POC Temporal and Anatomy file URLs (Draft Versions)

Sat May 4 22:15:58 EDT 2002

Hi Everyone,

Please have a look at the 
1.   temporal-PO at the files from 
ftp://www.gramene.org/pub/gramene/ontology/temporal_stages/
2.    anatomy-PO at the files from
ftp://www.gramene.org/pub/gramene/ontology/plant_anatomy/

Both the files were created by integration of TAIR and GRAMENE ontology versions
and also integrating from other resources. 

These are the draft versions. You may or may not see the extended relationships
in anatomy terms (like derived from types in some cases). But that should not be
a problem since it is just a matter of placing it under a different parent.
Important thing at the moment is that the term exists.

In the files there are three types of relationships (as follows) that have been
used

% - ISA
< - PARTOF
~ - DERIVED FROM

You may need to modify the configuration manager of your DAG EDIT

If you want to see the combined version of the two then go to 

for definition file
ftp://www.gramene.org/pub/gramene/ontology/POC_def

for ontology
ftp://www.gramene.org/pub/gramene/ontology/POC_ont

Statistics
total terms: 1208
anatomy: 982
temporal:223
89% of all terms have definition (1083 0f 1208) 

Looking forward to your feedback.

Pankaj

Pankaj Jaiswal wrote:
> 
> 
> The discussion on the draft versions will be the proposed agenda from my side. the two separate sections will be ---
> 1.   temporal-PO
> 2.    anatomy-PO
> 
> Both these ontologies were created by integration of TAIR and Gramene PO mainly and inclusion of  CVOs from other crops. I am proposing it to give a more generic structure to the PO instead of more crop specific. However, crop specificity has to be there for growth stages, but we can make the anatomy a more generic as the GO.
> 
> I will give you the URLs for anatomy files by Monday to be looked at.
> 
> Best regards
> 
> Pankaj
> 
> Sue Rhee wrote:
> 
> > sounds great! also it'd be nice to talk about pankaj's draft of the plant
> > temporal if folks have enough time to take a look at it before the
> > meeting.
> >
> > cheers,
> > sue
> >
> > On Fri, 3 May 2002, Vincent, Leszek wrote:
> >
> > > Hi colleagues
> > >
> > > Here are the details to confirm our POC conference call.
> > >
> > > Date: 07 May '02
> > >
> > > Time: 4 p.m. (CST) [16:00]; that's 2 p.m. for the TAIR folk, 5 p.m. for the Cornell/CSHL folk & 6 a.m. (Wed. 08 May) for Richard at IRRI.
> > >
> > > Duration:     I've reserved an hour (but we don't need to use all of that time ;-))
> > >
> > > Conference Number:    (573) 884-7102  - each participant/group will need to call in to the above number to get logged on to the conference call facility. I trust that 'your end' bearing the cost is still acceptable to you. I hope that one or more folk from each location will be able to participate in this discussion/update time:
> > >
> > > Tentative Agenda for Conference Call:
> > >
> > > 1. My thinking is that this would be a time for Pankaj to obtain an up-to-date overview of where each DB group is 'at' so that he can represent any relevant matters at the upcoming GO meeting at CSHL on May 12-13.
> > >
> > > 2. Any further thoughts/progress on Lincoln Stein's suggestion?: "that we  implement a site-neutral ontology browser on the Plant Ontology Consortium web site. This would be like the Gene Ontology web site in that it would not be associated with any particular group.
> > >
> > > 3. Interest in participating in a small POC meeting & 'phenotype w/shop' on Fri. August 09 with Michael Ashburner? This would be after the ISMB meeting (3-7 Aug., Edmonton, CA; http://www.ismb02.org/).
> > >
> > > 4. Any other relevant/pressing matters.
> > >
> > > I look forward to 'meeting' with you on Tuesday (Wednesday AM, Richard ;-) - hope that will work for you).
> > >
> > > - Leszek
> > > PS Susan McCouch has already sent me her apologies.
> > > 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
> > >
> >
> > -----------------------------------------------------------------------------
> > Sue Rhee                                rhee at acoma.stanford.edu
> > The Arabidopsis Information Resource    URL: www.arabidopsis.org
> > Carnegie Institution of Washington      FAX: +1-650-325-6857
> > Department of Plant Biology             Tel: +1-650-325-1521 ext. 251
> > 260 Panama St.
> > Stanford, CA 94305
> > U.S.A.
> > -----------------------------------------------------------------------------

-- 

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

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