Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

The Plant Ontology Database: A Community Resource For Plant Structure And Developmental Stages Controlled Vocabulary And Annotations

Chih-Wei Tung¹ , Pankaj Jaiswal¹ , Shulamit Avraham² , Katica Ilic³ , Elizabeth Kellogg ⁴ , Susan McCouch¹ , Anuradha Pujar¹ , Leonore Reiser⁵ , Seung Y Rhee³ , Martin M Sachs^6,7 , Mary Schaeffer^7,8 , Lincoln Stein² , Peter Stevens^4,9 , Leszek Vincent⁸ , Felipe Zapata^4,9 , Doreen Ware ²

¹  Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA

²  Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA

³  Department of Plant Biology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA

⁴  Department of Biology, University of Missouri at St. Louis, St. Louis MO 63121, USA

⁵  Molecular Sciences Institute, 2168 Shattuck Ave., Berkeley, CA 94704, USA

⁶  Maize Genetics Cooperation, Stock Center, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA

⁷  Agricultural Research Service, United States Department of Agriculture-Agricultural Research Service, Washington, DC 20250, USA.

⁸  Curtis Hall, University of Missouri at Columbia, Columbia, MO 65211, USA

⁹  Missouri Botanical Garden, 4344-Shaw Boulevard, St. Louis, MO 63110, USA

The Plant Ontology Consortium (POC) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons.
The Plant Ontology (PO) was initially developed based on the ontologies for the plant model species, Arabidopsis, rice and maize, developed by TAIR, Gramene, and MaizeGDB, respectively. Terms are continuously added as needed to describe other angiosperms such as Triticeae (wheat, oat and barley), Solanaceae (tomato, potato and peppers), Fabaceae (soybean and Medicago), Rutaceae (citrus), Asteraceae/Compositae (sunflower and lettuce) and Salicaceae (poplar, a tree species), to enable comparative plant genomics research. The PO is included in the open-source Open Biomedical Ontologies (OBO) project, a resource for sharing controlled vocabularies for different biological domains.
Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser for viewing, searching and querying.
The Consortium has implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current.