting one versus the
> > > other in what I can
> > > > > make out of the message below. The important issue about
> > > the identifier is
> > > > > that we divide up the numberspaces among the three groups
> > > such that we do
> > > > > not use the same number (accession). We reached an
> > > agreement on this
> > > > > yesterday, yes?
> > > > >
> > > > > We have been designating a seven digit number and if this
> > > is suitable for
> > > > > everyone, each group can take 10,000 numbers to start
> > > with (We've used up
> > > > > ~200 in Anatomy).
> > > > >
> > > > > In terms of the prefix, the reason I see for using a
> > > prefix to this number
> > > > > accession is to distinguish the shared plant anatomy ontology from
> > > > > different ontologies (e.g. GO, and inevitabley more
> > > ontologies to follow).
> > > > > Since we agreed on making a shared plant anatomy
> > > ontology, using PA as the
> > > > > prefix sounds ok to me so long as it is limited to 'Plant Anatomy
> > > > > Ontology' and that we stick to the numberspaces for the
> > > numbers (so that
> > > > > we don't create yet another accession for anatomy for
> > > Arabidopsis, for
> > > > > example).
> > > > >
> > > > > PO sounds a bit too general for this ontology. If we
> > > agree on making a
> > > > > combined plant ontology for Developmental Stages (or
> > > temporal), we can
> > > > > perhaps designate a different prefix. At this point, it
> > > is not clear to me
> > > > > that we can develop a combined temporal ontology for
> > > plants, but it is
> > > > > certainly worth a try if you are willing/interested. It
> > > is likely that the
> > > > > development of Trait and other types of ontologies would
> > > occur as a
> > > > > collaboration of more than plant groups, and may end up
> > > with a differnt
> > > > > prefix.
> > > > >
> > > > > Sue
> > > > >
> > > > > On Wed, 20 Mar 2002, Pankaj Jaiswal wrote:
> > > > >
> > > > > > Dear Everyone,
> > > > > >
> > > > > > I am forwarding you an e mail from Michael, Some of you
> > > must have seen it
> > > > > > earlier also. There he has tried to resolve the issue
> > > of identifiers (agenda no.
> > > > > > 2 from yesterday's conference call) and suggested to
> > > use PA "Plant Anatomy"
> > > > > > which is a more generic identifier. I am strongly
> > > seconding his suggestion and
> > > > > > would recommend using "PO" Plant Ontology instead of
> > > the PA or the identifiers
> > > > > > from respective databases. I would invite everyone to
> > > discuss pros and cons of
> > > > > > it while building up the database. It is infact has
> > > turned out to be a major
> > > > > > issue and should be resolved ASAP.
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > Pankaj
> > > > > >
> > > > > >
> > > > > > "Michael Ashburner (Genetics)" wrote:
> > > > > > >
> > > > > > > Curious what emails cross one's desk !
> > > > > > >
> > > > > > > If I may express a view, it for option 1. BUT John Richter
> > > > > > > should be consulted how DAGedit will cope with mixed
> > > if prefixes.
> > > > > > > The thing is for option 1 is that should any one want
> > > an ontology
> > > > > > > just for Arabidopsis then the Zea etc specific terms
> > > could be stripped
> > > > > > > in a thrice with an editor.
> > > > > > >
> > > > > > > The other way is to have a generic prefix for these
> > > terms, eg. PA
> > > > > > > for "Plant Anatomoy" and either use these in your
> > > individual databases
> > > > > > > or have your own id's as synonyms.
> > > > > > >
> > > > > > > Two points, one minor.
> > > > > > > Not
> > > > > > >              adult leaf sensu Arabidopsis thaliana TAIR:
> > > > > > > but
> > > > > > >              adult leaf (sensu Arabidopsis thaliana) TAIR:
> > > > > > >
> > > > > > > Two, I am no botanist but could these not be made a
> > > bit broader
> > > > > > > eg
> > > > > > > (sensu Brassicae)
> > > > > > > (sensu Graminae)
> > > > > > >
> > > > > > > (???or sensu dicots, senu monocots) and then only go to a more
> > > > > > > specific sense if the biology so demands ?
> > > > > > >
> > > > > > > Hope I am not butting in when inappropriate.
> > > > > > >
> > > > > > > Michael
> > > > > >
> > > > > > --
> > > > > >
> > > > > > ******************************************
> > > > > > 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.
> > > > >
> > > --------------------------------------------------------------
> > > ---------------
> > > >
> > > > --
> > > >
> > > > ******************************************
> > > > 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.
> > > --------------------------------------------------------------
> > > ---------------
> > >
> > >
> > >
> >
> 
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource    FAX: (650) 325-6857
> Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> Department of Plant Biology             URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------

-- 

******************************************
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 lreiser at acoma.Stanford.EDU  Mon Apr 15 22:15:41 2002
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Mon, 15 Apr 2002 19:15:41 -0700 (PDT)
Subject: Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
In-Reply-To: <B6DA66FE1BC3C14F8B6A4CBD66795AD12D564F@col-mailnode04.col.missouri.edu>
Message-ID: <Pine.GSO.4.44.0204151913500.11892-100000@acoma.Stanford.EDU>


I finally got around to changing the numberspace- I removed the leading
zeros so now TAIR terms start from 0000001-

since I only changed the 1111 to 0000 the  last 3 digits should be the
same.
I have updated this in gobo on GO cvs and will update files in TAIR's ftp
site and literature curation database tomrrow.

Leonore



On Fri, 22 Mar 2002, Vincent, Leszek wrote:

> Hi Colleagues
>
> Lots of good email 'dialogue' has been taking place during the past few days, predominantly regarding the questions of number space & prefix.
>
> Based on what's been offered here's my synthesis / proposal.
>
> Number Space: Allocation of groups of 5,000 numbers from within the 7 digit number space as follows:
>
> 0000001 - 0005000	TAIR
> 0005001 - 0010000	GRAMENE
> 0010001 - 0015000	IRRI
> 0015001 - 0020000	MAIZEDB
>
> This would seem to provide ample number space for each group's development of ontologies. It also provides lots of room for further number space allocations to be made to new plant ontologists.
>
> Prefix: PO is to be used as the prefix for all the ontologies originating from the various collaborating groups of the POC. Anatomy, development, temporal etc. ontologies will all be included under the PO umbrella prefix (this parallels the GO paradigm). The same applies to Trait ontologies (TO), however it is represented.
>
> May I suggest that we consider acknowledging the source of the relevant CV terms by inserting our database 'acronym' and perhaps the initials of the curator in the Dbxref field adjacent to the term definition field in DAG-Edit (e.g. MAIZEDB:pldv, GRAMENE:pj, TAIR:lr etc.). This would be in addition to the relevant Dbxref info. provided for the term being defined. Leonore did this for some of the terms in her anatomy ontology & I think it provides a useful link to the origins of the term - perhaps especially important with us working in a multi-species arena. It seems like the browser would need to be tweaked so that this Dbxref field is displayed. In any case I think it is very important that the Dbxref info. for the term definition be displayed as it's an important component of the definition. So also including the database abbreviation & curator initials from this Dbxref field should be feasible. Comments on this??
>
> The conference call stimulated considerable thought about matters raised during the call and it has been great reading the constructive dialogue that has followed. Thanks for working to reach consensus.
>
> I'll copy the recent emails to Victor Ulat, Richard's DB colleague at IRRI - add his email to your list (V.ULAT at CGIAR.ORG).
>
> If you think I've misrepresented something please don't hesitate to point this out to me - we're learning together.
>
> Sincerely,
> - Leszek
> xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> P. Leszek D. Vincent Ph.D., FLS
> Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
> 884-3716 (Agronomy), Fax:(573) 884-7850;
> Ph/Fax (Home): (573) 441-1228;
> Email: Leszek at missouri.edu
> Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> (http://www.cafnr.missouri.edu/mmp/ and  http://www.agron.missouri.edu/)
> xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
>
> > -----Original Message-----
> > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > Sent: Friday, March 22, 2002 2:42 PM
> > To: Pankaj Jaiswal
> > Cc: Vincent, Leszek; Coe, Edward H.; Polacco, Mary L.; Curator TAIR;
> > Leonor Reiser; Richard Bruskiewich; Tanya; Lincoln Stein;
> > Susan McCouch;
> > Doreen Ware; brie
> > Subject: Re: [Fwd: FW: suggestions for 'POC' methods]
> >
> >
> > Pankaj,
> >
> > Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> > Ontology accessions to be used with the PO prefix. And we are
> > also good
> > with leaving out trait ontolgies as a part of PO for now, particularly
> > because there may be a more general trait ontology developing
> > and it may
> > be more desirable to minimize the number of Accessions for
> > the same term.
> >
> > If we agree on the 7 digit integer, we would like to use up
> > 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR
> > temporal or
> > 0000001-0002000 and 0002001-0003000, respectively if you want
> > a leading
> > zero, since we already have these accessions associated to
> > the terms we
> > have.
> >
> > I'm not sure what you mean below when you say you will
> > provide PO IDs from
> > the database for TAIR terms and use TAIR IDs as synonyms.
> > Since we agree
> > on the namespace, there will be one and only one accession
> > for the TAIR
> > anatomy and temporal terms. We will have internal identifiers
> > but these
> > won't need to be used externally.
> >
> > > Lastly but not the least, since we are designating the
> > number space to every
> > > group, I am not hesitant in using the TAIR IDs as either
> > DBXref/synonyms. Next
> > > time when we update the DB I will provide the PO ID for the
> > anatomy/development
> > > term, and will use the TAIR ID as either the synonym or
> > DBXref, if you agree.
> > > Could you please tell me if you have already incorporated
> > these terms/IDs in
> > > your curation or still in the process of using them. It
> > will help us at Gramene
> > > in setting up the tables and browser. Even though I am
> > suggesting all these view
> > > points you will agree that it takes a certain amount of
> > resources and time and
> > > everyone of us is limited within the scope and mandate, we
> > will try our best.
> > >
> > > Thanks
> > >
> > > Pankaj
> > >
> > > Sue Rhee wrote:
> > > >
> > > > Hi, Pankaj,
> > > >
> > > > I don't see that Michael is suggesting one versus the
> > other in what I can
> > > > make out of the message below. The important issue about
> > the identifier is
> > > > that we divide up the numberspaces among the three groups
> > such that we do
> > > > not use the same number (accession). We reached an
> > agreement on this
> > > > yesterday, yes?
> > > >
> > > > We have been designating a seven digit number and if this
> > is suitable for
> > > > everyone, each group can take 10,000 numbers to start
> > with (We've used up
> > > > ~200 in Anatomy).
> > > >
> > > > In terms of the prefix, the reason I see for using a
> > prefix to this number
> > > > accession is to distinguish the shared plant anatomy ontology from
> > > > different ontologies (e.g. GO, and inevitabley more
> > ontologies to follow).
> > > > Since we agreed on making a shared plant anatomy
> > ontology, using PA as the
> > > > prefix sounds ok to me so long as it is limited to 'Plant Anatomy
> > > > Ontology' and that we stick to the numberspaces for the
> > numbers (so that
> > > > we don't create yet another accession for anatomy for
> > Arabidopsis, for
> > > > example).
> > > >
> > > > PO sounds a bit too general for this ontology. If we
> > agree on making a
> > > > combined plant ontology for Developmental Stages (or
> > temporal), we can
> > > > perhaps designate a different prefix. At this point, it
> > is not clear to me
> > > > that we can develop a combined temporal ontology for
> > plants, but it is
> > > > certainly worth a try if you are willing/interested. It
> > is likely that the
> > > > development of Trait and other types of ontologies would
> > occur as a
> > > > collaboration of more than plant groups, and may end up
> > with a differnt
> > > > prefix.
> > > >
> > > > Sue
> > > >
> > > > On Wed, 20 Mar 2002, Pankaj Jaiswal wrote:
> > > >
> > > > > Dear Everyone,
> > > > >
> > > > > I am forwarding you an e mail from Michael, Some of you
> > must have seen it
> > > > > earlier also. There he has tried to resolve the issue
> > of identifiers (agenda no.
> > > > > 2 from yesterday's conference call) and suggested to
> > use PA "Plant Anatomy"
> > > > > which is a more generic identifier. I am strongly
> > seconding his suggestion and
> > > > > would recommend using "PO" Plant Ontology instead of
> > the PA or the identifiers
> > > > > from respective databases. I would invite everyone to
> > discuss pros and cons of
> > > > > it while building up the database. It is infact has
> > turned out to be a major
> > > > > issue and should be resolved ASAP.
> > > > >
> > > > > Thanks
> > > > >
> > > > > Pankaj
> > > > >
> > > > >
> > > > > "Michael Ashburner (Genetics)" wrote:
> > > > > >
> > > > > > Curious what emails cross one's desk !
> > > > > >
> > > > > > If I may express a view, it for option 1. BUT John Richter
> > > > > > should be consulted how DAGedit will cope with mixed
> > if prefixes.
> > > > > > The thing is for option 1 is that should any one want
> > an ontology
> > > > > > just for Arabidopsis then the Zea etc specific terms
> > could be stripped
> > > > > > in a thrice with an editor.
> > > > > >
> > > > > > The other way is to have a generic prefix for these
> > terms, eg. PA
> > > > > > for "Plant Anatomoy" and either use these in your
> > individual databases
> > > > > > or have your own id's as synonyms.
> > > > > >
> > > > > > Two points, one minor.
> > > > > > Not
> > > > > >              adult leaf sensu Arabidopsis thaliana TAIR:
> > > > > > but
> > > > > >              adult leaf (sensu Arabidopsis thaliana) TAIR:
> > > > > >
> > > > > > Two, I am no botanist but could these not be made a
> > bit broader
> > > > > > eg
> > > > > > (sensu Brassicae)
> > > > > > (sensu Graminae)
> > > > > >
> > > > > > (???or sensu dicots, senu monocots) and then only go to a more
> > > > > > specific sense if the biology so demands ?
> > > > > >
> > > > > > Hope I am not butting in when inappropriate.
> > > > > >
> > > > > > Michael
> > > > >
> > > > > --
> > > > >
> > > > > ******************************************
> > > > > 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.
> > > >
> > --------------------------------------------------------------
> > ---------------
> > >
> > > --
> > >
> > > ******************************************
> > > 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.
> > --------------------------------------------------------------
> > ---------------
> >
> >
> >
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From lreiser at acoma.Stanford.EDU  Tue Apr 16 14:24:59 2002
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Tue, 16 Apr 2002 11:24:59 -0700 (PDT)
Subject: Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
In-Reply-To: <3CBC325D.538554F6@cornell.edu>
Message-ID: <Pine.GSO.4.44.0204161101210.13492-100000@acoma.Stanford.EDU>



Pankaj,

I think there should not be a problem. When I talked with Tanya and Sue we
all concurred that the agreement from the phone conference and subsequent
emails was that we at TAIR were OK with changing the numberspace as the
inculded email from Leszek indicates- that we would remove the leading
zeros and not worry about the previously assigned numbers. Also, that
since the prefix would be assigned based upon the term type (e.g. anatomy
and
development  as Plant Ontology terms-get a PO prefix)so that actually
changing the prefix in
the files was not necessary (ie. that it was a display issue where
anatomy/development terms were given a PO prefix). It seemed that the
important thing was that we used the assigned numberspace. This is an easy
remidy (a simple replace ) if need be.

Based upon  what you sent it looks like we have assigned  same
numberspace- just
different prefixes- is that your assessment?

We plan to change the files in our FTP and include that changes in the
readme file so people who have been using this understand that only the
leading numbers have changed.

For GOBO-wont PO be a new submission with its own prefixes?


I am also including the content of Sues email from March 25 for reference.


Leonore and Tanya

>From Sue:
Pankaj,

Great. I'm happy to stick to Plant Anatomy and Developmental Stage
Ontology accessions to be used with the PO prefix. And we are also good
with leaving out trait ontolgies as a part of PO for now, particularly
because there may be a more general trait ontology developing and it may
be more desirable to minimize the number of Accessions for the same term.

If we agree on the 7 digit integer, we would like to use up
1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR temporal or
0000001-0002000 and 0002001-0003000, respectively if you want a leading
zero, since we already have these accessions associated to the terms we
have.

I'm not sure what you mean below when you say you will provide PO IDs from
the database for TAIR terms and use TAIR IDs as synonyms. Since we agree
on the namespace, there will be one and only one accession for the TAIR
anatomy and temporal terms. We will have internal identifiers but these
won't need to be used externally.

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
On Tue, 16 Apr 2002, Pankaj Jaiswal wrote:

> Hi Leonore ,
>
> I saw the changes you made at GOBO on GOCVS. It is like
>
> !autogenerated-by:     DAG-Edit version 1.311
> !saved-by:             lreiser
> !date:                 Mon Apr 15 18:32:37 PDT 2002
> !version: $Revision: 1.2 $
> !editors: Leonore Reiser, Jonathan Clarke
> $TAIR_ontology_of_arabidopsis ; TAIR:0000001
>  %TAIR_anatomy_of_Arabidopsis ; TAIR:0000111
>   %whole organism ; TAIR:0000304
>    <cell type ; TAIR:0000298
>     %aerenchyma cell ; TAIR:0000294
>     %antipodal cell ; TAIR:0000192 < megagametophyte ; TAIR:0000188
>     %atrichoblast ; TAIR:0000263 ; synonym:non-hair cell < elongation zone ;
> TAIR:0000324 < root epidermis ; TAIR:0000361
>     %cambial initial ; TAIR:0000295
>     %central cell ; TAIR:0000194 < megagametophyte ; TAIR:0000188
>      <polar nucleus ; TAIR:0000196
>
> I am still surprised to see the identifiers that we agreed not to have, although
> it does make sense to have them, since it is representing Arabidopsis. In the
> past we agreed to have a PO identifier and an assigned number space similar to
> GO. However, what I could recollect from the conference call and some other e
> mails is that Sue (TAIR) did not want to create another accession and virtually
> agreed to use the PO identifier for the terms coming from anatomy and
> developmental stages. We also agreed and the same was again followed up when I
> had a talk with Tanya last week, that its fine. The reason, since TAIR has
> already released the arabidopsis anatomy and temporal ontology to the public
> which the people might have started using them. Given the situation its wise for
> us to use the terms with PO identifiers to make it generic for others to use
> (attributing the PO terms, with the original TAIR ID:1111xxx as a DBXref.) and
> identify it by the number space showing it was contributed by TAIR.
>
> Following our conversations on e mail, I am adopting the same strategy, while
> integrating the TAIR terms in a test release of PO.
>
> Here is an example of my flat file, (the example, helps me in integrating the
> TAIR terms in PO since it allows me to use DAG edit tool to drag and drop the
> DBXref field, that's why you see TAIR written twice once as DBXref and another
> as synonym). I will clean the flat file once I am done with the complete
> integration.
>
>
> $Plant ontology ; PO:0006561
>  %plant anatomy ; PO:0005025
>   %whole organism ; PO:0000304 ; TAIR:1111304 ; synonym:TAIR\:1111304
>    <cell type ; PO:0000298 ; TAIR:1111298 ; synonym:TAIR\:1111298
>     %aerenchyma cell ; PO:0000294 ; TAIR:1111294 ; synonym:TAIR\:1111294
>     %antipodal cell ; PO:0000192 ; TAIR:1111192 ; synonym:TAIR\:1111192 <
> megagametophyte ; PO:0000188
>
> I am in the process of compiling the integrated version and putting it up on the
> web (test version) for everyone from POC to look at it. At the moment my
> suggestion would be of not changing anything on our respective databases untill,
> the integration is complete. I wish we would be able to integrate the PO very
> soon.
>
> I will be happy to share my flat files, once I am satisfied with the draft
> version.
>
> With kind regards
>
> Pankaj
>
>
> Leonore Reiser wrote:
> >
> > I finally got around to changing the numberspace- I removed the leading
> > zeros so now TAIR terms start from 0000001-
> >
> > since I only changed the 1111 to 0000 the  last 3 digits should be the
> > same.
> > I have updated this in gobo on GO cvs and will update files in TAIR's ftp
> > site and literature curation database tomrrow.
> >
> > Leonore
> >
> > On Fri, 22 Mar 2002, Vincent, Leszek wrote:
> >
> > > Hi Colleagues
> > >
> > > Lots of good email 'dialogue' has been taking place during the past few days, predominantly regarding the questions of number space & prefix.
> > >
> > > Based on what's been offered here's my synthesis / proposal.
> > >
> > > Number Space: Allocation of groups of 5,000 numbers from within the 7 digit number space as follows:
> > >
> > > 0000001 - 0005000     TAIR
> > > 0005001 - 0010000     GRAMENE
> > > 0010001 - 0015000     IRRI
> > > 0015001 - 0020000     MAIZEDB
> > >
> > > This would seem to provide ample number space for each group's development of ontologies. It also provides lots of room for further number space allocations to be made to new plant ontologists.
> > >
> > > Prefix: PO is to be used as the prefix for all the ontologies originating from the various collaborating groups of the POC. Anatomy, development, temporal etc. ontologies will all be included under the PO umbrella prefix (this parallels the GO paradigm). The same applies to Trait ontologies (TO), however it is represented.
> > >
> > > May I suggest that we consider acknowledging the source of the relevant CV terms by inserting our database 'acronym' and perhaps the initials of the curator in the Dbxref field adjacent to the term definition field in DAG-Edit (e.g. MAIZEDB:pldv, GRAMENE:pj, TAIR:lr etc.). This would be in addition to the relevant Dbxref info. provided for the term being defined. Leonore did this for some of the terms in her anatomy ontology & I think it provides a useful link to the origins of the term - perhaps especially important with us working in a multi-species arena. It seems like the browser would need to be tweaked so that this Dbxref field is displayed. In any case I think it is very important that the Dbxref info. for the term definition be displayed as it's an important component of the definition. So also including the database abbreviation & curator initials from this Dbxref field should be feasible. Comments on this??
> > >
> > > The conference call stimulated considerable thought about matters raised during the call and it has been great reading the constructive dialogue that has followed. Thanks for working to reach consensus.
> > >
> > > I'll copy the recent emails to Victor Ulat, Richard's DB colleague at IRRI - add his email to your list (V.ULAT at CGIAR.ORG).
> > >
> > > If you think I've misrepresented something please don't hesitate to point this out to me - we're learning together.
> > >
> > > Sincerely,
> > > - Leszek
> > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > P. Leszek D. Vincent Ph.D., FLS
> > > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> > > University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
> > > 884-3716 (Agronomy), Fax:(573) 884-7850;
> > > Ph/Fax (Home): (573) 441-1228;
> > > Email: Leszek at missouri.edu
> > > Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> > > (http://www.cafnr.missouri.edu/mmp/ and  http://www.agron.missouri.edu/)
> > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > >
> > > > -----Original Message-----
> > > > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > > Sent: Friday, March 22, 2002 2:42 PM
> > > > To: Pankaj Jaiswal
> > > > Cc: Vincent, Leszek; Coe, Edward H.; Polacco, Mary L.; Curator TAIR;
> > > > Leonor Reiser; Richard Bruskiewich; Tanya; Lincoln Stein;
> > > > Susan McCouch;
> > > > Doreen Ware; brie
> > > > Subject: Re: [Fwd: FW: suggestions for 'POC' methods]
> > > >
> > > >
> > > > Pankaj,
> > > >
> > > > Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> > > > Ontology accessions to be used with the PO prefix. And we are
> > > > also good
> > > > with leaving out trait ontolgies as a part of PO for now, particularly
> > > > because there may be a more general trait ontology developing
> > > > and it may
> > > > be more desirable to minimize the number of Accessions for
> > > > the same term.
> > > >
> > > > If we agree on the 7 digit integer, we would like to use up
> > > > 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR
> > > > temporal or
> > > > 0000001-0002000 and 0002001-0003000, respectively if you want
> > > > a leading
> > > > zero, since we already have these accessions associated to
> > > > the terms we
> > > > have.
> > > >
> > > > I'm not sure what you mean below when you say you will
> > > > provide PO IDs from
> > > > the database for TAIR terms and use TAIR IDs as synonyms.
> > > > Since we agree
> > > > on the namespace, there will be one and only one accession
> > > > for the TAIR
> > > > anatomy and temporal terms. We will have internal identifiers
> > > > but these
> > > > won't need to be used externally.
> > > >
> > > > > Lastly but not the least, since we are designating the
> > > > number space to every
> > > > > group, I am not hesitant in using the TAIR IDs as either
> > > > DBXref/synonyms. Next
> > > > > time when we update the DB I will provide the PO ID for the
> > > > anatomy/development
> > > > > term, and will use the TAIR ID as either the synonym or
> > > > DBXref, if you agree.
> > > > > Could you please tell me if you have already incorporated
> > > > these terms/IDs in
> > > > > your curation or still in the process of using them. It
> > > > will help us at Gramene
> > > > > in setting up the tables and browser. Even though I am
> > > > suggesting all these view
> > > > > points you will agree that it takes a certain amount of
> > > > resources and time and
> > > > > everyone of us is limited within the scope and mandate, we
> > > > will try our best.
> > > > >
> > > > > Thanks
> > > > >
> > > > > Pankaj
> > > > >
> > > > > Sue Rhee wrote:
> > > > > >
> > > > > > Hi, Pankaj,
> > > > > >
> > > > > > I don't see that Michael is suggesting one versus the
> > > > other in what I can
> > > > > > make out of the message below. The important issue about
> > > > the identifier is
> > > > > > that we divide up the numberspaces among the three groups
> > > > such that we do
> > > > > > not use the same number (accession). We reached an
> > > > agreement on this
> > > > > > yesterday, yes?
> > > > > >
> > > > > > We have been designating a seven digit number and if this
> > > > is suitable for
> > > > > > everyone, each group can take 10,000 numbers to start
> > > > with (We've used up
> > > > > > ~200 in Anatomy).
> > > > > >
> > > > > > In terms of the prefix, the reason I see for using a
> > > > prefix to this number
> > > > > > accession is to distinguish the shared plant anatomy ontology from
> > > > > > different ontologies (e.g. GO, and inevitabley more
> > > > ontologies to follow).
> > > > > > Since we agreed on making a shared plant anatomy
> > > > ontology, using PA as the
> > > > > > prefix sounds ok to me so long as it is limited to 'Plant Anatomy
> > > > > > Ontology' and that we stick to the numberspaces for the
> > > > numbers (so that
> > > > > > we don't create yet another accession for anatomy for
> > > > Arabidopsis, for
> > > > > > example).
> > > > > >
> > > > > > PO sounds a bit too general for this ontology. If we
> > > > agree on making a
> > > > > > combined plant ontology for Developmental Stages (or
> > > > temporal), we can
> > > > > > perhaps designate a different prefix. At this point, it
> > > > is not clear to me
> > > > > > that we can develop a combined temporal ontology for
> > > > plants, but it is
> > > > > > certainly worth a try if you are willing/interested. It
> > > > is likely that the
> > > > > > development of Trait and other types of ontologies would
> > > > occur as a
> > > > > > collaboration of more than plant groups, and may end up
> > > > with a differnt
> > > > > > prefix.
> > > > > >
> > > > > > Sue
> > > > > >
> > > > > > On Wed, 20 Mar 2002, Pankaj Jaiswal wrote:
> > > > > >
> > > > > > > Dear Everyone,
> > > > > > >
> > > > > > > I am forwarding you an e mail from Michael, Some of you
> > > > must have seen it
> > > > > > > earlier also. There he has tried to resolve the issue
> > > > of identifiers (agenda no.
> > > > > > > 2 from yesterday's conference call) and suggested to
> > > > use PA "Plant Anatomy"
> > > > > > > which is a more generic identifier. I am strongly
> > > > seconding his suggestion and
> > > > > > > would recommend using "PO" Plant Ontology instead of
> > > > the PA or the identifiers
> > > > > > > from respective databases. I would invite everyone to
> > > > discuss pros and cons of
> > > > > > > it while building up the database. It is infact has
> > > > turned out to be a major
> > > > > > > issue and should be resolved ASAP.
> > > > > > >
> > > > > > > Thanks
> > > > > > >
> > > > > > > Pankaj
> > > > > > >
> > > > > > >
> > > > > > > "Michael Ashburner (Genetics)" wrote:
> > > > > > > >
> > > > > > > > Curious what emails cross one's desk !
> > > > > > > >
> > > > > > > > If I may express a view, it for option 1. BUT John Richter
> > > > > > > > should be consulted how DAGedit will cope with mixed
> > > > if prefixes.
> > > > > > > > The thing is for option 1 is that should any one want
> > > > an ontology
> > > > > > > > just for Arabidopsis then the Zea etc specific terms
> > > > could be stripped
> > > > > > > > in a thrice with an editor.
> > > > > > > >
> > > > > > > > The other way is to have a generic prefix for these
> > > > terms, eg. PA
> > > > > > > > for "Plant Anatomoy" and either use these in your
> > > > individual databases
> > > > > > > > or have your own id's as synonyms.
> > > > > > > >
> > > > > > > > Two points, one minor.
> > > > > > > > Not
> > > > > > > >              adult leaf sensu Arabidopsis thaliana TAIR:
> > > > > > > > but
> > > > > > > >              adult leaf (sensu Arabidopsis thaliana) TAIR:
> > > > > > > >
> > > > > > > > Two, I am no botanist but could these not be made a
> > > > bit broader
> > > > > > > > eg
> > > > > > > > (sensu Brassicae)
> > > > > > > > (sensu Graminae)
> > > > > > > >
> > > > > > > > (???or sensu dicots, senu monocots) and then only go to a more
> > > > > > > > specific sense if the biology so demands ?
> > > > > > > >
> > > > > > > > Hope I am not butting in when inappropriate.
> > > > > > > >
> > > > > > > > Michael
> > > > > > >
> > > > > > > --
> > > > > > >
> > > > > > > ******************************************
> > > > > > > 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.
> > > > > >
> > > > --------------------------------------------------------------
> > > > ---------------
> > > > >
> > > > > --
> > > > >
> > > > > ******************************************
> > > > > 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.
> > > > --------------------------------------------------------------
> > > > ---------------
> > > >
> > > >
> > > >
> > >
> >
> > -------------------------------------------------------------------------------
> > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology             URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------------
>
> --
>
> ******************************************
> 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
> ******************************************
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------




From lreiser at acoma.Stanford.EDU  Tue Apr 16 15:04:35 2002
From: lreiser at acoma.Stanford.EDU (Leonore Reiser)
Date: Tue, 16 Apr 2002 12:04:35 -0700 (PDT)
Subject: Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
In-Reply-To: <3CBC7304.F5CD94AF@cornell.edu>
Message-ID: <Pine.GSO.4.44.0204161203520.13492-100000@acoma.Stanford.EDU>


It could be the curator or maybe better the database that is the source of
the term....
Leonore


On Tue, 16 Apr 2002, Pankaj Jaiswal wrote:

> Hi Leonore,
>
> Now, since you have cleared my doubts about getting rid of previous TAIR IDs
> altogether. It becomes easy for me to integrate the terms from your files. This
> also means that we are not going to store TAIR IDs as DBXref in the PO database
> which we will have for POC, instead the terms coming from TAIR files will be
> identified by their number space and the curator who submitted the term (as
> DBXref for definition of a term).
>
> For GOBO, PO will definitely be a new submission. We will see when that happens,
> when we submit.
>
> Pankaj
>
> Leonore Reiser wrote:
> >
> > Pankaj,
> >
> > I think there should not be a problem. When I talked with Tanya and Sue we
> > all concurred that the agreement from the phone conference and subsequent
> > emails was that we at TAIR were OK with changing the numberspace as the
> > inculded email from Leszek indicates- that we would remove the leading
> > zeros and not worry about the previously assigned numbers. Also, that
> > since the prefix would be assigned based upon the term type (e.g. anatomy
> > and
> > development  as Plant Ontology terms-get a PO prefix)so that actually
> > changing the prefix in
> > the files was not necessary (ie. that it was a display issue where
> > anatomy/development terms were given a PO prefix). It seemed that the
> > important thing was that we used the assigned numberspace. This is an easy
> > remidy (a simple replace ) if need be.
> >
> > Based upon  what you sent it looks like we have assigned  same
> > numberspace- just
> > different prefixes- is that your assessment?
> >
> > We plan to change the files in our FTP and include that changes in the
> > readme file so people who have been using this understand that only the
> > leading numbers have changed.
> >
> > For GOBO-wont PO be a new submission with its own prefixes?
> >
> > I am also including the content of Sues email from March 25 for reference.
> >
> > Leonore and Tanya
> >
> > >From Sue:
> > Pankaj,
> >
> > Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> > Ontology accessions to be used with the PO prefix. And we are also good
> > with leaving out trait ontolgies as a part of PO for now, particularly
> > because there may be a more general trait ontology developing and it may
> > be more desirable to minimize the number of Accessions for the same term.
> >
> > If we agree on the 7 digit integer, we would like to use up
> > 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR temporal or
> > 0000001-0002000 and 0002001-0003000, respectively if you want a leading
> > zero, since we already have these accessions associated to the terms we
> > have.
> >
> > I'm not sure what you mean below when you say you will provide PO IDs from
> > the database for TAIR terms and use TAIR IDs as synonyms. Since we agree
> > on the namespace, there will be one and only one accession for the TAIR
> > anatomy and temporal terms. We will have internal identifiers but these
> > won't need to be used externally.
> >
> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > On Tue, 16 Apr 2002, Pankaj Jaiswal wrote:
> >
> > > Hi Leonore ,
> > >
> > > I saw the changes you made at GOBO on GOCVS. It is like
> > >
> > > !autogenerated-by:     DAG-Edit version 1.311
> > > !saved-by:             lreiser
> > > !date:                 Mon Apr 15 18:32:37 PDT 2002
> > > !version: $Revision: 1.2 $
> > > !editors: Leonore Reiser, Jonathan Clarke
> > > $TAIR_ontology_of_arabidopsis ; TAIR:0000001
> > >  %TAIR_anatomy_of_Arabidopsis ; TAIR:0000111
> > >   %whole organism ; TAIR:0000304
> > >    <cell type ; TAIR:0000298
> > >     %aerenchyma cell ; TAIR:0000294
> > >     %antipodal cell ; TAIR:0000192 < megagametophyte ; TAIR:0000188
> > >     %atrichoblast ; TAIR:0000263 ; synonym:non-hair cell < elongation zone ;
> > > TAIR:0000324 < root epidermis ; TAIR:0000361
> > >     %cambial initial ; TAIR:0000295
> > >     %central cell ; TAIR:0000194 < megagametophyte ; TAIR:0000188
> > >      <polar nucleus ; TAIR:0000196
> > >
> > > I am still surprised to see the identifiers that we agreed not to have, although
> > > it does make sense to have them, since it is representing Arabidopsis. In the
> > > past we agreed to have a PO identifier and an assigned number space similar to
> > > GO. However, what I could recollect from the conference call and some other e
> > > mails is that Sue (TAIR) did not want to create another accession and virtually
> > > agreed to use the PO identifier for the terms coming from anatomy and
> > > developmental stages. We also agreed and the same was again followed up when I
> > > had a talk with Tanya last week, that its fine. The reason, since TAIR has
> > > already released the arabidopsis anatomy and temporal ontology to the public
> > > which the people might have started using them. Given the situation its wise for
> > > us to use the terms with PO identifiers to make it generic for others to use
> > > (attributing the PO terms, with the original TAIR ID:1111xxx as a DBXref.) and
> > > identify it by the number space showing it was contributed by TAIR.
> > >
> > > Following our conversations on e mail, I am adopting the same strategy, while
> > > integrating the TAIR terms in a test release of PO.
> > >
> > > Here is an example of my flat file, (the example, helps me in integrating the
> > > TAIR terms in PO since it allows me to use DAG edit tool to drag and drop the
> > > DBXref field, that's why you see TAIR written twice once as DBXref and another
> > > as synonym). I will clean the flat file once I am done with the complete
> > > integration.
> > >
> > >
> > > $Plant ontology ; PO:0006561
> > >  %plant anatomy ; PO:0005025
> > >   %whole organism ; PO:0000304 ; TAIR:1111304 ; synonym:TAIR\:1111304
> > >    <cell type ; PO:0000298 ; TAIR:1111298 ; synonym:TAIR\:1111298
> > >     %aerenchyma cell ; PO:0000294 ; TAIR:1111294 ; synonym:TAIR\:1111294
> > >     %antipodal cell ; PO:0000192 ; TAIR:1111192 ; synonym:TAIR\:1111192 <
> > > megagametophyte ; PO:0000188
> > >
> > > I am in the process of compiling the integrated version and putting it up on the
> > > web (test version) for everyone from POC to look at it. At the moment my
> > > suggestion would be of not changing anything on our respective databases untill,
> > > the integration is complete. I wish we would be able to integrate the PO very
> > > soon.
> > >
> > > I will be happy to share my flat files, once I am satisfied with the draft
> > > version.
> > >
> > > With kind regards
> > >
> > > Pankaj
> > >
> > >
> > > Leonore Reiser wrote:
> > > >
> > > > I finally got around to changing the numberspace- I removed the leading
> > > > zeros so now TAIR terms start from 0000001-
> > > >
> > > > since I only changed the 1111 to 0000 the  last 3 digits should be the
> > > > same.
> > > > I have updated this in gobo on GO cvs and will update files in TAIR's ftp
> > > > site and literature curation database tomrrow.
> > > >
> > > > Leonore
> > > >
> > > > On Fri, 22 Mar 2002, Vincent, Leszek wrote:
> > > >
> > > > > Hi Colleagues
> > > > >
> > > > > Lots of good email 'dialogue' has been taking place during the past few days, predominantly regarding the questions of number space & prefix.
> > > > >
> > > > > Based on what's been offered here's my synthesis / proposal.
> > > > >
> > > > > Number Space: Allocation of groups of 5,000 numbers from within the 7 digit number space as follows:
> > > > >
> > > > > 0000001 - 0005000     TAIR
> > > > > 0005001 - 0010000     GRAMENE
> > > > > 0010001 - 0015000     IRRI
> > > > > 0015001 - 0020000     MAIZEDB
> > > > >
> > > > > This would seem to provide ample number space for each group's development of ontologies. It also provides lots of room for further number space allocations to be made to new plant ontologists.
> > > > >
> > > > > Prefix: PO is to be used as the prefix for all the ontologies originating from the various collaborating groups of the POC. Anatomy, development, temporal etc. ontologies will all be included under the PO umbrella prefix (this parallels the GO paradigm). The same applies to Trait ontologies (TO), however it is represented.
> > > > >
> > > > > May I suggest that we consider acknowledging the source of the relevant CV terms by inserting our database 'acronym' and perhaps the initials of the curator in the Dbxref field adjacent to the term definition field in DAG-Edit (e.g. MAIZEDB:pldv, GRAMENE:pj, TAIR:lr etc.). This would be in addition to the relevant Dbxref info. provided for the term being defined. Leonore did this for some of the terms in her anatomy ontology & I think it provides a useful link to the origins of the term - perhaps especially important with us working in a multi-species arena. It seems like the browser would need to be tweaked so that this Dbxref field is displayed. In any case I think it is very important that the Dbxref info. for the term definition be displayed as it's an important component of the definition. So also including the database abbreviation & curator initials from this Dbxref field should be feasible. Comments on this??
> > > > >
> > > > > The conference call stimulated considerable thought about matters raised during the call and it has been great reading the constructive dialogue that has followed. Thanks for working to reach consensus.
> > > > >
> > > > > I'll copy the recent emails to Victor Ulat, Richard's DB colleague at IRRI - add his email to your list (V.ULAT at CGIAR.ORG).
> > > > >
> > > > > If you think I've misrepresented something please don't hesitate to point this out to me - we're learning together.
> > > > >
> > > > > Sincerely,
> > > > > - Leszek
> > > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > > P. Leszek D. Vincent Ph.D., FLS
> > > > > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> > > > > University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
> > > > > 884-3716 (Agronomy), Fax:(573) 884-7850;
> > > > > Ph/Fax (Home): (573) 441-1228;
> > > > > Email: Leszek at missouri.edu
> > > > > Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> > > > > (http://www.cafnr.missouri.edu/mmp/ and  http://www.agron.missouri.edu/)
> > > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > >
> > > > > > -----Original Message-----
> > > > > > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > > > > Sent: Friday, March 22, 2002 2:42 PM
> > > > > > To: Pankaj Jaiswal
> > > > > > Cc: Vincent, Leszek; Coe, Edward H.; Polacco, Mary L.; Curator TAIR;
> > > > > > Leonor Reiser; Richard Bruskiewich; Tanya; Lincoln Stein;
> > > > > > Susan McCouch;
> > > > > > Doreen Ware; brie
> > > > > > Subject: Re: [Fwd: FW: suggestions for 'POC' methods]
> > > > > >
> > > > > >
> > > > > > Pankaj,
> > > > > >
> > > > > > Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> > > > > > Ontology accessions to be used with the PO prefix. And we are
> > > > > > also good
> > > > > > with leaving out trait ontolgies as a part of PO for now, particularly
> > > > > > because there may be a more general trait ontology developing
> > > > > > and it may
> > > > > > be more desirable to minimize the number of Accessions for
> > > > > > the same term.
> > > > > >
> > > > > > If we agree on the 7 digit integer, we would like to use up
> > > > > > 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR
> > > > > > temporal or
> > > > > > 0000001-0002000 and 0002001-0003000, respectively if you want
> > > > > > a leading
> > > > > > zero, since we already have these accessions associated to
> > > > > > the terms we
> > > > > > have.
> > > > > >
> > > > > > I'm not sure what you mean below when you say you will
> > > > > > provide PO IDs from
> > > > > > the database for TAIR terms and use TAIR IDs as synonyms.
> > > > > > Since we agree
> > > > > > on the namespace, there will be one and only one accession
> > > > > > for the TAIR
> > > > > > anatomy and temporal terms. We will have internal identifiers
> > > > > > but these
> > > > > > won't need to be used externally.
> > > > > >
> > > > > > > Lastly but not the least, since we are designating the
> > > > > > number space to every
> > > > > > > group, I am not hesitant in using the TAIR IDs as either
> > > > > > DBXref/synonyms. Next
> > > > > > > time when we update the DB I will provide the PO ID for the
> > > > > > anatomy/development
> > > > > > > term, and will use the TAIR ID as either the synonym or
> > > > > > DBXref, if you agree.
> > > > > > > Could you please tell me if you have already incorporated
> > > > > > these terms/IDs in
> > > > > > > your curation or still in the process of using them. It
> > > > > > will help us at Gramene
> > > > > > > in setting up the tables and browser. Even though I am
> > > > > > suggesting all these view
> > > > > > > points you will agree that it takes a certain amount of
> > > > > > resources and time and
> > > > > > > everyone of us is limited within the scope and mandate, we
> > > > > > will try our best.
> > > > > > >
> > > > > > > Thanks
> > > > > > >
> > > > > > > Pankaj
> > > > > > >
> > > > > > > Sue Rhee wrote:
> > > > > > > >
> > > > > > > > Hi, Pankaj,
> > > > > > > >
> > > > > > > > I don't see that Michael is suggesting one versus the
> > > > > > other in what I can
> > > > > > > > make out of the message below. The important issue about
> > > > > > the identifier is
> > > > > > > > that we divide up the numberspaces among the three groups
> > > > > > such that we do
> > > > > > > > not use the same number (accession). We reached an
> > > > > > agreement on this
> > > > > > > > yesterday, yes?
> > > > > > > >
> > > > > > > > We have been designating a seven digit number and if this
> > > > > > is suitable for
> > > > > > > > everyone, each group can take 10,000 numbers to start
> > > > > > with (We've used up
> > > > > > > > ~200 in Anatomy).
> > > > > > > >
> > > > > > > > In terms of the prefix, the reason I see for using a
> > > > > > prefix to this number
> > > > > > > > accession is to distinguish the shared plant anatomy ontology from
> > > > > > > > different ontologies (e.g. GO, and inevitabley more
> > > > > > ontologies to follow).
> > > > > > > > Since we agreed on making a shared plant anatomy
> > > > > > ontology, using PA as the
> > > > > > > > prefix sounds ok to me so long as it is limited to 'Plant Anatomy
> > > > > > > > Ontology' and that we stick to the numberspaces for the
> > > > > > numbers (so that
> > > > > > > > we don't create yet another accession for anatomy for
> > > > > > Arabidopsis, for
> > > > > > > > example).
> > > > > > > >
> > > > > > > > PO sounds a bit too general for this ontology. If we
> > > > > > agree on making a
> > > > > > > > combined plant ontology for Developmental Stages (or
> > > > > > temporal), we can
> > > > > > > > perhaps designate a different prefix. At this point, it
> > > > > > is not clear to me
> > > > > > > > that we can develop a combined temporal ontology for
> > > > > > plants, but it is
> > > > > > > > certainly worth a try if you are willing/interested. It
> > > > > > is likely that the
> > > > > > > > development of Trait and other types of ontologies would
> > > > > > occur as a
> > > > > > > > collaboration of more than plant groups, and may end up
> > > > > > with a differnt
> > > > > > > > prefix.
> > > > > > > >
> > > > > > > > Sue
> > > > > > > >
> > > > > > > > On Wed, 20 Mar 2002, Pankaj Jaiswal wrote:
> > > > > > > >
> > > > > > > > > Dear Everyone,
> > > > > > > > >
> > > > > > > > > I am forwarding you an e mail from Michael, Some of you
> > > > > > must have seen it
> > > > > > > > > earlier also. There he has tried to resolve the issue
> > > > > > of identifiers (agenda no.
> > > > > > > > > 2 from yesterday's conference call) and suggested to
> > > > > > use PA "Plant Anatomy"
> > > > > > > > > which is a more generic identifier. I am strongly
> > > > > > seconding his suggestion and
> > > > > > > > > would recommend using "PO" Plant Ontology instead of
> > > > > > the PA or the identifiers
> > > > > > > > > from respective databases. I would invite everyone to
> > > > > > discuss pros and cons of
> > > > > > > > > it while building up the database. It is infact has
> > > > > > turned out to be a major
> > > > > > > > > issue and should be resolved ASAP.
> > > > > > > > >
> > > > > > > > > Thanks
> > > > > > > > >
> > > > > > > > > Pankaj
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > "Michael Ashburner (Genetics)" wrote:
> > > > > > > > > >
> > > > > > > > > > Curious what emails cross one's desk !
> > > > > > > > > >
> > > > > > > > > > If I may express a view, it for option 1. BUT John Richter
> > > > > > > > > > should be consulted how DAGedit will cope with mixed
> > > > > > if prefixes.
> > > > > > > > > > The thing is for option 1 is that should any one want
> > > > > > an ontology
> > > > > > > > > > just for Arabidopsis then the Zea etc specific terms
> > > > > > could be stripped
> > > > > > > > > > in a thrice with an editor.
> > > > > > > > > >
> > > > > > > > > > The other way is to have a generic prefix for these
> > > > > > terms, eg. PA
> > > > > > > > > > for "Plant Anatomoy" and either use these in your
> > > > > > individual databases
> > > > > > > > > > or have your own id's as synonyms.
> > > > > > > > > >
> > > > > > > > > > Two points, one minor.
> > > > > > > > > > Not
> > > > > > > > > >              adult leaf sensu Arabidopsis thaliana TAIR:
> > > > > > > > > > but
> > > > > > > > > >              adult leaf (sensu Arabidopsis thaliana) TAIR:
> > > > > > > > > >
> > > > > > > > > > Two, I am no botanist but could these not be made a
> > > > > > bit broader
> > > > > > > > > > eg
> > > > > > > > > > (sensu Brassicae)
> > > > > > > > > > (sensu Graminae)
> > > > > > > > > >
> > > > > > > > > > (???or sensu dicots, senu monocots) and then only go to a more
> > > > > > > > > > specific sense if the biology so demands ?
> > > > > > > > > >
> > > > > > > > > > Hope I am not butting in when inappropriate.
> > > > > > > > > >
> > > > > > > > > > Michael
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > >
> > > > > > > > > ******************************************
> > > > > > > > > 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.
> > > > > > > >
> > > > > > --------------------------------------------------------------
> > > > > > ---------------
> > > > > > >
> > > > > > > --
> > > > > > >
> > > > > > > ******************************************
> > > > > > > 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.
> > > > > > --------------------------------------------------------------
> > > > > > ---------------
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > >
> > > > -------------------------------------------------------------------------------
> > > > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > > > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > > > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> > > > Department of Plant Biology             URL: http://arabidopsis.org/
> > > > 260 Panama St.
> > > > Stanford, CA 94305
> > > > -------------------------------------------------------------------------------
> > >
> > > --
> > >
> > > ******************************************
> > > 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
> > > ******************************************
> > >
> >
> > -------------------------------------------------------------------------------
> > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> > Department of Plant Biology             URL: http://arabidopsis.org/
> > 260 Panama St.
> > Stanford, CA 94305
> > -------------------------------------------------------------------------------
>
> --
>
> ******************************************
> 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
> ******************************************
>

-------------------------------------------------------------------------------
Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
The Arabidopsis Information Resource	FAX: (650) 325-6857
Carnegie Institution of Washington	Tel: (650) 325-1521 ext. 311
Department of Plant Biology		URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
-------------------------------------------------------------------------------



From pj37 at cornell.edu  Tue Apr 16 14:52:52 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 16 Apr 2002 14:52:52 -0400
Subject: Synthesis - RE: [Fwd: FW: suggestions for 'POC' methods]
References: <Pine.GSO.4.44.0204161101210.13492-100000@acoma.Stanford.EDU>
Message-ID: <3CBC7304.F5CD94AF@cornell.edu>

Hi Leonore,

Now, since you have cleared my doubts about getting rid of previous TAIR IDs
altogether. It becomes easy for me to integrate the terms from your files. This
also means that we are not going to store TAIR IDs as DBXref in the PO database
which we will have for POC, instead the terms coming from TAIR files will be
identified by their number space and the curator who submitted the term (as
DBXref for definition of a term).

For GOBO, PO will definitely be a new submission. We will see when that happens,
when we submit.

Pankaj

Leonore Reiser wrote:
> 
> Pankaj,
> 
> I think there should not be a problem. When I talked with Tanya and Sue we
> all concurred that the agreement from the phone conference and subsequent
> emails was that we at TAIR were OK with changing the numberspace as the
> inculded email from Leszek indicates- that we would remove the leading
> zeros and not worry about the previously assigned numbers. Also, that
> since the prefix would be assigned based upon the term type (e.g. anatomy
> and
> development  as Plant Ontology terms-get a PO prefix)so that actually
> changing the prefix in
> the files was not necessary (ie. that it was a display issue where
> anatomy/development terms were given a PO prefix). It seemed that the
> important thing was that we used the assigned numberspace. This is an easy
> remidy (a simple replace ) if need be.
> 
> Based upon  what you sent it looks like we have assigned  same
> numberspace- just
> different prefixes- is that your assessment?
> 
> We plan to change the files in our FTP and include that changes in the
> readme file so people who have been using this understand that only the
> leading numbers have changed.
> 
> For GOBO-wont PO be a new submission with its own prefixes?
> 
> I am also including the content of Sues email from March 25 for reference.
> 
> Leonore and Tanya
> 
> >From Sue:
> Pankaj,
> 
> Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> Ontology accessions to be used with the PO prefix. And we are also good
> with leaving out trait ontolgies as a part of PO for now, particularly
> because there may be a more general trait ontology developing and it may
> be more desirable to minimize the number of Accessions for the same term.
> 
> If we agree on the 7 digit integer, we would like to use up
> 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR temporal or
> 0000001-0002000 and 0002001-0003000, respectively if you want a leading
> zero, since we already have these accessions associated to the terms we
> have.
> 
> I'm not sure what you mean below when you say you will provide PO IDs from
> the database for TAIR terms and use TAIR IDs as synonyms. Since we agree
> on the namespace, there will be one and only one accession for the TAIR
> anatomy and temporal terms. We will have internal identifiers but these
> won't need to be used externally.
> 
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> On Tue, 16 Apr 2002, Pankaj Jaiswal wrote:
> 
> > Hi Leonore ,
> >
> > I saw the changes you made at GOBO on GOCVS. It is like
> >
> > !autogenerated-by:     DAG-Edit version 1.311
> > !saved-by:             lreiser
> > !date:                 Mon Apr 15 18:32:37 PDT 2002
> > !version: $Revision: 1.2 $
> > !editors: Leonore Reiser, Jonathan Clarke
> > $TAIR_ontology_of_arabidopsis ; TAIR:0000001
> >  %TAIR_anatomy_of_Arabidopsis ; TAIR:0000111
> >   %whole organism ; TAIR:0000304
> >    <cell type ; TAIR:0000298
> >     %aerenchyma cell ; TAIR:0000294
> >     %antipodal cell ; TAIR:0000192 < megagametophyte ; TAIR:0000188
> >     %atrichoblast ; TAIR:0000263 ; synonym:non-hair cell < elongation zone ;
> > TAIR:0000324 < root epidermis ; TAIR:0000361
> >     %cambial initial ; TAIR:0000295
> >     %central cell ; TAIR:0000194 < megagametophyte ; TAIR:0000188
> >      <polar nucleus ; TAIR:0000196
> >
> > I am still surprised to see the identifiers that we agreed not to have, although
> > it does make sense to have them, since it is representing Arabidopsis. In the
> > past we agreed to have a PO identifier and an assigned number space similar to
> > GO. However, what I could recollect from the conference call and some other e
> > mails is that Sue (TAIR) did not want to create another accession and virtually
> > agreed to use the PO identifier for the terms coming from anatomy and
> > developmental stages. We also agreed and the same was again followed up when I
> > had a talk with Tanya last week, that its fine. The reason, since TAIR has
> > already released the arabidopsis anatomy and temporal ontology to the public
> > which the people might have started using them. Given the situation its wise for
> > us to use the terms with PO identifiers to make it generic for others to use
> > (attributing the PO terms, with the original TAIR ID:1111xxx as a DBXref.) and
> > identify it by the number space showing it was contributed by TAIR.
> >
> > Following our conversations on e mail, I am adopting the same strategy, while
> > integrating the TAIR terms in a test release of PO.
> >
> > Here is an example of my flat file, (the example, helps me in integrating the
> > TAIR terms in PO since it allows me to use DAG edit tool to drag and drop the
> > DBXref field, that's why you see TAIR written twice once as DBXref and another
> > as synonym). I will clean the flat file once I am done with the complete
> > integration.
> >
> >
> > $Plant ontology ; PO:0006561
> >  %plant anatomy ; PO:0005025
> >   %whole organism ; PO:0000304 ; TAIR:1111304 ; synonym:TAIR\:1111304
> >    <cell type ; PO:0000298 ; TAIR:1111298 ; synonym:TAIR\:1111298
> >     %aerenchyma cell ; PO:0000294 ; TAIR:1111294 ; synonym:TAIR\:1111294
> >     %antipodal cell ; PO:0000192 ; TAIR:1111192 ; synonym:TAIR\:1111192 <
> > megagametophyte ; PO:0000188
> >
> > I am in the process of compiling the integrated version and putting it up on the
> > web (test version) for everyone from POC to look at it. At the moment my
> > suggestion would be of not changing anything on our respective databases untill,
> > the integration is complete. I wish we would be able to integrate the PO very
> > soon.
> >
> > I will be happy to share my flat files, once I am satisfied with the draft
> > version.
> >
> > With kind regards
> >
> > Pankaj
> >
> >
> > Leonore Reiser wrote:
> > >
> > > I finally got around to changing the numberspace- I removed the leading
> > > zeros so now TAIR terms start from 0000001-
> > >
> > > since I only changed the 1111 to 0000 the  last 3 digits should be the
> > > same.
> > > I have updated this in gobo on GO cvs and will update files in TAIR's ftp
> > > site and literature curation database tomrrow.
> > >
> > > Leonore
> > >
> > > On Fri, 22 Mar 2002, Vincent, Leszek wrote:
> > >
> > > > Hi Colleagues
> > > >
> > > > Lots of good email 'dialogue' has been taking place during the past few days, predominantly regarding the questions of number space & prefix.
> > > >
> > > > Based on what's been offered here's my synthesis / proposal.
> > > >
> > > > Number Space: Allocation of groups of 5,000 numbers from within the 7 digit number space as follows:
> > > >
> > > > 0000001 - 0005000     TAIR
> > > > 0005001 - 0010000     GRAMENE
> > > > 0010001 - 0015000     IRRI
> > > > 0015001 - 0020000     MAIZEDB
> > > >
> > > > This would seem to provide ample number space for each group's development of ontologies. It also provides lots of room for further number space allocations to be made to new plant ontologists.
> > > >
> > > > Prefix: PO is to be used as the prefix for all the ontologies originating from the various collaborating groups of the POC. Anatomy, development, temporal etc. ontologies will all be included under the PO umbrella prefix (this parallels the GO paradigm). The same applies to Trait ontologies (TO), however it is represented.
> > > >
> > > > May I suggest that we consider acknowledging the source of the relevant CV terms by inserting our database 'acronym' and perhaps the initials of the curator in the Dbxref field adjacent to the term definition field in DAG-Edit (e.g. MAIZEDB:pldv, GRAMENE:pj, TAIR:lr etc.). This would be in addition to the relevant Dbxref info. provided for the term being defined. Leonore did this for some of the terms in her anatomy ontology & I think it provides a useful link to the origins of the term - perhaps especially important with us working in a multi-species arena. It seems like the browser would need to be tweaked so that this Dbxref field is displayed. In any case I think it is very important that the Dbxref info. for the term definition be displayed as it's an important component of the definition. So also including the database abbreviation & curator initials from this Dbxref field should be feasible. Comments on this??
> > > >
> > > > The conference call stimulated considerable thought about matters raised during the call and it has been great reading the constructive dialogue that has followed. Thanks for working to reach consensus.
> > > >
> > > > I'll copy the recent emails to Victor Ulat, Richard's DB colleague at IRRI - add his email to your list (V.ULAT at CGIAR.ORG).
> > > >
> > > > If you think I've misrepresented something please don't hesitate to point this out to me - we're learning together.
> > > >
> > > > Sincerely,
> > > > - Leszek
> > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > > P. Leszek D. Vincent Ph.D., FLS
> > > > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
> > > > University of Missouri-Columbia, Columbia, MO 65211-7020, USA. Ph: (573)
> > > > 884-3716 (Agronomy), Fax:(573) 884-7850;
> > > > Ph/Fax (Home): (573) 441-1228;
> > > > Email: Leszek at missouri.edu
> > > > Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
> > > > (http://www.cafnr.missouri.edu/mmp/ and  http://www.agron.missouri.edu/)
> > > > xoxoxoxoxoxoxoxoxoxoxoxoxoxoxox
> > > >
> > > > > -----Original Message-----
> > > > > From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
> > > > > Sent: Friday, March 22, 2002 2:42 PM
> > > > > To: Pankaj Jaiswal
> > > > > Cc: Vincent, Leszek; Coe, Edward H.; Polacco, Mary L.; Curator TAIR;
> > > > > Leonor Reiser; Richard Bruskiewich; Tanya; Lincoln Stein;
> > > > > Susan McCouch;
> > > > > Doreen Ware; brie
> > > > > Subject: Re: [Fwd: FW: suggestions for 'POC' methods]
> > > > >
> > > > >
> > > > > Pankaj,
> > > > >
> > > > > Great. I'm happy to stick to Plant Anatomy and Developmental Stage
> > > > > Ontology accessions to be used with the PO prefix. And we are
> > > > > also good
> > > > > with leaving out trait ontolgies as a part of PO for now, particularly
> > > > > because there may be a more general trait ontology developing
> > > > > and it may
> > > > > be more desirable to minimize the number of Accessions for
> > > > > the same term.
> > > > >
> > > > > If we agree on the 7 digit integer, we would like to use up
> > > > > 1111111-1112000 for TAIR anatomy and 1112001-1113000 for TAIR
> > > > > temporal or
> > > > > 0000001-0002000 and 0002001-0003000, respectively if you want
> > > > > a leading
> > > > > zero, since we already have these accessions associated to
> > > > > the terms we
> > > > > have.
> > > > >
> > > > > I'm not sure what you mean below when you say you will
> > > > > provide PO IDs from
> > > > > the database for TAIR terms and use TAIR IDs as synonyms.
> > > > > Since we agree
> > > > > on the namespace, there will be one and only one accession
> > > > > for the TAIR
> > > > > anatomy and temporal terms. We will have internal identifiers
> > > > > but these
> > > > > won't need to be used externally.
> > > > >
> > > > > > Lastly but not the least, since we are designating the
> > > > > number space to every
> > > > > > group, I am not hesitant in using the TAIR IDs as either
> > > > > DBXref/synonyms. Next
> > > > > > time when we update the DB I will provide the PO ID for the
> > > > > anatomy/development
> > > > > > term, and will use the TAIR ID as either the synonym or
> > > > > DBXref, if you agree.
> > > > > > Could you please tell me if you have already incorporated
> > > > > these terms/IDs in
> > > > > > your curation or still in the process of using them. It
> > > > > will help us at Gramene
> > > > > > in setting up the tables and browser. Even though I am
> > > > > suggesting all these view
> > > > > > points you will agree that it takes a certain amount of
> > > > > resources and time and
> > > > > > everyone of us is limited within the scope and mandate, we
> > > > > will try our best.
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > Pankaj
> > > > > >
> > > > > > Sue Rhee wrote:
> > > > > > >
> > > > > > > Hi, Pankaj,
> > > > > > >
> > > > > > > I don't see that Michael is suggesting one versus the
> > > > > other in what I can
> > > > > > > make out of the message below. The important issue about
> > > > > the identifier is
> > > > > > > that we divide up the numberspaces among the three groups
> > > > > such that we do
> > > > > > > not use the same number (accession). We reached an
> > > > > agreement on this
> > > > > > > yesterday, yes?
> > > > > > >
> > > > > > > We have been designating a seven digit number and if this
> > > > > is suitable for
> > > > > > > everyone, each group can take 10,000 numbers to start
> > > > > with (We've used up
> > > > > > > ~200 in Anatomy).
> > > > > > >
> > > > > > > In terms of the prefix, the reason I see for using a
> > > > > prefix to this number
> > > > > > > accession is to distinguish the shared plant anatomy ontology from
> > > > > > > different ontologies (e.g. GO, and inevitabley more
> > > > > ontologies to follow).
> > > > > > > Since we agreed on making a shared plant anatomy
> > > > > ontology, using PA as the
> > > > > > > prefix sounds ok to me so long as it is limited to 'Plant Anatomy
> > > > > > > Ontology' and that we stick to the numberspaces for the
> > > > > numbers (so that
> > > > > > > we don't create yet another accession for anatomy for
> > > > > Arabidopsis, for
> > > > > > > example).
> > > > > > >
> > > > > > > PO sounds a bit too general for this ontology. If we
> > > > > agree on making a
> > > > > > > combined plant ontology for Developmental Stages (or
> > > > > temporal), we can
> > > > > > > perhaps designate a different prefix. At this point, it
> > > > > is not clear to me
> > > > > > > that we can develop a combined temporal ontology for
> > > > > plants, but it is
> > > > > > > certainly worth a try if you are willing/interested. It
> > > > > is likely that the
> > > > > > > development of Trait and other types of ontologies would
> > > > > occur as a
> > > > > > > collaboration of more than plant groups, and may end up
> > > > > with a differnt
> > > > > > > prefix.
> > > > > > >
> > > > > > > Sue
> > > > > > >
> > > > > > > On Wed, 20 Mar 2002, Pankaj Jaiswal wrote:
> > > > > > >
> > > > > > > > Dear Everyone,
> > > > > > > >
> > > > > > > > I am forwarding you an e mail from Michael, Some of you
> > > > > must have seen it
> > > > > > > > earlier also. There he has tried to resolve the issue
> > > > > of identifiers (agenda no.
> > > > > > > > 2 from yesterday's conference call) and suggested to
> > > > > use PA "Plant Anatomy"
> > > > > > > > which is a more generic identifier. I am strongly
> > > > > seconding his suggestion and
> > > > > > > > would recommend using "PO" Plant Ontology instead of
> > > > > the PA or the identifiers
> > > > > > > > from respective databases. I would invite everyone to
> > > > > discuss pros and cons of
> > > > > > > > it while building up the database. It is infact has
> > > > > turned out to be a major
> > > > > > > > issue and should be resolved ASAP.
> > > > > > > >
> > > > > > > > Thanks
> > > > > > > >
> > > > > > > > Pankaj
> > > > > > > >
> > > > > > > >
> > > > > > > > "Michael Ashburner (Genetics)" wrote:
> > > > > > > > >
> > > > > > > > > Curious what emails cross one's desk !
> > > > > > > > >
> > > > > > > > > If I may express a view, it for option 1. BUT John Richter
> > > > > > > > > should be consulted how DAGedit will cope with mixed
> > > > > if prefixes.
> > > > > > > > > The thing is for option 1 is that should any one want
> > > > > an ontology
> > > > > > > > > just for Arabidopsis then the Zea etc specific terms
> > > > > could be stripped
> > > > > > > > > in a thrice with an editor.
> > > > > > > > >
> > > > > > > > > The other way is to have a generic prefix for these
> > > > > terms, eg. PA
> > > > > > > > > for "Plant Anatomoy" and either use these in your
> > > > > individual databases
> > > > > > > > > or have your own id's as synonyms.
> > > > > > > > >
> > > > > > > > > Two points, one minor.
> > > > > > > > > Not
> > > > > > > > >              adult leaf sensu Arabidopsis thaliana TAIR:
> > > > > > > > > but
> > > > > > > > >              adult leaf (sensu Arabidopsis thaliana) TAIR:
> > > > > > > > >
> > > > > > > > > Two, I am no botanist but could these not be made a
> > > > > bit broader
> > > > > > > > > eg
> > > > > > > > > (sensu Brassicae)
> > > > > > > > > (sensu Graminae)
> > > > > > > > >
> > > > > > > > > (???or sensu dicots, senu monocots) and then only go to a more
> > > > > > > > > specific sense if the biology so demands ?
> > > > > > > > >
> > > > > > > > > Hope I am not butting in when inappropriate.
> > > > > > > > >
> > > > > > > > > Michael
> > > > > > > >
> > > > > > > > --
> > > > > > > >
> > > > > > > > ******************************************
> > > > > > > > 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.
> > > > > > >
> > > > > --------------------------------------------------------------
> > > > > ---------------
> > > > > >
> > > > > > --
> > > > > >
> > > > > > ******************************************
> > > > > > 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.
> > > > > --------------------------------------------------------------
> > > > > ---------------
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > > -------------------------------------------------------------------------------
> > > Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> > > The Arabidopsis Information Resource    FAX: (650) 325-6857
> > > Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> > > Department of Plant Biology             URL: http://arabidopsis.org/
> > > 260 Panama St.
> > > Stanford, CA 94305
> > > -------------------------------------------------------------------------------
> >
> > --
> >
> > ******************************************
> > 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
> > ******************************************
> >
> 
> -------------------------------------------------------------------------------
> Leonore Reiser, Ph.D.                   lreiser at acoma.stanford.edu
> The Arabidopsis Information Resource    FAX: (650) 325-6857
> Carnegie Institution of Washington      Tel: (650) 325-1521 ext. 311
> Department of Plant Biology             URL: http://arabidopsis.org/
> 260 Panama St.
> Stanford, CA 94305
> -------------------------------------------------------------------------------

-- 

******************************************
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 ware at stein.cshl.org  Mon Apr 22 10:48:58 2002
From: ware at stein.cshl.org (Doreen Ware)
Date: Mon, 22 Apr 2002 10:48:58 -0400
Subject: QTL schema
Message-ID: <002d01c1ea0c$d5b858a0$d51f308f@D6GXP911>

Hi Cornell,

I am working with Kuan this morning.  My understanding is that on Friday you had a meeting discussing  the QTL and mutant database structure.  Kuan has communicated with me that there was some agreement that the QTL structure would not accomodate the mutants.  Can you please generate a list of items that were in disagreement and a list of items that were confusing so Kuan and I can take a look at these together. 


Thanks,

Doreen 

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From noelyap at ascus.plbr.cornell.edu  Tue Apr 23 17:05:06 2002
From: noelyap at ascus.plbr.cornell.edu (Immanuel Yap)
Date: Tue, 23 Apr 2002 17:05:06 -0400
Subject: QTL schema
In-Reply-To: <002d01c1ea0c$d5b858a0$d51f308f@D6GXP911>
References: <002d01c1ea0c$d5b858a0$d51f308f@D6GXP911>
Message-ID: <15557.52354.352815.7513@ascus.plbr.cornell.edu>

On Mon Apr 22, 2002, Doreen Ware wrote:
> Hi Cornell,
> 
> I am working with Kuan this morning.  My understanding is that on
> Friday you had a meeting discussing the QTL and mutant database
> structure.  Kuan has communicated with me that there was some
> agreement that the QTL structure would not accomodate the mutants.
> Can you please generate a list of items that were in disagreement
> and a list of items that were confusing so Kuan and I can take a
> look at these together.

Hello Doreen,

The consensus was that mutant and QTL studies, although conceptually
related, are operationally quite different and need to be curated
differently.  The closer you get to locus/sequence, of course, the
more similar they become, but getting down to that level involves a
very dissimilar data trail.  Trying to force one into the other
doesn't make a whole lot of sense.

A QTL study is an instance of a map study.  You cannot separate a QTL
from its underlying genetic map.  A QTL is inherently defined as a
statistically signficant correlation between mapped markers and
phenotype.  The critical part is that the mapped markers define the
distribution of parental alleles in a population of segregants and the
information derived from those markers allows you to divide the
population into genotypic categories that are compared to the
phenotypic differences between groups.  If the difference is
significant, a putative QTL is declared.

In a mutant study, there is a much simpler kind of comparison employed
- a mutant individual is compared to its isogenic "wild type"
("reference variety").  This requires no map, no markers and no
statistics.  The mutation is defined as a variant of the reference
phenotype.

For these reasons, the schema required to curate these types of
studies are fundamentally different, though the same controlled
vocabulary can be used to describe the phenotypes, the environments in
which the phenotypes are observed, the germplasm, the developmental
stages, the locations (GIS, etc), and indeed, many of the mutants are
themselves variants at the same loci as the QTLs.

Though there is still little data that allows us to determine which
variant sequences are responsible for the mutant or quantitative
phenotypes we are curating, Gramene should facilitate the users'
ability to make inferences about the relationship between genotype and
phenotype by showing positional, phenotypic, functional, etc.,
correspondences.

There are certainly items in the mutant schema that Kuan is presenting
that are general-purpose enough and should be reused, not only for
QTL, but for Gramene as a whole:

    object_to_*
    geographical_location
    image
    developmental_stage

Some need to be modified to make them more general-purpose, because
they appear to be quite mutant-specific at the moment:

    germplasm_info
    allele

These tables are mutant-specific, and probably should remain so:

    study [rename to mutant study?]
    mutant
    rough_mutant_data
    mutant_synonym
    mutagenesis

Here are some strange tables:

    phenotype_expression
        - has a field for trait_score; what is it supposed to be used for?

    map_panel
        - This is a term used in MaizeDB for mapping populations, but
          as defined herein appears to be a quite different concept.
          This should be defined as in Ken's cmap_map_study.  

We might also want to separate the map_study from the map_panel info.
Also, us Cornellian dislike the term "mapping panel" and prefer to use
"mapping population".  So for maps and markers we may have:

    map_study
    map_population
    linkage_group
    locus
    marker
    marker_correspondence

Locus/marker go into the map viewer as "features".  Currently, the
distinction between locus and marker is rather blurred in Gramene.
I'd really like to maintain them as discrete objects: A marker is an
actual physical probe or phenotype while a (genetic) locus is the
position to which it maps.  This will make it easier to infer
correspondences based on marker+position.  A QTL can then be
associated with a particular set of loci on a particular linkage group
mapped in a specific population.

I'm developing some QTL-specific tables:

    qtl_experiment
    trait_description [or link to trait ontology?]
    trait_evaluation
    environment
    qtl_analysis
    qtl

Give me some time to do the conversion to SQL.  I'm also going to
develop some HTML mockups for QTL, so you can see how it all hangs
together.

Noel [& Susan]
-- 
Immanuel V. Yap <ivy1 at cornell.edu>        | It is the fate of 
Department of Plant Breeding and Biometry | operating systems 
Cornell University                        | to become free.  
G15 Bradfield Hall, Ithaca, NY 14853      |    - Neal Stephenson
office: 1-607-255-3103                    | 


From Denirossi at aol.com  Tue Apr 23 18:45:42 2002
From: Denirossi at aol.com (Denirossi at aol.com)
Date: Tue, 23 Apr 2002 18:45:42 EDT
Subject: SSSRIT
Message-ID: <4a.a6a6b05.29f73e16@aol.com>

Dear Gramene Administrator,

I have been using the SSRIT software from the Gramene site for a while but 
recently, aaround last friday or so, the site is not responding anymore.  I 
wonder if is there any other alternative link for that tool.
I would appreciate any help since it has been very important for my research.
Thank you very much,

Jorge A. DaSilva, PhD
Sugarcane Leader
Texas A&M University
Soil and Cro[p Science Department
Weslaco Center


From teytelma at stein.cshl.org  Wed Apr 24 00:38:58 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Wed, 24 Apr 2002 00:38:58 -0400 (EDT)
Subject: SSSRIT
In-Reply-To: <4a.a6a6b05.29f73e16@aol.com>
Message-ID: <Pine.GSO.4.05.10204240037060.21804-100000@phage.cshl.org>

Dear Dr. DaSilva,

Thank you very much for pointing out the error.  We have fixed the SSRIT
script and it should now work fine.

Sincerely,

Lenny Teytelman

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

On Tue, 23 Apr 2002 Denirossi at aol.com wrote:

> Dear Gramene Administrator,
> 
> I have been using the SSRIT software from the Gramene site for a while but 
> recently, aaround last friday or so, the site is not responding anymore.  I 
> wonder if is there any other alternative link for that tool.
> I would appreciate any help since it has been very important for my research.
> Thank you very much,
> 
> Jorge A. DaSilva, PhD
> Sugarcane Leader
> Texas A&M University
> Soil and Cro[p Science Department
> Weslaco Center
> 



From pj37 at cornell.edu  Fri Apr 26 09:08:10 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 26 Apr 2002 09:08:10 -0400
Subject: Gramene citation and Publication
Message-ID: <3CC9513A.84042AB2@cornell.edu>


Hi Everyone,

Gramene is cited at following places for its work

http://www3.interscience.wiley.com/cgi-bin/fulltext/91016048/FILE?TPL=ftx_start
http://www3.interscience.wiley.com/cgi-bin/fulltext/91015355/FILE?TPL=ftx_start

Our publication (now the PDF is available)
http://www3.interscience.wiley.com/cgi-bin/fulltext/91016047/FILE?TPL=ftx_start

and as collaborators in POC
http://www3.interscience.wiley.com/cgi-bin/fulltext/91016119/FILE?TPL=ftx_start

We already have an NAR paper.

Pankaj


From liuxx175 at tc.umn.edu  Thu Apr 25 17:41:27 2002
From: liuxx175 at tc.umn.edu (Sixin Liu)
Date: Thu, 25 Apr 2002 14:41:27 -0700
Subject: wheat EST
Message-ID: <l03130300b8ee272aa259@[134.84.43.63]>

Hello,

I am wondering if there is a near plan to update the wheat EST in Gramene
web site. The number of wheat EST deposited in Genebank was doubled in the
last few weeks.

Thanks,

Sixin Liu
University of Minnesota




From lgarner at nal.usda.gov  Tue Apr 30 08:34:27 2002
From: lgarner at nal.usda.gov (Lena Garner)
Date: Tue, 30 Apr 2002 08:34:27 -0400
Subject: Rice genetics newsletter
Message-ID: <D16710276837D211BDA20008C7FAB8BC05854CC0@aurora.nal.usda.gov>

Dear Sirs,

We are interested in purchasing the more recent issues of your newsletter.
The last issue we received was Vol 17 2000.  If there are any issues more
current, please invoice us at the following address:

National Agricultural Library                      
Current Serial Records, Room 002
10301 Baltimore Avenue            
Beltsville, MD 20710     

If there any questions, please do not hesitate to contact us.

Thank you,

Lena Garner
Lead Technician
National Agricultural Library                       Work (301) 504-5691
10301 Baltimore Avenue, Room 002            Fax   (301 504-5243
Beltsville, MD 20710                                  
                             



From matthews at greengenes.cit.cornell.edu  Fri Apr 26 16:03:42 2002
From: matthews at greengenes.cit.cornell.edu (Dave Matthews)
Date: Fri, 26 Apr 2002 16:03:42 -0400 (EDT)
Subject: Possible problem on gramene.org
Message-ID: <200204262003.QAA26021@greengenes.cit.cornell.edu>

The Klez virus fakes its From: address, based on what the user/victim
has in his address book.  I've gotten a couple dozen of them in the
last three days.
- Dave


From ware at stein.cshl.org  Fri Apr 26 10:11:18 2002
From: ware at stein.cshl.org (Doreen Ware)
Date: Fri, 26 Apr 2002 10:11:18 -0400
Subject: wheat EST
References: <l03130300b8ee272aa259@[134.84.43.63]>
Message-ID: <002401c1ed2c$3c6aca20$499bb918@D6GXP911>

Lenny,

Can you resond to this with regard to the timing and availability of the EST
on the live site.

It may be useful to set up chron job to look for new ESTs based upon the
last date the chron job was run. If new ESTs are deposited it can send you
an email.

Dor

From: "Sixin Liu" <>
To: <gramene at gramene.org>
Sent: Thursday, April 25, 2002 5:41 PM
Subject: wheat EST


> Hello,
>
> I am wondering if there is a near plan to update the wheat EST in Gramene
> web site. The number of wheat EST deposited in Genebank was doubled in the
> last few weeks.
>
> Thanks,
>
> Sixin Liu
> University of Minnesota
>
>
>



From lazo at pw.usda.gov  Fri Apr 26 13:54:16 2002
From: lazo at pw.usda.gov (Gerard R Lazo)
Date: Fri, 26 Apr 2002 10:54:16 -0700 (PDT)
Subject: Possible problem on gramene.org
Message-ID: <200204261754.g3QHsGj12628@wheat.pw.usda.gov>

You may want to know that your machine appears to be distributing 
rogue e-mails, possibly due to some kind of virus.

I received a file with the subject line:

--------------------------------------------------------------
Date: Thu, 25 Apr 2002 22:34:57 -0400 (EDT)
From: gramene <gramene at gramene.org>

Subject: A special  nice game

with attachments:

install.exe
whoami.cornell
--------------------------------------------------------------

Apparantly something is going around, I had an unusual number of 
virus associated e-mails this morning.

-                                                                      -
Gerard R Lazo    / USDA-ARS-Western Regional Research Ctr \ 510.559.5640
lazo at pw.usda.gov \ 800 Buchanan St, Albany, CA 94710-1105 / 510.559.6449




From teytelma at stein.cshl.org  Fri Apr 26 11:29:08 2002
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Fri, 26 Apr 2002 11:29:08 -0400 (EDT)
Subject: wheat EST
In-Reply-To: <l03130300b8ee272aa259@[134.84.43.63]>
Message-ID: <Pine.GSO.4.05.10204261117260.25702-100000@phage.cshl.org>

Dear Sixin,

Thank you very much for letting us know about the ESTs.  We will update
the Wheat alignments in the next few weeks.

In general, we update alignments on quarterly basis, and have just
finished an update last night.  It is unfortunate that the data wasn't
released a few weeks earlier.

On a good note, yesterday's release includes alignments of the TIGR Maize
Gene Index and the Dupont Maize Unigene Clusters.

Sincerely,

Lenny Teytelman

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

On Thu, 25 Apr 2002, Sixin Liu wrote:

> Hello,
> 
> I am wondering if there is a near plan to update the wheat EST in Gramene
> web site. The number of wheat EST deposited in Genebank was doubled in the
> last few weeks.
> 
> Thanks,
> 
> Sixin Liu
> University of Minnesota
> 
> 
> 



From schmidt at stein.cshl.org  Tue Apr 30 13:06:10 2002
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Tue, 30 Apr 2002 13:06:10 -0400
Subject: Possible problem on gramene.org
In-Reply-To: <200204261754.g3QHsGj12628@wheat.pw.usda.gov>
References: <200204261754.g3QHsGj12628@wheat.pw.usda.gov>
Message-ID: <200204301706.NAA15245@cshl.org>

The gramene list is moderated, so viruses shouldn't get through.
I think Dave Matthews is right that the headers were bogus.
We do get a lot of viruses.  Most of them are obvious, such as those
with attachments of type MIDI with extension .pif


On Friday 26 April 2002 13:54, Gerard R Lazo wrote:
> You may want to know that your machine appears to be distributing
> rogue e-mails, possibly due to some kind of virus.
>
> I received a file with the subject line:
>
> --------------------------------------------------------------
> Date: Thu, 25 Apr 2002 22:34:57 -0400 (EDT)
> From: gramene <gramene at gramene.org>
>
> Subject: A special  nice game
>
> with attachments:
>
> install.exe
> whoami.cornell
> --------------------------------------------------------------
>
> Apparantly something is going around, I had an unusual number of
> virus associated e-mails this morning.
>
> -                                                                      -
> Gerard R Lazo    / USDA-ARS-Western Regional Research Ctr \ 510.559.5640
> lazo at pw.usda.gov \ 800 Buchanan St, Albany, CA 94710-1105 / 510.559.6449

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


From pj37 at cornell.edu  Tue Apr 30 12:05:26 2002
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Tue, 30 Apr 2002 12:05:26 -0400
Subject: Possible problem on gramene.org
References: <200204261754.g3QHsGj12628@wheat.pw.usda.gov>
Message-ID: <3CCEC0C6.12ADB574@cornell.edu>

Dear Gerard,

We assure you that no such viruses have been forwarded from Gramene mailing
list. The reason, its a moderated mailing list and any such spurious mails are
either deleted/rejected.

However, a better explanation is sent by Dave Mathews as follows..

Sincerely,

Pankaj

Dave Matthews wrote:
> 
> The Klez virus fakes its From: address, based on what the user/victim
> has in his address book.  I've gotten a couple dozen of them in the
> last three days.
> - Dave

Gerard R Lazo wrote:
> 
> You may want to know that your machine appears to be distributing
> rogue e-mails, possibly due to some kind of virus.
> 
> I received a file with the subject line:
> 
> --------------------------------------------------------------
> Date: Thu, 25 Apr 2002 22:34:57 -0400 (EDT)
> From: gramene <gramene at gramene.org>
> 
> Subject: A special  nice game
> 
> with attachments:
> 
> install.exe
> whoami.cornell
> --------------------------------------------------------------
> 
> Apparantly something is going around, I had an unusual number of
> virus associated e-mails this morning.
> 
> -                                                                      -
> Gerard R Lazo    / USDA-ARS-Western Regional Research Ctr \ 510.559.5640
> lazo at pw.usda.gov \ 800 Buchanan St, Albany, CA 94710-1105 / 510.559.6449

--


