New node in the Plant Structure Ontology

[Katica Ilic]

Pankaj,

We came to the conclusion on having a separate node
for in vitro term back last spring, and this idea of propagating annotations from
'cell culture' term all the way up to the cell node just does't make
sense to me.

However, I would consider renaming the terms like 'root cell
culture' to 'cultured root cell', or 'protoplast culture' to cultured
protoplast'. I wouldn't call it just 'protoplast', to avoid possible
confusion (if this term is to stay in 'in vitro ' node).

Def from K. Esau:
Protoplast: The organized living unit of a single cell including
protoplasmic and nonprotoplasmic contents of a cell but excluding the cell
wall.

(PO) suggested def: In vitro isolated cells from which the entire cell wall has been enzymatically removed.

I am not sure about annotations to 'somatic embryos'; if we want those
appearing under 'embryo', but we can certainly discuss this.

Also, callus is NOT a meristem, even in tissue culture, researchers don't
refer to it as  meristem. K Esau described it as a tissue (see her
definition), and in a broad sense it is tissue.

Esau def:
Callus: A tissue composed of large thin-walled cells developing as a result
of injury, as in wound healing or grafting, and in tissue culture.

I don't know what is the best solution for the term 'callus'; in a strict
sense, it doesn't belong to the 'in vitro' node, but it dsoesn't belong
to the rest of the structure ontology either. I've been thinking
of defining this top node in a broad way that would acomodate terms like 'callus',
which means it wouldn't be specifically called "in vitro cell, tissue,
organ culture".

Any ideas?


Katica



On Tue, 25 Jan 2005, Lincoln Stein wrote:

> Hi all,
>
> I think we hashed through this at the spring meeting and the issue
> that came up is that there are cultured lines that don't correspond
> directly to any normal tissue.  The equivalent in human would be the
> HeLa cell line, which was derived (a long long time ago) from an
> ovarian cancer, but would hardly be described as "ovarian tissue"
> now.
>
> Certainly for primary cultures an annotator might want to describe the
> source of a microarray tissue as "derived from primary culture of
> leaf tissue", where "leaf tissue" uses the appropriate PO term.  For
> established lines, though, I would be more comfortable descending
> from an "in vitro cell, tissue, organ culture" node.
>
> Lincoln
>
> On Tuesday 25 January 2005 01:58 pm, Pankaj Jaiswal wrote:
> > 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.
> > > -----------------------------------------------------------------
> > >---------
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
>
> NOTE: Please copy Sandra Michelsen <michelse at cshl.edu> on
> all emails regarding scheduling and other time-critical topics.
>

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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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