Submitted to: Plant Physiology
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/21/2007
Publication Date: 6/11/2007
Citation: Ilic, K., Kellogg, E., Jaiswal, P., Zapata, F., Stevens, P., Vincent, L., Avraham, S., Reiser, L., Pujar, A., Sachs, M.M., Whitman, N., Mccouch, S., Schaeffer, M.L., Ware, D., Stein, L., Rhee, S. 2007. Plant Structure Ontology, Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology. 143:587-599. Interpretive Summary: This manuscript describes the development and use of the Plant Structure Ontology (PSO). The PSO is a set of terms that describe plant anatomy and morphology. The terms were developed as a collaborative effort between several groups that represent model and agronomically important crop species. The terms are intended to provide a set of descriptors that can be used across different plant taxa; to describe data sets such as the tissues used in a microarray experiment or for the generation of a complementary DNA (cDNA) library for expressed sequence tagging (ESTs). The use of a common vocabulary will facilitate comparing and combining data sets, within species or between species ability in a meaningful way. At this time several Plant databases are using the Plant Structure Ontology to describe expression patterns of genes and phenotypes of mutants and natural variants. In addition to using the information at their own site they also regularly contributing new annotations to the Plant Ontology (PO) database. Over 10,000 associations to gene annotations and phenotype are currently available at the PO website. The association data sets as well as the PSO can be queried and retrieved using the Plant Ontology browser at www.plantontology.org.
Technical Abstract: 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.