progress and thought questions

[Toby Kellogg]

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