New terms in the Plant Structure Ontology

[Katica Ilic]

Anu,

Just send me a list of the terms you need, if you need more time, we can
add them in the next cvs round. I just don't want to postpone this any
longer, we discussed primordia terms a couple of months ago, and I took
some of the Pankaj
suggestion at that time (I don't know exactly what terms he suggested). I
can look into that. Easiest would be just to see what you have.

I'll be commiting new terms all week
(hopefuly). If you have comments or suggestions for the listed terms,
proposed structure, or definition, please, send it to me asap.

Again, additional terms can be added at later time (even this week).

Katica

P.S. Besides, Shuly is waiting for me to commit the new ontology files.

On Wed, 26 Jan
2005, Anuradha Pujar wrote:

> Primordium terms needs further discussion, there are additional xx
> primordium terms that are required for cereals and i am working on it, to
> see, if it fits in with the relationship and definition that you are
> suggesting.
>  anu
> >
> > 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
> >
> > --------------------------------------------------------------------------
> > 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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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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