New terms in the Plant Structure Ontology

[Katica Ilic]

pankaj, please see below,
On Wed, 26 Jan 2005, Pankaj Jaiswal wrote:

>
>
> Katica Ilic wrote:
>
> >
> > 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.
> >
>
> There are two instances of callus, one developing as a result of injury,
> and another instance is the same as you have. So you may like to add both.

In my e-mail, I mentioned that we shall discuss this on the ontology conf
call.

> In the definition you may want to rephrase " cell aggregates" to
> undifferentiated mass of cells/tissue.

I think cell aggregates is OK, that more descriptive than
undifferentiated mass of cells/tissue (at least for us who accually had a
hands-on experience  with cell suspensions).

> > 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.
> >
>
> Under the comments in place of Arabidopsis, can we say Brassicaceae?

I would leave it as it is for now, since I am not really sure if it is
aplicable to all Brassicaceae.
>
> > 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.
> >
>
> This still needs further discussion, wait until we have come to a
> conclusion. I am not sure if we can call XX-primordium as an instance of
> XX, where XX is a mature organ.

For the time being, there is no harm in having them as instances (we have
them as instance_of in TAIR).
Once they are in the PO, and we agreeed that we need these terms, right,
we can discuss the relationships and adding additional terms.

Katica

>
> -Pankaj
>

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Katica Ilic             		katica at acoma.stanford.edu
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