Abstract Detail

Developmental and Structural Section

Kellogg, Elizabeth [1], Stein, Lincoln [2], McCouch, Susan [3], Rhee, Seung [4], Jaiswal, Pankaj [3], Stevens, Peter [7], Ware, Doreen [2], Vincent, Leszek [5], Polacco, Mary [5], Reiser, Leonore [4], Sachs, Marty [6], Zapata, Felipe [1], Avraham, Shulamit [2], Ilic, Katica [4].

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

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.

1 - University of Missouri-St. Louis, Biology, 8001 Natural Bridge Road, St. Louis, Missouri, 631321, USA
2 - Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
3 - Cornell University, Department of Plant Breeding, Bradfield Hall, Ithaca, New York, 14853
4 - Arabidopsis Information Resource, 260 Panama Street, Stanford, California, 94305
5 - University of Missouri-Columbia, Department of Agronomy, 215 Curtis Hall, Columbia, Missouri, 65211-7020
6 - University of Illinois, Department of Crop Sciences, Maize Genetics Cooperation - Stock Center, Urbana, Illinois, 61801-4798
7 - Missouri Botanical Garden, PO Box 299, St. Louis, Missouri, 63166-0299, USA

Keywords:
bioinformatics
characters
comparative genomics
morphology.

Presentation Type: Paper
Session: 1-12
Location: Alpine A (Snowbird Center)
Date: Monday, August 2nd, 2004
Time: 11:15 AM
Abstract ID:347