Comments on anatomy and temporal ontologies

[Pankaj Jaiswal]

I have made some changes in growth stage ontology files as suggested. The files
are now on CVS POC/temporal/ 
Don't worry about  the folder name, i will rename it later.

Changes made: Modifications were done under PO:0007140, PO:0007001 and
PO:0007139. did not touch the Ath section. You have the choice to adopt any
framework to build the integrated version.

Added 
  %ripening stage PO:0007001
   %fruit ripening stage PO:0007003

Did not add terms endosperm / embryo development stage , since its difficult to
discretely define them in some of the cereals. Reason is, most of the time,
their definition suggests recognition of stage by looking at the endosperm
hardness. There is no mention of what's happening to the embryo (except some of
the terms from maize). The best i could suggest is to put all of them under
"embryonic stages", otherwise it may give a wrong impression that most of the
cereals don't have any embryo development stage (which is not true).


vegetative lag stage (sensu Poaceae) PO:0007146 and 
stem elongation stage (sensu Poaceae) PO:0007048 are now
instances of vegetative stage and also part of reproductive stage. Do you think
its OK to have it this way.


Modifications for flowering stages
deleted the synonyms (anthesis and anthesis stage) of flowering stage now
flowering stage (sensu Poaceae)PO:0007151, because we are recognizing anthesis
as instance of flowering stage PO:0007021

introduced new term 
  %flowering stagePO:0007151


CVS check out:

the growth stage ontology files are now available on Poc CVS under the folder
temporal
file names: temporal_poc_ont.txt and temporal_poc_def.txt

Pankaj


Leonore Reiser wrote:
> 
> Pankaj-
> Thank you for all the comments! It is really helpful in getting some
> clarity. Tanya and I will go over them in more
> detail and start working out changes. You mentioned in your mail that you
> would change some things- would you like to go ahead and make those
> changes and we will work on that version (so we dont end up having to
> merge two sets of changes?).
> 
> Are these ontologies in the CVS repository? Can we use that to keep/share
> development versions rather than via email or ftp?
> 
> Regarding the naming- I think there is no problem with using the term
> plant growth stages.Go for it!
> 
> Leonore
> 
> -------------------------------------------------------------------------------
> 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
> -------------------------------------------------------------------------------

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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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