Nodal root innstances (crown and seminal roots)

[Vincent, Leszek]

Katica (& colleagues),

Just for clarification - The references in the definitions associated
with the two terms (crown roots & seminal roots) came from my Zea
ontology 'sand box' - an excel spreadsheet. They're not included in the
Zea ontology file.

- Leszek
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
P. Leszek D. Vincent Ph.D., FLS
Division of Plant Sciences
Res. Prof. Dept. of Horticulture
215 Curtis Hall
University of Missouri-Columbia
Columbia
MO 65211-7020
USA
Ph: (573) 884-3716; Fax:(573) 884-7850;
Email: Leszek at missouri.edu
Associate Curator, Dunn-Palmer Herbarium (UMO);
Research Associate, Missouri Botanical Garden (MO), USA;
Plant Systematist on The Plant Ontology Consortium - NSF award 0321666
(www.plantontology.org)
*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*
 

-----Original Message-----
From: owner-po-dev at brie4.cshl.org [mailto:owner-po-dev at brie4.cshl.org]
On Behalf Of Katica Ilic
Sent: Tuesday, May 03, 2005 4:31 PM
To: po-dev at plantontology.org; Pankaj Jaiswal
Cc: Kellogg, Elizabeth A.
Subject: Re: Nodal root innstances (crown and seminal roots)


Hi all,

I apologize for not responding to this thread on time, the e-mail was
sent
on the day of the ontology release and I simply didn't have time to
respond. In fact, I would greatly appreciate if internal ontology
requests
are not sent off on the day of the ontology release, unless they are
urgent.


Now that Pankaj is suggesting to bring back terms crown and seminal
root,
the question is: do we then need term 'nodal root'; it is now just a
grouping term?

Could we make crown and seminal root instances of adventitious root
(obsoleting nodal root), with definitions that Toby provided? And
perhaps
adding 'brace root' too if needed.

adventitious root
   % crown root ; PO:0003008
   % seminal root ; PO:0003009
   % brace root (new)

Regarding Leszek's definitions, I don't think we should be providing
references as part of definitions, and definitions should be short and
concise, if possible (considering the AmiGO display of definitions).

Katica

P.S. Pankaj, once we agree on this, if you don't mind, I can do these
changes in the file, together with a few other corrections and typos (on
Friday).



On Tue, 3 May 2005, Pankaj Jaiswal wrote:

> Sounds good to me. If everyone agrees, I will add the terms on Friday.
> -Pankaj
>
>
>
> kellogge wrote:
>
> > Seems reasonable to me to bring these back.
> > How about:
> > crown root (definition): adventitious root initiating from one of
the
> > earliest-formed nodes on the plant. (Comment: these roots are
normally
> > formed at or just above ground level.)
> > seminal root (definition): adventitious root initiating from the
> > scutellar node in a grass.
> > Toby
> >
> > On Apr 27, 2005, at 12:40 PM, Pankaj Jaiswal wrote:
> >
> >
> >
<http://www.plantontology.org/amigo/go.cgi?view=details&show_association
s=terms&search_constraint=terms&depth=0&query=PO:0003005>
> >
> >
> >     Can we bring back the two instances of the nodal root,
> >
> >     nodal root ; PO:0003005
> >     ---%crown root ; PO:0003008
> >     ---seminal root ; PO:0003009
> >
> >     These terms were merged to nodal root (PO:0003005) as synonyms.
They
> >     were introduced to the anatomy.ontology in version 1.11
> >
> >     Their development is genetically controlled
> >
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dop
t=Abstract&list_uids=14980975
> >
> >
> >     Also I need these terms for annotating the genes expressed in
them
> >
> >
> >     #1
> >     cDNA-AFLP analysis of inducible gene expression in rice
> >     seminal root tips under a water deficit
> >     doi:10.1016/S0378-1119(03)00713-3
> >     http://www.paper.edu.cn/scholar/download.jsp?file=wuping-5
> >
> >
> >     #2
> >     The Crown rootless1 Gene in Rice Is Essential for Crown Root
> >     Formation and Is a Target of an AUXIN RESPONSE FACTOR in Auxin
> >     Signaling.
> >     Plant Cell. 2005 Apr 13
> >
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dop
t=Abstract&list_uids=15829602
> >
> >
> >
> >     --
> >     ************************
> >     Pankaj Jaiswal, PhD
> >     G15-Bradfield Hall
> >     Dept. of Plant Breeding
> >     Cornell University
> >     Ithaca, NY-14853, USA
> >
> >     Tel: +1-607-255-3103
> >     +1-607-255-4109
> >     Fax: +1-607-255-6683
> >     http://www.gramene.org
> >     ************************
> >
> >
> > Elizabeth A. Kellogg
> > E. Desmond Lee and Family Professor of Botanical Studies
> > Department of Biology
> > University of Missouri-St. Louis
> > St. Louis, MO 63121
> > Tel: 314-516-6217
> > FAX: 314-516-6233
> >
http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/home.ht
ml
> >
>
> --
> ************************
> Pankaj Jaiswal, PhD
> G15-Bradfield Hall
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
>
> Tel: +1-607-255-3103
>       +1-607-255-4109
> Fax: +1-607-255-6683
> http://www.gramene.org
> ************************
>

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Katica Ilic             		katica at acoma.stanford.edu
The Arabidopsis Information Resource 	Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington 	FAX: (650) 325-6857
Department of Plant Biology 		URL: http://arabidopsis.org/
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