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BIOINFORMATICS

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology^1,[OA]

Department of Plant Breeding, Cornell University, Ithaca, New York 14853 (A.P., P.J., S.M.); Department of Biology, University of Missouri, St. Louis, Missouri 63121 (E.A.K., P.S., F.Z.); Department of Plant Biology, Carnegie Institution, Stanford, California 94305 (K.I., L.R., S.Y.R.); Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211 (L.V., M.S.); Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (S.A., L.S., D.W.); Missouri Botanical Garden, St. Louis, Missouri 63110 (P.S., F.Z.); Maize Genetics Cooperation-Stock Center, Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801 (M.M.S.); and Agricultural Research Service, United States Department of Agriculture, Washington, DC 20250 (M.M.S., M.S., D.W.)

Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and development. Each species or family specific community developed distinct terminologies for describing whole-plant growth stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org) was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the development of a generic whole-plant growth stage ontology that describes the spatiotemporal stages of plant growth as a set of landmark events that progress 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 Plant Ontology Consortium used the plant ontology growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resource, Gramene database, and MaizeGDB.

² These authors contributed equally to the paper.

³ Present address: Molecular Sciences Institute, 2168 Shattuck Ave., Berkeley, CA 94704.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Susan McCouch (srm4@cornell.edu).

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.106.085720

^* Corresponding author; e-mail srm4{at}cornell.edu; fax 1–607–255–6683.

Received June 23, 2006; accepted July 28, 2006; published August 25, 2006.

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