New node in the Plant Structure Ontology

[Pankaj Jaiswal]

I still do not think that we need to create a separate node "In vitro 
cell, tissue and organ culture". All the instances of this term can 
easily go under either cell/tissue/sprorophyte depending on the cultured 
plant structure.

Also I would rephrase them as below, because one studies the expression 
of the genes or extracts enzymes/proteins/RNA from the actual cells or a 
tissue that were grown in an in-vitro culture, where the use of term 
"culture" is a recognition of method. The methodology can be described 
in the definition.

leaf cell culture > cultured leaf cell
root cell culture > cultured root cell
protoplast culture > protoplast

and appear in the tree as

cell
..i..cultured leaf cell
..i..cultured root cell
..i..protoplast

tissue
..i..callus-->I am sure it is an instance of meristem.

embryo
..i..somatic embryo

-Pankaj

Katica Ilic wrote:

> Hi all,
> 
> I finally put together In vitro (experimental) node for the Plant
> Structure Ontology.
> 
> Additional terms can be introduced later, these are the terms needed for
> annotations in TAIR, Gramene and maizeGDB. I've had second thoughts about
> terms that have 'culture' in the name, but these are already existing
> terms, at least in TAIR and MaizeDGB.
> 
> I would greatly appreciate your suggestions and comments, especially
> regarding the definitions.
> 
> The top node term is 'In vitro cell, tissue and organ culture' and this
> term will go under the 'plant structure', as sibling to the four top
> nodes:
> 
> PO:0009002 : cell
> PO:0009004 : gametophyte
> PO:0009003 : sporophyte
> PO:0009007 : tissue
> New term: In vitro cell, tissue and organ culture
> 	(i) protoplast culture
> 	(i) cell culture
> 		(i) leaf cell culture
> 		(i) root cell culture
> 	(i) callus
> 		(i) callus culture
> 	(i) embryo culture
> 		(i) somatic embryo
> 
> 
> Suggested definitions for the new terms:
> 
> Term: in vitro cell, tissue and organ culture
> Definition:
> Experimentaly isolated and grown plant protoplast, cell, tissue and
> organ, that involves, as a common factor, growth of microbe-free
> plant material in an aseptic (sterile) environment, such as
> sterilized nutrient medium in a test tube or petri dish.
> 
> Term: protoplast culture
> Def: In vitro isolation and maintenance of the cells from which the entire
> cell wall has been enzymatically removed.
> 
> Term: cell culture
> Synonym: Cell suspension culture (cell suspension, carrot cell suspension,
> tobacco cell suspension, maize 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: leaf cell culture
> 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: root cell culture
> 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: Callus: An unorganized, proliferative mass of large, thin-walled
> cells; a wound response.
> 
> Term: Callus culture
> 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: embryo culture:
> Def: In vitro development or maintenance of isolated mature or
> immature zygotic embryos, or somatic embryos.
> 
> 
> 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.
> --------------------------------------------------------------------------
> 
> 
> 

-- 
************************
Pankaj Jaiswal, PhD
G15-Bradfield Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
************************