Botany meeting: Abstracts

[Felipe Zapata]

Hello,

I am sending the abstracts for the 2 presentations we (Peter, Toby and 
I) are planning to give at Botany 2004 (Botanical Society of 
America/American Society of Plant Taxonomists/American Fern 
Society/American Bryological and Lichenological Society). Toby or Peter 
would give the first talk and I would give the second one.

Please send us your comments.

Thanks,

Felipe

Overview of the Plant Ontology Consortium: goals and general structure.
Kellogg etc.

As genomic data accumulate, databases have been established to 
coordinate and disseminate information about specific plant species, 
primarily Arabidopsis (The Arabidopsis Information Resource, TAIR), 
rice (OryzaBase and Gramene), and maize (Maize Genome Database, 
MaizeGDGB), although others exist for other species as well.  One goal 
of these databases is to provide an index of genes, such that a user 
could, for example, find all genes known to affect fruit morphology, or 
all genes known to be expressed in young roots.  However, the databases 
have developed largely independently of each other, so that 
descriptions of phenotypes are not uniform.  Searching TAIR with the 
word "fruit" will produce no results, because all fruit-related genes 
are connected to the word "silique," and in Gramene a similar search 
would have to be conducted using the word "caryopsis."  The Plant 
Ontology Consortium (POC) is a collaborative effort that will provide a 
standard vocabulary to be applied across multiple plant databases, such 
that one could search each one using the same descriptor.  The POC 
(www.plantontology.org) currently involves several plant databases and 
workers in plant systematics, development and genomics.  Our first 
efforts are to unite terminology for Arabidopsis and the cereals; in 
subsequent years we will expand the descriptors as necessary to include 
tomato and legumes, and we will develop ontologies for describing plant 
growth and developmental stages.  The goal is to provide a set of 
"bins" into which genes and associated phenotypes can be placed.  The 
Plant Ontology is not designed to recapitulate or replace the entire 
rich vocabulary of plant taxonomy. It will also not provide a full set 
of morphological descriptors, although those it uses will be familiar.  
Rather it will provide a framework for connecting genotypic data with 
phenotypes in a way that permits comparisons across databases and among 
plants.
The project is supported by National Science Foundation grant No. 
0321666 to the Plant Ontology Consortium.

Developing the Plant Ontology: examples and computational tools
F. Zapata, et al.

The Plant Ontology follows an existing structure and set of rules 
already developed for the Gene Ontology.  It includes a set of terms 
related according to a Directed Acyclic Graph (DAG), in which parent 
terms can have multiple children (like a conventional hierarchy), but 
child terms can also have multiple parents (unlike a strict hierarchy 
or classification).  For example, the gynoecium (a parent term) is 
composed of carpel, ovary, style and stigma (all of them child terms).  
A carpel is also a particular kind of modified leaf, a megasporophyll.  
Hence, carpel, a child term, has multiple parents: gynoecium and 
megasporophyll.  The resulting structure is quite flexible and can 
accommodate plant morphological data that are not strictly hierarchical 
in nature. For instance, some wholes cannot be defined exhaustively by 
their parts; not all embryos have cotyledons, and the only thing common 
to all embryos would be a mass of four cells.  We use the computer 
program DAG Edit, an application that creates and maintains the files 
in a standard format for describing and modifying DAGs (DAG-edit 
format).  Individual members of the consortium are assigned particular 
sets of terms (nodes) in the hierarchy.  The hierarchy is not intended 
to be exhaustive even for the organisms currently under focus, but care 
is taken not to label nodes in such a way that subsequent inclusion of 
plants with very different morphologies will necessitate a 
restructuring of the hierachy. As portions of the ontology are drafted 
they are submitted to the CVS (control version system) repository, 
where all versions of the working files and documents are stored. There 
they can be viewed, compared with older versions, discussed and edited 
simultaneously by all members of the group.
The project is supported by National Science Foundation grant No. 
0321666 to the Plant Ontology Consortium.



~~~~~~
Felipe Zapata
University of Missouri St. Louis
Department of Biology
8001 Natural Bridge Rd.
St. Louis, MO 63121
314 516-6200
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