progress and thought questions

[Peter Stevens]

>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).


I have made a little progress in disentangling pollen terms since the 
version of the glossary of about three weeks ago - which, 
incidentally, owing to a snafu lacked any introductory material at 
all. As far as I can work out the numerous terms in part represent 
two different ways of looking at pollen walls - morphology and 
staining properties. We will try and hash this out some more using in 
part a very good web glossary.

P.

>
>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