progress and thought questions

[Pankaj Jaiswal]

Hi Toby, Peter and Felipe,

This version looks great. It is a great beginning. I will go through it in
detail sometime this week. Following are my comments, though not many.

Cheers

Pankaj

Toby Kellogg said:
> Hi folks -
>   Felipe has posted or is about to post an updated version of the plant
> ontology to the CVS, with more bits of the hierarchy filled in and also
> definitions for everything so far.  When you compare it to TAIR and
> GRAMENE, you'll see that we've omitted from the organ ontology any terms
> that refer to tissue types, and also have avoided including attributes of
> organs unless they seem absolutely necessary.  (For example, we haven't
> included even-pinnate compound leaves and odd-pinnate compound leaves,
> since the parts of each are the same - leaflet, petiolule, stipel.)  This
> lack of attributes also makes it much more "skeletal" than the Maize
> Ontology.
>     You'll see in the notes that we keep running up against the question
> of
> detail and attributes of organs.  If the ontology is a tool for binning
> genetic/genomic data, rather than for describing all aspects of all
> angiosperms in detail, then we want something with minimal elaboration.
> However, I'm still not really clear how an end user (as opposed to an
> annotator) will actually use this ontology, so I could be way off base
> here.
>    A number of specific questions have come up, so I'll list them below
> for
> you to think about and discuss at some point in the future.
> 1.  In this most recent version, parts of the embryo are egg cell,
> synergid
> cell, polar nucleus, and antipodal cell (just four terms), and central
> cell
> develops from polar nuclei.  Alternatively, we could introduce another
> hierarchical level such that parts of the embryo are egg apparatus,
> central
> cell, and antipodal cells, with egg cell and synergid cell part of egg
> apparatus and polar nuclei part of central cell.  Are things ever
> annotated
> to "egg apparatus" or is it always "egg plus synergid"?  If the latter,
> then the former is superfluous.
> 2.  Sporoderm is part of pollen, exine and intine are parts of sporoderm.
> There are then a whole bunch of terms for all the components of the pollen
> wall (endexine, ectexine, etc. etc. etc.).  Do we really want all of those
> terms?  It seems like overkill to me,  but maybe they are necessary.

I guess we need these terms. Sometimes the insitu hybridization
experiments  on gene expression identify such structures.



> 3.  How are we going to define microgametophyte?  e.g. does pollen =
> microgametophyte even though it contains some tissue (the pollen wall)
> that
> is of sporophytic origin?  What about microspore?

We agreed on the PART_OF relationship type that POC will not use it in a
strict way. Our definition was that "a term could be a part of another
term but is not necessarily always a part of it".

> 4.  Is it important to include endothelium as part of the inner
> integument?
> This is the same issue as #2 - how detailed do we want (need) to be?
> 5.  In the version that Felipe has posted, we dispensed with apocarpous
> gynoecium and syncarpous gynoecium as instances of gynoecium, because it
> made it easier to handle the terms carpel, ovary, stigma and style.  Also
> apocarpous and syncarpous are attributes of gynoecium, not really a
> separate structure.  Is there any reason to re-instate them?  (There are
> reasons *not* to, which Felipe or I can explain if anyone wants.)


No problem as of now.

> 6.  Do we need to include leaf margin, leaf base, and leaf apex as parts
> of
> a leaf?  They are obviously used for description of plants, but are they
> (or will they be) used for annotation of genes?

We want them. There are several reports on gene expression/mutant studies
on these parts.


> 7.  Is it worth including perigynium as an instance of a prophyll?  The
> term is used only for species in the family Cyperaceae, specifically
> species of Carex.

My argument would be to include the terms on usage/requirement basis
unless absolutely necessary to clarify some other node in the ontology.


> 8.  Capsules are currently divided into circumscissile, poricidal,
> septifragal, septicidal, and lodulicidal, with silique being an instance
> of
> a septifragal capsule.  Do we need all those types of capsules, or can we
> just use capsule (with silique as a instance)?  (Same issue as #s 2 and
> 4.)

These are all based on mode/type of dehiscence. We had this discussion
when dehiscence term was introduced in the Gene ontology's biological
process section. My suggestion is to go with you and if somebody realy
identifies a gene associated with the process we can modify the structure.


> 9.  What are the relationships among epicotyl, plumule, coleoptile, and
> embryonic axis?  Are all in common use?

I believe so. All are part of embryo or shoot of a seedling.

> 10.  Inflorescence can be defined with panicle, raceme, tassel, ear, and
> cob as synonyms.  Alternatively, we can divide inflorescences into racemes
> (which do not terminate in a flower) and cymes (which do).  Panicle,
> tassel, ear, and cob would thus be synonyms of raceme.  Or we can keep
> dividing the inflorescence categories more and more finely depending on
> which axes end in flowers and which don't, and could end up with a
> plethora
> of terms.  (Same issue as #s 2, 4, and 8.)  How complex do we get?

I agree with you. My question here is how do we deal with terms like
primary/secondary inflorescence branches? There are many mutants/genes
responsible for the branching organization.


> Cheers -
> Toby
>
> Elizabeth A. Kellogg
> Department of Biology
> University of Missouri-St. Louis
> 8001 Natural Bridge Road
> St. Louis, MO 63121
> phone: 314-516-6217
> fax: 314-516-6233
> http://www.umsl.edu/divisions/artscience/biology/Kellogg/Kellogg/
>
>
>


-- 
Pankaj Jaiswal
Gramene Database
www.gramene.org