New revision of Plant Ontology is in cvs

[Katica Ilic]

Hi all,

I just committed ontology files to cvs:

anatomy.ontology, revision 1.31
anatomy.definition, revision 1.30
temporal.ontology (no changes), 1.2

New terms:
whole plant
in vitro cell, tissue and organ culture
cultured protoplast
cultured cell (Synonym: cell suspension)
cultured leaf cell
cultured root cell
somatic embryo
cultured callus
cultured embryo
cauline leaf
apical hook (Synonym: hypocotyl hook)
cotyledon primordium
lateral root primordium
leaf primordium
ovule primordium
gynoecium primordium
petal primordium

Definitions:
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

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 isolated and maintained mature or immature zygotic embryos,
somatic embryos or haploid embryos (derived from male gametophyte).

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.

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.


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 an outgrowth in the shoot apex (flanking the meristem).

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

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

Felipe's updated definitions:
Stem: the axial system of plants that bears leaves and buds.
Comment: it is usually above ground and more or less negatively geotropic,
is exogenous in origin, often indeterminate in growth and with secondary
thickening.

Inflorescence: That part of the axial system of plants above the uppermost
foliage leaf/pair of foliage leaves that bears flowers.

Peduncle: The stalk of an inflorescence; that part of the inflorescence
below the first flower or inflorescence branch and above the last foliage
leaf/pair of foliage leaves.

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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