Plant Physiology Preview
Published on December 1, 2006; 10.1104/pp.106.092825
OPEN ACCESS ARTICLE
Received November 8, 2006
Accepted November 26, 2006
Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant
Katica Ilic , Elizabeth A. Kellogg , Pankaj Jaiswal , Felipe Zapata , Peter F. Stevens , Leszek P. Vincent , Shulamit Avraham , Leonore Reiser , Anuradha Pujar , Martin M. Sachs , Noah T. Whitman , Susan R. McCouch , Mary L. Schaeffer , Doreen H. Ware , Lincoln D. Stein , and Seung Y. Rhee *
Carnegie Institution, Department of Plant Biology, Stanford, California, 94305
Department of Biology, University of Missouri - St Louis, St Louis, Missouri, 63121
Department of Plant Breeding, Cornell University, Ithaca, New York, 14853
Missouri Botanical Garden, St. Louis, MO, 63121
University of Missouri - Columbia, Columbia, Missouri, 65211
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724
Maize Genetics Cooperation - Stock Center & Department of Crop Sciences, University of Illinois, Urbana, Illinois, 61801; USDA-ARS
University of Missouri - Columbia, Columbia, Missouri, 65211; USDA-ARS
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 11724; USDA-ARS
* Corresponding author; email: rhee{at}acoma.stanford.edu.
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that would accurately describe plant anatomy and morphology. This will facilitate 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. 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. PSO is intended for a broad plant research community including bench scientists, curators in genomic databases and bioinformaticians. The initial releases of PSO integrated existing ontologies for Arabidopsis, maize and rice; more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and Populus (poplar). Databases such as TAIR, NASC, Gramene, MaizeGDB and SGN are using Plant Structure Ontology to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology (PO) database. 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. PSO as well as contributed gene associations can be obtained at www.plantontology.org.
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