Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Controlled Vocabularies For Describing And Comparing Phenotypes And Gene Expression In Angiosperms

Pankaj Jaiswal¹ , Katica Ilic² , Leonore Reiser² , Felipe Zapata³ , Leszek Vincent⁵ , Anuradha Pujar¹ , Peter Stevens⁴ , Elizabeth Kellogg³ , Mary Polacco⁵ , Shulamit Avraham⁷ , Seung Y. Rhee² , Marty Sachs⁶ , Doreen Ware⁷ , Susan R. McCouch¹ , Lincoln Stein⁷

¹  Department of Plant Breeding, Cornell University, Ithaca, NY, 14853

²  Carnegie Institution of Washington, Department of Plant Biology, 260 Panama St, Stanford, CA, 94305

³  Dept of Biology, Univ of Missouri - St Louis, 8001 Natural Bridge Rd, Saint Louis, MO, 63121

⁴  Missouri Botanical Garden, University of Missouri-St. Louis, St. Louis, MO, 63121

⁵  University of Missouri-Columbia, Columbia, MO, 65211

⁶  Maize Genetics Cooperation - Stock Center, USDA-ARS & Department of Crop Sciences,University of Illinois, Urbana, IL, 61801

⁷  Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724

The number and complexity of plant genomic databases has dramatically increased, providing an array of resources for plant comparative genomics. However, among these databases, each uses a variable terminology to describe plant structure and development. In order to permit cross-species comparisons and effectively take advantage of these databases, there is a need for a uniform set of descriptors. In response to this need, the Plant Ontology Consortium (POC) (www.plantontology.org) was formed. The POC is a collaboration among plant databases and experts in plant systematics, botany and genomics. The goal of the POC is to develop a common set of controlled vocabularies to describe anatomical and developmental stages described for both experimentally and agronomically important flowering plant species.. Our first task was to integrate existing species-specific vocabulary terms into unified flowering-plants ontologies, providing a semantic framework for meaningful cross-species queries across databases such as Gramene, TAIR, MaizeGDB and others. The first version of the plant structure ontology and developmental stage ontologies incorporates terms for cereals and Arabidopsis representing monocots and dicot respectively. The organizing principles and rules followed in developing the plant ontology will be summarized, along with our plans to extend these controlled vocabularies to encompass legumes, Solanaceae and other plant species. The project is supported by National Science Foundation grant No. 0321666 to the Plant Ontology Consortium.