Plant & Animal Genomes XIII Conference

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

Using The Plant Ontologies: Searching/Browsing Terms And Annotations And Methods For Annotation Of Gene Expression And Phenotypes

Leonore Reiser¹ , Katica Ilic¹ , Pankaj Jaiswal³ , Elizabeth Kellogg⁵ , Mary Polacco⁶ , Anuradha Pujar³ , Seung Yon Rhee¹ , Marty Sachs⁴ , Lincoln Stein² , Peter Stevens⁵ , Leszek Vincent⁶ , Doreen Ware² , Felipe Zapata⁵

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

²  Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor,NY ,11724-2212, USA

³  Department of Plant Breeding,Cornell University, Ithaca, NY,14853, USA,

⁴  Maize Genetics Cooperation - Stock Center, USDA-ARS & Department of Crop Sciences,University of Illinois, Urbana, IL, 61801

⁵  Department of Biology, University of Missouri-St. Louis, 8001 Natural Bridge Rd, St.Louis, MO,63121, USA

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

A primary goal of the Plant Ontology Consortium (www.plantontology.org) is to develop simple, yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. Biologists can then use these controlled vocabularies to describe plant phenotypes and gene expression by making associations/annotations to genes that are supported by experimental evidence. The first part of the tutorial will focus on tools to search and browse the plant ontologies and annotations. Using the modified AmiGO ontology browser and the PO database, we will demonstrate how to visualize the ontology structure, find terms and genes/germplasms associated to these terms. Participants will learn how to perform simple queries of annotations in the PO database to find similarly expressed genes and mutants with similar phenotypes in different organisms. We will show how corresponding data from member database for can be utilized for gene discovery, predicting phenotypes and determining functions of gene products. For the PO annotations to be maximally useful for comparative genomics it is important that the ontologies be consistently applied for annotation of genes and germplasms. The second half of the tutorial will address standards and methods for annotation of gene expression and phenotypes using the Plant Ontologies. Using specific examples from the literature, participants will annotate plant phenotypes and gene expression using two different software; PubSearch (www.gmod.org/pubsearch.shtml) and Gramene’s curation tool. Finally, we will discuss strategies and future plans to integrate annotations and terms from other plant species.