New terms in the Plant Structure Ontology

[Katica Ilic]

Hi Anu,

Just brief comments, see below

On Mon, 31 Jan 2005, Anuradha Pujar wrote:

> Hello,
> In complete awareness that the primordium terms have been committed, I
> wish to draw attention to the fact that these terms will have an implicit
> link with the body part development stage ontology and having the
> develops_from relationship is significant.
>
> All plant body part develops from a primordium and the primordium itself
> is defined as a stage by Esau.  Nevertheless, the larger scientific
> community uses this term as an anatomical entity. Strictly, by Esau’s
> definition, a primordium could be a cell, organ or an organized series of
> cells, in their earliest stage of differentiation. E.g. leaf primordium,
> sclerid primordium, vessel member primordium.
>
> Therefore our suggestion is
>
> 1.The term primordium is botanically defined and should be available on
> the PO per se.
> Though Pankaj suggested xx-primordium as a grouping term, we should
> consider making it more generic i.e. "primordium". Any instances of it
> suggesting cell/tissue/organ primordium should then be listed with IS_A
> relationship.


Term primordium is more appropriate that organ primordium (in sync wiuth
the decision to obsolete top node 'organ'), though we do not necessarilly
need the groping term if all the primordia terms have instance_of
relationships.

 >
> 2. In defining, composite terms like ‘leaf primordium’ both ‘leaf’ and
> ‘primordium’ should be defined independently, as in the case of every
> other composite term in the PO such as ‘leaf epidermis’.
> This will make it easier for the developers and the automation script to
> use SLOTS (today's e mail from Lincoln) and make cross products.
>
>
> 3.The temporal development stages of body part ontology, will have a
> number of anatomical structures as a part of their developmental history.
> BUT the exact definition of those terms (primordium included) will be
> retrieved from the structure ontology.
>
> Would, having the term ‘primordium’ at the same level of sporophyte be
> justified for the above reasons? With children terms that could be  a
> cell, tissue or organs?
>
> I agree with Pankaj, that, develops_from relationship is more appropriate
> biologically, to say, that leaf develops from a leaf primordium, rather
> than the suggested relationship, of leaf primordium is_a instance of leaf.


I don't agree to include develops_from with primordia terms in the
structure thet you and Pankaj are suggesting, for two main reasons:

1. Develops_from relationship has a considerable limitations (see
Documentation on the POC live site, True path rule), and should be used
only when absolutely necessary, since annotations should not be propagated
beyong the firs parental node. This proposition imply revoking
develops_from relationships all over the ontology (if we are to be
consistent), that would lead to potential violations of the true path
rule, and creating cyclic structures, as oppose to hierarchy. After all,
as we stated before, everything develops from zygote, and we decided not
to follow this 'logics' when creating the top nodes.

2. Instance_of is not a wrong relationship, but a truly appropriate one
ontologicaly and biologicaly as well, and we have several examples of
similar situations, all with instance_of.

Embryo
 (p) embryo proper (though this should be instance_of, considering
remarks from Tereza Tykarska in my personal communications with her)

sporophyte
 (i) seed

leaf
  (i) embryonic leaf

...and perhaps others I cannot remeber now, since I am leaving for a
meeting..


Katica


 > > > Plant structure
>   i--cell
>   i--tissue
>   i--sporophyte
>   i--gametophyte
>   i--Primordium
>       i-Phyllome primordium
>         i-leaf primordium
>         i- bract primordium
>         i-sporophyll primordium
>         i--carpel primordium
>         i--stamen primordium
>
> The current state of structure, committed last week suggests that a gene
> that is expressed in a leaf primordium is also  expressed in the leaf or
> any of its
> instances. Whereas the relationships suggested by Pankaj and here in this
> mail, suggests, that a given primordium is in its earliest stages of
> differentiation, which means, it has not yet fully differentiated into an
> actual organ. Thus if we go by, the develops from relationship, the
> annotations as well as the concept remains intact, validating the
> statement that a gene expressed in leaf primordium is not necessarily
> expressed in  leaf or its instances.
>
> Individual definitions of gynoecium and petal primordium also requires
> changes.
>
> anu
>
>
> >
> > 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
> >>
> >> --------------------------------------------------------------------------
> >> 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.
> >> --------------------------------------------------------------------------
> >>
> >>
> >>
> >
> >
> >
>
>

--------------------------------------------------------------------------
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.
--------------------------------------------------------------------------