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<h2> The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant<a title="RFN1"></a><sup>1</sup><a title="RFN4"></a><sup>,[W]</sup><a title="RFN5"></a><sup>,[OA]</sup> </h2> <em><strong></strong>Katica Ilic<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Elizabeth A. Kellogg<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Pankaj Jaiswal<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Felipe Zapata<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Peter F. Stevens<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Leszek P. Vincent<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Shulamit Avraham<a title="RFN2"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN2">2</a></sup>, Leonore Reiser<a title="RFN3"></a><sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#FN3">3</a></sup>, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. McCouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein and Seung Y. Rhee<sup><a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#COR1">*</a></sup></em> <p> <em> Department of Plant Biology, Carnegie Institution, Stanford, California 94305 (K.I., L.R., N.T.W., S.Y.R.); Department of Biology, University of Missouri, St. Louis, Missouri 63121 (E.A.K.); Department of Plant Breeding, Cornell University, Ithaca, New York 14853 (P.J., A.P., S.R.M.); Missouri Botanical Garden, St. Louis, Missouri 63121 (F.Z., P.F.S.); Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (S.A., D.H.W., L.D.S.); University of Missouri, Columbia, Missouri 65211 (L.P.V., M.L.S.); Maize Genetics Cooperation, Stock Center, and Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801 (M.M.S.); and United States Department of Agriculture-Agricultural Research Service, Washington, DC 20250 (M.M.S., M.L.S., D.H.W.) </em> </p> <p> <em>An Open Access article from Plant Physiology 143:587-599 (2007).</em> </p> <p> </p> <h4> Abstract </h4> <p> Formal description of plant phenotypes and standardized annotation<sup></sup>of gene expression and protein localization data require uniform<sup></sup>terminology that accurately describes plant anatomy and morphology.<sup></sup>This facilitates cross species comparative studies and quantitative<sup></sup>comparison of phenotypes and expression patterns. A major drawback<sup></sup>is variable terminology that is used to describe plant anatomy<sup></sup>and morphology in publications and genomic databases for different<sup></sup>species. The same terms are sometimes applied to different plant<sup></sup>structures in different taxonomic groups. Conversely, similar<sup></sup>structures are named by their species-specific terms. To address<sup></sup>this problem, we created the Plant Structure Ontology (PSO),<sup></sup>the first generic ontological representation of anatomy and<sup></sup>morphology of a flowering plant. The PSO is intended for a broad<sup></sup>plant research community, including bench scientists, curators<sup></sup>in genomic databases, and bioinformaticians. The initial releases<sup></sup>of the PSO integrated existing ontologies for Arabidopsis (<em>Arabidopsis<sup></sup>thaliana</em>), maize (<em>Zea mays</em>), and rice (<em>Oryza sativa</em>); more recent<sup></sup>versions of the ontology encompass terms relevant to Fabaceae,<sup></sup>Solanaceae, additional cereal crops, and poplar (<em>Populus</em> spp.).<sup></sup>Databases such as The Arabidopsis Information Resource, Nottingham<sup></sup>Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics<sup></sup>Network are using the PSO to describe expression patterns of<sup></sup>genes and phenotypes of mutants and natural variants and are<sup></sup>regularly contributing new annotations to the Plant Ontology<sup></sup>database. The PSO is also used in specialized public databases,<sup></sup>such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over<sup></sup>10,000 gene annotations and phenotype descriptions from participating<sup></sup>databases can be queried and retrieved using the Plant Ontology<sup></sup>browser. The PSO, as well as contributed gene associations,<sup></sup>can be obtained at www.plantontology.org. </p> <p> <br> </p> <hr> <p> </p> <p> </p> <p> </p> <p> Angiosperms are one of the most diverse groups of plants that<sup></sup>vary greatly in morphology, size, habitat, and longevity. Agriculture<sup></sup>is almost entirely dependent on angiosperms. Besides providing<sup></sup>food and fiber, angiosperms are important sources for pharmaceuticals,<sup></sup>lumber, paper, and biofuel. Understanding the origins, mechanisms,<sup></sup>and functions of morphological diversity in flowering plants<sup></sup>is one of the fundamental questions in plant biology. Modern<sup></sup>approaches to studying plant development integrate classical<sup></sup>knowledge in plant anatomy and development with molecular genetics<sup></sup>and genomics tools. Among powerful tools, analyses of mutants<sup></sup>that affect developmental processes have shed new light on our<sup></sup>understanding of the complexity of plant development. More recently,<sup></sup>high-throughput, genome-wide phenomic screens in Arabidopsis<sup></sup>(<em>Arabidopsis thaliana</em>; for review, see Alonso and Ecker, 2006<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB1"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>),<sup></sup>and large-scale gene expression-profiling technologies (for<sup></sup>review, see Rensink and Buell, 2005<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB21"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>) generated a huge amount<sup></sup>of data in plant science. These tools and resources have the<sup></sup>potential to contribute to efforts to link genes with developmental<sup></sup>morphology (i.e. genotype with phenotype) and make an impact<sup></sup>on our understanding of functions of genes involved in plant<sup></sup>development. However, an accurate interpretation of the function<sup></sup>of genes that control various aspects of plant development must<sup></sup>be embedded in detailed knowledge of the anatomy and morphology<sup></sup>of a plant. Explicitly, the structural features of plant cells,<sup></sup>tissues, and organs need to be correctly understood and uniformly<sup></sup>described. Accurate and standardized nomenclature for plant<sup></sup>anatomy and morphology is also required for comparative purposes<sup></sup>(i.e. for comparisons of genes involved in plant development<sup></sup>among related or evolutionarily distant taxa). Semantic perplexity<sup></sup>presents a major obstacle for conducting such comparative studies<sup></sup>in plants; similar plant structures are described by their species-specific<sup></sup>terms. For example, in scientific publications, fruit is often<sup></sup>referred to as silique in Arabidopsis, grain or caryopsis in<sup></sup>rice (<em>Oryza sativa</em>), and kernel in maize (<em>Zea mays</em>). Conversely,<sup></sup>the inherent ambiguity of some plant anatomical terms led to<sup></sup>the same or similar terms being applied to different structures<sup></sup>(e.g. cork cell in the epidermis of grasses and cork cell in<sup></sup>the periderm in all other angiosperms).<sup></sup> </p> <p> Standard vocabulary for describing anatomy and developmental<sup></sup>stages was developed for several plant species at major plant<sup></sup>genomic databases, such as Arabidopsis at The Arabidopsis Information<sup></sup>Resource (TAIR; Berardini et al., 2004<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB4"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>), rice and other cereals<sup></sup>at Gramene (Yamazaki and Jaiswal, 2005<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB28"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>), and maize at MaizeGDB<sup></sup>(Vincent et al., 2003<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB27"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>). These vocabularies have been used to<sup></sup>describe gene expression data and mutant or natural variant<sup></sup>phenotypes in several plant databases. However, they were developed<sup></sup>independently of each other and were based on different principles<sup></sup>and rules. In addition, variation in nomenclature used for different<sup></sup>taxonomic groups in angiosperms presented obstacles for conducting<sup></sup>queries in more than one plant database and retrieving meaningful<sup></sup>results. For the purpose of comparative genomics, diverse terminology<sup></sup>needed to be organized into a standardized language that could<sup></sup>be shared among individual databases and used for accurate description<sup></sup>of phenotypes and gene expression data.<sup></sup> </p> To address these problems, the Plant Ontology Consortium (POC;<sup></sup>Jaiswal et al., 2005<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB16"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>) has developed a simple and extensible<sup></sup>controlled vocabulary that describes anatomy, morphology, and<sup></sup>growth and developmental stages of a generic flowering plant.<sup></sup>In addition, the POC has established a database through which<sup></sup>the data curated using this vocabulary can be accessed in a<sup></sup>one-stop manner. Here, we describe the first representation<sup></sup>of anatomy and morphology of a generic flowering plant, the<sup></sup>Plant Structure Ontology (PSO). This ontology represents the<sup></sup>morphological-anatomical aspect of the Plant Ontology (PO);<sup></sup>the temporal aspect and the Plant Growth and Developmental Stages<sup></sup>Ontology have been described elsewhere (Pujar et al., 2006<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&fulltext=open+access&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB20"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>).<sup></sup>We also discuss the guiding principles and rationale for the<sup></sup>development and maintenance of the PSO and its importance for<sup></sup>describing phenotypes and large-scale gene expression data in<sup></sup>reference plants and crop species.<br> <p> </p>
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