02941nas a2200397   4500000000100000000000100001008004100002260001300043653001600056653003800072653001900110653002100129653002500150653002800175100001600203700002200219700001900241700001800260700001800278700001900296700002100315700001900336700001900355700001700374700001700391700001800408700001900426700001600445700001800461700001500479245010300494300001100597490000800608520191300616022001402529       2007                            d  c2007 Feb10aAngiosperms10aGene Expression Regulation, Plant10aPlant Proteins10aPlant Structures10aTerminology as Topic10aUser-Computer Interface1 aKatica Ilic1 aElizabeth Kellogg1 aPankaj Jaiswal1 aFelipe Zapata1 aPeter Stevens1 aLeszek Vincent1 aShulamit Avraham1 aLeonore Reiser1 aAnuradha Pujar1 aMartin Sachs1 aNoah Whitman1 aSusan McCouch1 aMary Schaeffer1 aDoreen Ware1 aLincoln Stein1 aSeung Rhee00aThe plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.  a587-990 v1433 aFormal 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.  a0032-0889