Plant ontology updates

Wed May 4 17:39:45 EDT 2005

Hi all,

I have no problem leaving 'root vascular bundle' out for now, and I like
the idea of clarifying the usage of the 'vascular' terms, once we decide
on the root vascular bundle. Right now, there is 'root vascular system'
and 'root stele', and it is not too confusing to decide which one of the two
to use in particular cases (at least for Arabidopsis annotations).

We can include in Comment section Toby's clarification once the vascular
terms are revisited.

After the comments I got today, here is the new version of this week
ontology update:

I. To bring back terms crown root seminal root, and obsoleting nodal rot

adventitious root
  % crown root ; PO:0003008
  % seminal root ; PO:0003009

II. From St Louis meeting, add the following terms (which we already
agreed on):
New term:
1. stem vascular system
NEW def: Vascular tissues in their specific arrangements in the stem.

2. Renaming the term 'nodule' to 'root nodule' and adding a new structure
for the term 'nodule:

3. New term: adventitious root nodule (syn. stem nodule)

NEW def: Enlargement or swelling on adventitious aerial roots, inhabited
by nitrogen-fixing bacteria.

Comment: Unlike the root nodules, these contain functioning chloroplasts
in the nodule cortex and are therefore capable of carbon fixation.

Ontology structure:

root
 (p) root nodule
 (i) adventitious root
     (p) adventitious root nodule (synonym: stem nodule)

4. Corrections of typos in the ontology file (as described earlier).

I appreciate your comments and your prompt responses to this thread.

Katica

On Wed, 4 May 2005, Peter Stevens wrote:

> >Ummm, I think Homer nodded.  As  far as I can work out, differences
> >between young roots in monocots and BLAs, certainly in eudicots, has
> >to do more with the number of protoxylem poles than anything else;
> >BLAs are 1-few, monocots tend to be many (and to have a pith, too,
> >although this is certainly at least sporadic in BLAs).  Furthermore,
> >roots don't really have vascular bundles at all, so the term should
> >not be used here; the aylem and phloem poles alternate regularly
> >around the circumference of the stele.  So the vascular system of
> >the root consists of the vascular tissue, initially alternating
> >xylem and phloem, which may take up the whole of the central part of
> >the root - or not.  The stele can be clearly recognised, unlike in
> >many stems (strictly speaking, 'stele' and 'vascular system' are not
> >synonyms, although they have been treated as such).  Incidentally,
> >the direction of development of the xylem in the root and stem
> >differs; the root is exarch, the stem endarch; this is true of all
> >seed plants.
>
>
> What goes on in the stem is roughly what Toby described; most
> monocots and things like Piperaceae tend to have scattered vbs;
> Ranunculaceae Cucurbitaceae Asteraceae (e.g.) have initially a ring
> of separate bundles, whether or not later joined by vascular cambium,
> while other BLAs have a ring of vascular tissue from the beginning -
> but I am not sure of the distribution of this latter feature.
>
> P.
>
>
>
>
>
> >The difficulty with the root terms is created by the differences in root
> >anatomy.  In monocots plus a few of the early-diverging angiosperms
> >(e.g. Piperaceae), the vascular system of the root is made up of
> >vascular bundles scattered all over the place as seen in cross section,
> >and not organized into a central cylinder.  In eudicots, the term root
> >vascular bundle doesn't have much meaning, since the stele is a
> >cylindrical unit without separate bundles.  Thus for monocots and
> >Piperaceae, you'd need the terms root vascular bundle and root vascular
> >system (all the bundles as a group), whereas in eudicots and other of
> >the early diverging lineages you'd need stele (which would include the
> >endodermis) and root vascular system, which would be the vascular tissue
> >encompassed by the stele.  So the accurate definition of the terms - to
> >avoid confusing the annotators - would have to include some sort of
> >comment on where the terms are to be applied.
> >Toby
> >
> >On May 3, 2005, at 7:09 PM, Katica Ilic wrote:
> >
> >
> >>  Hi all,
> >>
> >>  The following changes to the Plant Structure Ontology are to be made
> >>  this
> >>  week:
> >>
> >>  I. Bringing back from the obsolete node terms 'crown root' and
> >>  'seminal
> >>  root', and obsoleting 'nodal root'
> >>
> >>  Ontology structure:
> >>
> >>  adventitious root
> >>    % crown root ; PO:0003008
> >>    % seminal root ; PO:0003009
> >>
> >>  Please, let me know if term 'brace root' is needed at present time.
> >>
> >>  II. From St Louis meeting, the following terms are to be added (which
> >>  we
> >>  already agreed on):
> >>
> >>  New term:
> >>  1. stem vascular system
> >>  Def: Total of the vascular tissues in their specific arrangements in
> >>  the
> >>  stem.
> >>
> >>  2. root vascular bundle (new term, requested by Pankaj)
> >>  Def: A strandlike part of vascular system of root, composed of phloem,
> >>
> >>  xylem and associated transfusion tissue
> >>
> >>  3. add 'leaf vascular bundle' as a synonym of 'leaf vein'
> >>
> >>  NOTE: we now have three highly redundant terms: root vascular system,
> >>  root
> >>  stele and root vascular bundle. For a curator, it is going to be a
> >>  very
> >>  arbitrary decision to make on which one to use for annotation.
> >>
> >>  4. Renaming the term 'nodule' to 'root nodule' and adding a new
> >>  structure
> >>  for the term 'nodule:
> >>
> >>  New term: adventitious root nodule (syn. stem nodule)
> >>  Def:  Enlargement or swelling on adventitious aerial roots in some
> >>  legumes
> >>  (e.g., Sesbania rostrata), inhabited by nitrogen-fixing bacteria.
> >>  Unlike
> >>  the root nodules, these contain functioning chloroplasts in the nodule
> >>
> >>  cortex and are therefore capable of carbon fixation. (TAIR:ki)
> >  >
> >>  Ontology structure:
> >>
> >>  root
> >>   (p) root nodule
> >>   (i) adventitious root
> >>       (p) adventitious root nodule (synonym: stem nodule)
> >>
> >>
> >>  IV. Corrections of typos and minor errors in the ontology file :
> >>  1. Term: stem cortex
> >>  Definition: The primary tissue located between the vascular system and
> >>  the
> >>  epidermis of the root.
> >>  (It should be 'of the stem").
> >>
> >>  2.	Sillica cell to silica cell
> >>
> >>  3. Cotyledon vascular system (to correct the definition)
> >>
> >>  4. Also, several minor typos in the text of the following:
> >>  Terms: stolon, valve, phloem, chlorenchyma, and shoot procambium.
> >>
> >>  Thanks,
> >>
> >>  Katica
> >>
> >>
> >>  ----------------------------------------------------------------------
> >>  ----
> >>  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/
> >>  260 Panama St.
> >>  Stanford, CA 94305
> >>  U.S.A.
> >>  ----------------------------------------------------------------------
> >>  ----
> >>
> >>
> >>
> >>
> >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
>

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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/
260 Panama St.
Stanford, CA 94305
U.S.A.
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