Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Applications Of Plant Ontologies For Describing And Comparing Phenotypes And Gene Expression In Angiosperms

Katica Ilic¹ , Shulamit Avraham⁴ , Anuradha Pujar⁵ , Leonore Reiser¹ , Marty Sachs⁷ , Peter Stevens² , Leszek Vincent⁶ , Felipe Zapata² , Pankaj Jaiswal⁵ , Elizabeth Kellogg³ , Susan McCouch⁵ , Seung Rhee¹ , Mary Schaeffer⁶ , Doreen Ware⁴ , Lincoln Stein⁴

¹  Carnegie Institution of Washington, Department of Plant Biology, 260 Panama St, Stanford, CA, 94305

²  Missouri Botanical Garden, University of Missouri - St. Louis, St. Louis, MO, 63121

³  Department of Biology, University of Missouri - St Louis, 8001 Natural Bridge Rd, Saint Louis, MO, 63121

⁴  Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724

⁵  Department of Plant Breeding, Cornell University, Ithaca, NY, 14853

⁶  University of Missouri - Columbia, Columbia, MO, 65211

⁷  Maize Genetics Cooperation - Stock Center, USDA-ARS & Department of Crop Sciences, University of Illinois, Urbana, IL, 61801

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort of several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop generic controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. Consistent use of these ontologies would reduce the problem of heterogeneity of terminology used to describe comparable object types in plant databases - an obvious obstacle for conducting queries for multiple species across databases such as Gramene, TAIR, Maize GDB and others. The initial releases of the Plant Structure Ontology (July 2004) and Plant Growth and Developmental Stages Ontology (July 2005) included integration of existing ontologies for Arabidopsis, maize and rice, thus spanning the eudicot/monocot divide. Currently, we are expanding PO to encompass legumes, Solanaceae and other plant families.
As a part of ongoing functional annotation efforts, participating databases (TAIR, Gramene and MaizeGDB) have been actively using Plant Ontologies to annotate gene expression data, describe mutant phenotypes and biological samples. So far, over 4,000 gene annotations have been contributed to the POC database. These annotations can be queried using our ontology browser, the Plant Ontology AmiGO. We will present a summary of the organizing principles and rules followed in developing Plant Ontologies. Standards and methods for using Plant Ontologies to annotate gene expression patterns and mutant phenotypes will be addressed with examples from member databases, demonstrating how the PO supports gene discovery, phenotype prediction, and gene product functions, while also accessing mutant stocks and germplasm.