The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant

Ilic, K., Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., Avraham, S., Reiser, L., Pujar, A., Sachs, M. M., Whitman, N. T., McCouch, S. R., Schaeffer, M. L., Ware, D. H., Stein, L. D., Rhee, S. Y. (February 2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology, 143 (2). pp. 587-599. ISSN 0032-0889

Abstract

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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > annotation
bioinformatics > genomics and proteomics > annotation > phylogenetic tree annotation
organism description > plant
CSHL Authors:
Communities: CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: CSHL Librarian
Date: February 2007
Date Deposited: 14 Nov 2011 19:10
Last Modified: 23 Feb 2017 19:26
PMCID: PMC1803752
Related URLs:
URI: https://repository.cshl.edu/id/eprint/23047

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