New terms in the Plant Structure Ontology

[Anuradha Pujar]

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
>
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