progress and thought questions

[Katica Ilic]

Hi Toby,

I've looked at updated anatomy.ontlogy, it looks great! What a nice job!
I've gone through some of the issues you raised, and below are the minor
comments. I may have some more later.

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.

- I would go with the first. Although I am not aware of any
annotation using term egg apparatus yet, I found a couple of abstracts coming
from Thomas Dresselhaus' lab refering to genes expressed in the egg
apparatus in maize and wheat (PMB meeting in Barcelona, 2003, see
http://www.ispmb2003.com/abst/obtimpres.php?idAbst=422). So, we may need
egg apparatus as a term, with childrens egg cell and synergids.

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 agree with you, they are overkill to me too, but then again, we may
need these terms. I'll look to see what is in the published literature
(if people actaully use these terms).

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?

- I would go with synonym here (polen=microgametophyte), especially with
the few options that we now have when it comes to synonyms.  As for the
microspores, I would include it in the micosporangium node, with
microsporocyte as a_part_of, then microspore as its child (develops_from),
and then pollen (which you already have there as a child of
microsporangium). I could look into this in more details later.

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

- I agree with Pankaj, we need these terms since they are all in common
use.

At the end, very minor points, there is a typo in embryo sac node
(symergids), and also, I would put sperm cell(s) instead sperm in the
microgametophyte node (unless I am missing something here).

Cheers,

Katica