Nodal root innstances (crown and seminal roots)

[Katica Ilic]

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_associations=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&dopt=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&dopt=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.html
> >
>
> --
> ************************
> 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
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