Plant Physiology Preview
Published on August 11, 2006; 10.1104/pp.106.085720
Received June 23, 2006
Accepted July 28, 2006
Whole Plant Growth Stage Ontology for Angiosperms and its Application in Plant Biology
Anuradha Pujar , Pankaj Jaiswal , Elizabeth A Kellogg , Katica Ilic , Leszek Vincent , Shulamit Avraham , Peter Stevens , Felipe Zapata , Leonore Reiser , Seung Y Rhee , Martin M. Sachs , Mary Schaeffer , Lincoln Stein , Doreen Ware , and Susan McCouch *
Department of Department of Plant Breeding, 240 Emerson Hall, Cornell University, Ithaca, NY, 14853, USA
Department of Biology, University of Missouri at St. Louis, St. Louis MO 63121, USA
Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA
Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
Department of Biology, University of Missouri at St. Louis, St. Louis MO 63121, USA; Missouri Botanical Garden, 4344-Shaw Boulevard, St. Louis, MO 63110
Maize Genetics Cooperation - Stock Center, Department of Crop Sciences - University of Illinois, Urbana, IL 61801, USA; Agricultural Research Service, United States Department of Agriculture, USA
Division of Plant Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA; Agricultural Research Service, United States Department of Agriculture, USA
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Agricultural Research Service, United States Department of Agriculture, USA
* Corresponding author; email: srm4{at}cornell.edu.
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 lifecycle. 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 (POC) (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 paper, we describe the development of a generic whole-plant growth stage ontology that describes the spatio-temporal 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 POC used the PO growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The Arabidopsis Information Resource (TAIR), Gramene database and MaizeGDB.
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