A delayed response on "POC observations so far"

Tue Oct 14 14:51:16 EDT 2003

Hi,

Our goal is to be as generic as possible and have a single ontology. No synonymy 
in different ontology sets. If a particular node requires a species specific 
string, then it can be created within the same Ontology tree by effectively 
using the "sensu" rule. Atleast that is what we are going to have in POC and 
encourage others to use it.

Best
Pankaj

Toby Kellogg wrote:

> 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/
> 
> 
> 

-- 
******************************************
Pankaj Jaiswal, Ph.D.
Research Associate
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org
******************************************