New terms for the Plant Ontology

[Katica Ilic]

Hi all,

Here is the latest set of terms that are either requested by users or
needed for annotations. As you can see, there are subcellular structures
listed below; these terms are not present in GO and are plant specific, so
we need to consider them.

I am not sure about filiform apparatus, does it go as a child of synergid
cell or egg apparatus (or both). My recollection is that this structure is
not just part of two synergid cells, but also exceed to the egg cell.

Also, I am not sure about terms 'septum' and 'valve', where exactly to put
these (see below).

Your suggestions and comments are very appreciated.

Many thanks,

Katica

Term: cuticle
Def: A layer of fatty material, cutin, rather impervious to water, located
on the outer walls of epidermal cells.

Cell
  (i) epidermal cell
	(p) cuticle

Term: casparian strip
Def: A band-like wall formation within primary walls that contains suberin
and lignin; typical of endodermal cells in roots, in which it occurs in
radial and transverse anticlinal walls.
root
  (p) root cortex
     (p) root endodermis
         (p) casparian strip

Term: filiform apparatus
Def: A complex of cell wall invaginations in a synergid cell similar to
those in transfer cells.

Synergid cell
  (p) filiform apparatus

or
egg apparatus
  (p) filiform apparatus

Term: lateral root tip
Def: The portion of the lateral root including the meristem and root cap.
Term: root tip
Def:  Top portion of the root including meristem and root cap.

This is the case were we need to instantiate 'root tip' (creating three
terms, root tip, primary root tip, lateral root tip).

root
  (p) root tip
  (i) lateral root
       (p) lateral root tip
   (i) primary root
        (p) primary root tip

root tip
(i) lateral root tip
(i) primary root tip

Term: pollen tube tip
Tip portion of the pollen tube that is rapidly growing.

male gametophyte
 (p) pollen tube
    (p) pollen tube tip

Term: root hair tip
Tip portion of an outgrowth of a root epidermal cell

epidermis
(p) epidermal cell
  (i) root hair
     (p) root hair tip

I think we don't need to propagate 'root hair tip' everywhere
where 'root hair' is present as 'develops_from' (it's optional).

Term: septum - A thin partition or membrane that divides two cavities or
soft masses of tissue of anther, ovary or fruit.

Since we have three terms for each, carpel and anther, my suggestion is to
add 'septum' as a child of generic term only, and not to instantiate under
any 'sensu' term.

carpel
  (p) septum

and

anther
(p) septum

and

fruit
(p) septum

Term: lenticel
Def: Loosely-packed mass of cork cells occurring especially in the young
stem, bark or even leaf of a plant, visible on the surface as a raised,
often powdery-appearing spot, through which gaseous exchange occurs.

stem
(p) lenticel

also,

leaf
(p) lenticel

Term: tetrad of microspores
A group of four haploid cells that remained joined together shortly after
meiosis. Each cell will give rise to the male gametophyte.

androecium
 (p) stamen
     (p) anther
         (p) microsporangium
            (p) microsporocyte
               (d) tetrads of microspore
                    (d) microspore

In this case, we have 'tetrad of microspores' with only develops_from
relationship.

Term: valve
Def: valve: a portion of an organ that is fragmented; in capsule, the
portions into which the pericarp splits at maturity.

fruit
 (p) fruit abscission zone
 (p) pericarp
 (p) seed
 (p) valve

and

flower
 (p) gynoecium
 (p) carpel
 (p) ovary


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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
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