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BIOINFORMATICS

The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant^1,[W],[OA]

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

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated existing ontologies for Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa); more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and poplar (Populus spp.). Databases such as The Arabidopsis Information Resource, Nottingham Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics Network are using the PSO to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database. The PSO is also used in specialized public databases, such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over 10,000 gene annotations and phenotype descriptions from participating databases can be queried and retrieved using the Plant Ontology browser. The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org.

² These authors contributed equally to the development of the Plant Structure Ontology.

³ Present address: Molecular Sciences Institute, 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: Seung Y. Rhee (rhee{at}acoma.stanford.edu).

^[W] The online version of this article contains Web-only data.

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

www.plantphysiol.org/cgi/doi/10.1104/pp.106.092825

^* Corresponding author; e-mail rhee{at}acoma.stanford.edu; fax 650–325–6857.

Received November 8, 2006; accepted November 26, 2006; published December 1, 2006.

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