Plant & Animal Genomes XIV Conference

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

Development Of A Generic Plant Growth Stage Ontology And Its Application For Comparative And Functional Genomics.

Anuradha Pujar¹ , Shulamit Avraham² , Katica Ilic³ , Pankaj Jaiswal¹ , Elizabeth Kellog⁴ , Susan McCouch¹ , Leonore Reiser³ , Sueng Rhee³ , Martin Sachs^5,6 , Mary Schaeffer^6,7 , Lincoln Stein² , Peter Stevens^4,8 , Leszek Vincent⁷ , Doreen Ware² , Felipe Zapata^4,8

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

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

³  Carnegie Institution of Washington, Stanford, CA 94305, USA

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

⁵  Maize Genetics Cooperation - Stock Center, Department of Crop Sciences - University of Illinois, Urbana, IL 61801, USA

⁶  Agricultural Research Service, United States Department of Agriculture, USA

⁷  Curtis Hall University of Missouri-Columbia, Columbia, MO 65211, USA

⁸  Missouri Botanical Garden, 4344-Shaw Boulevard, St. Louis, MO 63110

Diverse plant species have distinct terminologies associated with their growth stage vocabularies and this semantic heterogeneity has made it impossible to make meaningful computational comparisons across species or databases. Yet there are specific problems in plant science such as nitrogen fixation in legumes, inflorescence architecture in grasses, fruit formation in tomato and others that need to be studied in specific plants rather than in any one particular model species. The Plant Ontology Consortium (POC) www.plantontology.org has developed an ontology to specify growth and developmental stages of a generic flowering plant. The whole-plant growth stage ontology describes the spatial-temporal stages of plant growth arranged as progressive landmark events from germination to senescence. This ontology represents a synthesis and integration of terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic information. It provides a common platform for annotating gene function and gene expression in relation to the developmental trajectory of a plant described at the organismal level. As proof of concept the POC has used the emerging growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resources, Gramene Database and MaizeGDB. We will discuss the role of the plant research community in developing, evaluating and expanding this ontology to become a community standard and we will demonstrate its utility for comparative genomics using curated examples from POC member databases and literature.