New terms in the Plant Structure Ontology

[Katica Ilic]

Hi all,

I am planning to commit changes in PO this afternoon. To avoid mistakes
from the past, here is what I am going to do regarding new terms in PO
(based on your comments and suggestions so far):

Note: this is not the list that Simon Yupp suggested; these are the terms
I brought up to your attention earlier this week.
Also, I am adding the following unresolved) items on the agenda for next
ontology group conf call:

1. Terms: callus, whole plant, somatic embryo -what is the most
appropriate place in the PO?
2. Apical hook - does it refer to hypogeal seeds?
3. Propagating terms from 'in vitro' node, such as 'cultured cell' to
the other nodes in the PO (see Pankaj's suggestion, Jan  25, po-dev
thread).

There are the new terms in PO (with short explanation for some terms):

1. I'll add the term 'whole plant' to the PO as a child of 'Plant
structure', sibling of 'cell' gametophyte' 'sporophyte' and 'tissue'
nodes.
On the next conf call we shall discuss the appropriate place for this
term.

Term: Whole plant
Def: The entire plant, including roots, shoots and leaves, at any stage of
its life cycle.
Comment: This term is so general that it should be avoided whenever
possible.

2. New node in PO
I am adding top node 'In vitro cell, tissue and organ culture' (under the
'plant structure'), and most of the terms in this node are needed for
annotations. I am leaving out term 'callus' for now, till we decide where
to put this term.

Plant structure
(i) In vitro cell, tissue and organ culture
	(i) cultured cell
		(i) cultured protoplast
		(i) cultured leaf cell
		(i) cultured root cell
	(i) cultured callus
	(i) cultured embryo
		(i) somatic embryo


Term: in vitro cell, tissue and organ culture
Definition:
Isolated and grown plant protoplast, cell, tissue and organ, involving, as
a common factor, growth of microbe-free plant material in sterile
environment, such as sterilized nutrient medium in a test tube or petri
dish.

Term: cultured protoplast
Def: In vitro isolated cells from which the entire cell wall has been
enzymatically removed.

Term: cultured cell
Synonym: cell suspension
Def: In vitro grown isolated cells and small cell aggregates that
proliferate while suspended in liquid sterile medium or spread on a solid
agar medium.
Comment:  In cell cultures, the cells are no longer organized into
tissues.

Term: cultured leaf cell
Def: In vitro grown isolated cells and small cell aggregates that
originated from isolated leaf protoplasts (after they re-established cell
wall, or from callus that was induced from leaf tissue).

Term: cultured root cell
Def: In vitro grown isolated cells and small cell aggregates that
originated from isolated protoplasts after they re-established cell wall,
or from callus that was induced from segment of root.

Term: somatic embryo:
Def: An embryo arising from previously differentiated somatic cells in
vitro, rather than from fused haploid gametes, i.e., zygote.

Term: cultured callus
Def: In vitro grown cell aggregates that originated from isolated
protoplasts, cell suspensions, or from callus that was induced in sterile
medium the supplemented by plant growth regulators.

Term: cultured embryo
Def: In vitro development or maintenance of isolated mature or immature
zygotic embryos, somatic embryos or haploid embryos (derived from male
gametophyte).

3. Old terms revisited:
These two terms will go under 'leaf' node as an instance_of.

Term: Cauline leaf
Def: Leaf or pairs/whorls of leaves borne on the stem.
Comment: In Arabidopsis, refers to the leaves that are borne on the
elongated inflorescence branches.

Term: Rosette leaf
Def: One of multiple leaves borne in a rosette. Rosette - a group of
leaves, generally borne at the base of the plant, that are separated by
very short internodes.
Comment:  In Arabidopsis, vegetative development is characterized by the
production of the rosette leaves.

This term is part_of 'primary shoot'.
Term: apical hook

Synonym: hypocotyl hook
Def: hook-like structure which develops at the apical part of the
hypocotyl in dark-grown seedlings in dicots.

4. Primordial terms

I am adding the following terms under respective organs as instance_of.
For the time being, I am leaving out top node term 'organ primordium',
since we voted not to have node 'organ', the 'organ primordium is not
needed fro similar reasons.

Term: organ primordium
Def: An organized group of cells from which an organ develops.

Term: cotyledon primordium
Def: An organized group of cells that will differentiate into a cotyledon.

Term: lateral root primordium
Def: An organized group of cells derived from the root pericycle that will
differentiate into a new root.

Term: leaf primordium
Def: An organized group of cells that will differentiate into leaf that
are emerging as a outgrowth in the shoot apex (flanking the meristem).


Term: ovule primordium
Def: An organized group of cells that will differentiate into ovule.


Term: gynoecium primordium
Def: The very first appearance of gynoecium.


Term: petal primordium
Def: The very first appearance of a petal.

Many thanks,

Katica

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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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