A delayed response on "POC observations so far"

Tue Oct 14 14:21:22 EDT 2003

Hi all -
  this correspondence raises a question - are we trying to get all the
various databases to conform to a single ontology, or are we just trying to
establish some sort of synonymy so that one can move easily among them?
The ontology that Leszek proposes seems quite maize-specific, which is of
course not a problem until the maize database needs to connect with the
rice or Arabidopsis ones.
Toby

>Sue (& possibly others),
>
>The "bottom line" (elevator pitch) is that the Zea mays Plant Structure
>ontology has attempted to represent the biological reality of monoecy
>via incorporating ontogenetic data & reflecting phylogenetic theory &
>satisfies the 'true path rule'- check it out.
>
>- Leszek
>
>> -----Original Message-----
>> From: owner-po-dev at brie4.cshl.org
>> [mailto:owner-po-dev at brie4.cshl.org] On Behalf Of Sue Rhee
>> Sent: Wednesday, October 08, 2003 4:54 PM
>> To: po-dev at plantontology.org
>> Subject: Re: A delayed response on "POC observations so far"
>>
>>
>> give me the bottom line in three sentences or less.
>>
>> thanks,
>> sue
>>
>> On Wed, 8 Oct 2003, Vincent, Leszek wrote:
>>
>> > Hi POC colleagues,
>> >
>> > Here's some 'bedtime reading'.
>> >
>> > Recently there was discussion about the representation of unisexual
>> > florets in a taxon which bears both functionally male &
>> female florets
>> > in separate flowering structures e.g. adequate representation of
>> > monoecy in taxa such as Zea mays. Furthermore concern was
>> raised about
>> > querying an ontology, involving a monoecious taxon, for the term
>> > gynoecium - that such a search should be able to retrieve
>> > gynoecium-related info. associated with the tassel as well
>> as the ear
>> > as in Zea mays.
>> >
>> > Pankaj & possibly some others may recall that some of us
>> visited this
>> > area sometime last year & the synthesis of that dialogue
>> was recorded
>> > in the current ontology for Zea mays (freely available from
>> > plantontology.org). But to show you an example of the tentative
>> > solution to the challenge I've reproduced a portion of the
>> > representation below:
>> >
>> > organ
>> >   %tassel (functionally male inflorescence)
>> >     <pedicellate spikelet of tassel
>> >       <lower floret of pedicellate spikelet of tassel
>> >         <gynoecial tissue (abortive) of lower floret of pedicellate
>> > spikelet of tassel
>> >         <lodicules of lower floret of ....
>> >         <palea of lower floret of .....
>> >         <stamens of lower floret of ....
>> >       <lower glume of pedicellate spikelet of tassel
>> >       <upper glume of .....
>> >     <sessile spikelet of tassel
>> >       etc.
>> >   %lateral branch
>> >     <ear (functionally female inflorescence)
>> >       <pedicellate spikelet of ear
>> > etc....
>> >
>> > Yes, it is a little complex (view it via DAG-Edit for a clearer
>> > representation than that provided here) but it is my/our
>> best attempt
>> > yet at capturing the biological complexity such that the true path
>> > rule is met for this biological reality in Zea mays.
>> Furthermore, it
>> > should satisfy the query needs referred to above. Of course
>> there may
>> > be other considerations that have since transpired...
>> >
>> > For me, as a botanist & plant systematist, I think it is a good
>> > solution because it captures the ontogenetic detail for these
>> > structures and it is also consistent with phylogenetic argument
>> > concerning these structures - and consequently should be
>> applicable to
>> > taxa, other than Zea, where monoecy & dioecy is found.
>> >
>> > It is true that some folk may not (at first) appreciate the
>> biological
>> > relevance of including both the androecium & gynoecium in both the
>> > tassel & ear. My attempt to cover that 'base' is provided in the
>> > definition for "floret". In this definition I spell out the
>> > ontogenetic reality of both the androecium & gynoecium
>> being initially
>> > present in both the tassel & ear florets - hence their need to be
>> > included in both the tassel & lateral branch/ear nodes. It
>> also draws
>> > attention to the putative phylogenetic necessity for such a
>> > representation. Implicitly what I'm practicing is that
>> ontogenetic &
>> > phylogenetic information are both extremely important for
>> inclusion in
>> > the application of the 'true path rule'.
>> >
>> > Here's the definition for floret (yes, it is detailed):
>> > "The floret is the individual flower of the Zea mays plant. In the
>> > grass family (Poaceae, alt. Gramineae) each floret is typically
>> > bisexual (perfect), possessing both an androecium and a gynoecium.
>> > Each floret typically has a pair of bracts, the lemma and
>> palea, which
>> > subtend the floret. It is important to note that In Zea mays the
>> > florets of the 'tassel' are functionally male (the female component
>> > (gynoecium) having aborted early on in development). The florets of
>> > the 'ear' are functionally female (the male components (androecium)
>> > having aborted early on in development). The possession of
>> > functionally male and functionally female florets (or
>> flowers) on the
>> > same plant is a condition called monoecy. While Zea mays is
>> > functionally monoecious, the presence of both androecial
>> and gynoecial
>> > tissue in the early stages of floret ontogeny is phylogenetically
>> > significant. Consequently, the androecium is represented in the
>> > florets of the ear and the gynoecium is represented in the
>> florets of
>> > the tassel, even though either of these whorls is absent in the
>> > functional florets. The inclusion of both whorls in the floret
>> > ontology for the florets of ears and spikelets is based on this
>> > phylogenetically significant ontogeny. East and Hayes (1911, p.
>> > 134-135) provided the following: "Perhaps it should be mentioned in
>> > passing that the immature sex organs, so called, of maize
>> seem endowed
>> > with the power of becoming either stamens or carpels. One
>> often finds a
>> > normal ear ending in stamens, and nearly every plant
>> produces lateral
>> > branches which have carpels and stamens mixed together
>> > indiscriminantly." Studies of mutants have explored these
>> occurrences
>> > and similar occurrences in tassels, corroborating the
>> inherent bisexual
>> > nature of the floret meristem prior to the subsequent
>> development of the
>> > monoecious condition." (the length of this defn. possibly provides
>> > argument for the inclusion of some sort of comment field closely
>> > associated with the definition?).
>> >
>> > I've also been using the Derived/Develops_from relationship
>> in the Zea
>> > ontology. This relationship accommodates the temporal &
>> spatial needs
>> > associated with ontogeny e.g. the development of primordia.
>> >
>> > You'll note, when browsing the ontology via DAG-Edit, that I still
>> > need to provide definitions for some terms - an ever pressing need.
>> >
>> > Let me have your candid comments/thoughts.
>> >
>> > Leszek
>> >
>> > ===========================
>> > P. Leszek D. Vincent Ph.D., FLS
>> > Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
>> University of
>> > Missouri-Columbia, Columbia, MO 65211-7020, USA.
>> > Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
>> > Ph/Fax (Home): (573) 441-1228;
>> > Email: Leszek at missouri.edu
>> > Yahoo! Messenger: leszekvincent
>> > Plant Systematist on the Plant Ontology Consortium
>> > Associate Curator, Dunn-Palmer Herbarium (UMO)
>> > Research Associate, Missouri Botanical Garden, USA
>> > CEO - PhytoSynergy, LLC
>> > =======================
>> >
>> >
>>
>> --------------------------------------------------------------
>> ---------------
>> Sue Rhee                         	rhee at acoma.stanford.edu
>> The Arabidopsis Information Resource	URL: www.arabidopsis.org
>> Carnegie Institution of Washington	FAX: +1-650-325-6857
>> Department of Plant Biology		Tel: +1-650-325-1521 ext. 251
>> 260 Panama St.
>> Stanford, CA 94305
>> U.S.A.
>> --------------------------------------------------------------
>> ---------------
>>
>>

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/