Submit a Revision

*your email :**
page name* : such as "Introduction", "Conclusion"..etc
An ontology is a concise and unambiguous description of relevant<sup></sup>entities and their explicit relations to each other (Schulze-Kremer,<sup></sup>2002<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB22"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>). Entities (terms) are linked by specific relationships,<sup></sup>with paths from more specific to more general terms upward in<sup></sup>the ontology tree. Thus, the information from one hierarchical<sup></sup>level can be propagated up to the next level, allowing users<sup></sup>to make inferences and to perform queries at different levels.<sup></sup>Each term in the ontology has a textual definition, an accession<sup></sup>number (identifier or ontology ID), and a specific relationship<sup></sup>to at least one parental term (Bard and Rhee, 2004<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB2"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>). The unique<sup></sup>identifier and relationships in the ontology are interpretable<sup></sup>by a computer, which makes possible computational processing<sup></sup>and retrieval of information associated with each term. For<sup></sup>example, lists of genes annotated to the terms in an ontology<sup></sup>can be compared and terms that are overrepresented in one list<sup></sup>over another can be determined using statistical tests. This<sup></sup>underscores their main appeal in the field of biology and, to<sup></sup>a large extent, explains the recent increase in the number of<sup></sup>bioontologies (Blake, 2004<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB5"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>).<sup></sup><p> The best known bioontology, the Gene Ontology (GO), was the<sup></sup>first to offer a practical solution for describing gene products<sup></sup>in a human- and computer-comprehensible manner spanning diverse<sup></sup>taxonomic groups (Gene Ontology Consortium, 2006<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB12"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>; <a href="http://www.geneontology.org/">http://www.geneontology.org</a>).<sup></sup>The GO consists of three mutually independent ontologies; each<sup></sup>describes cellular components, biological processes, or molecular<sup></sup>functions that occur in organisms. Over the years, the GO has<sup></sup>become a standard for describing functional aspects of gene<sup></sup>products in a consistent way in various genomic databases. Following<sup></sup>the GO paradigm and embracing the idea of generic, standardized<sup></sup>terminology that can be used across diverse taxonomic groups,<sup></sup>the POC has largely adopted the ontology design model and rules<sup></sup>established by the GO consortium. However, the PSO is conceptually<sup></sup>different and is governed independently from the GO. Some important<sup></sup>differences between the PO and GO are discussed in more detail<sup></sup>below.<sup></sup></p> <p> The PSO is the first multispecies ontology of plant anatomy<sup></sup>and morphology. Its main purpose is to provide a standardized<sup></sup>set of terms describing plant structures—a tool for annotation<sup></sup>of gene expression patterns and phenotypes of germplasms across<sup></sup>angiosperms. Hence, this vocabulary is intended for a broad<sup></sup>plant research community, including curators in genomic databases,<sup></sup>bioinformaticians, and bench scientists. The PSO initially integrated<sup></sup>existing species-specific ontologies for Arabidopsis, maize,<sup></sup>and rice; however, it is not intended only for a few model plant<sup></sup>organisms. Rather, we envision it as a continuously expanding<sup></sup>ontology that will gradually encompass crop species and woody<sup></sup>species. Recently, the ontology has been expanded to include<sup></sup>terms for Fabaceae, Solanaceae, additional cereal crops (wheat<sup></sup>[<em>Triticum aestivum</em>], oat [<em>Avena sativa</em>], barley [<em>Hordeum vulgare</em>]),<sup></sup>and poplar (<em>Populus</em> spp.), a model plant organism for woody<sup></sup>species.<sup></sup></p> <p> A common set of criteria was established to ensure that the<sup></sup>PSO would be biologically accurate and adequately meet practical<sup></sup>requirements for annotation. Analysis of the three original<sup></sup>species-specific plant ontologies—predecessors of the<sup></sup>PSO—greatly influenced our decisions on the rationale<sup></sup>and design for the PSO. Foremost, we defined the scope of this<sup></sup>ontology to be limited to anatomical and morphological structures<sup></sup>pertinent to flowering plants during their normal course of<sup></sup>development. Botanical terms, from the cellular to the whole<sup></sup>organism level, are entities (i.e. terms [in italics in this<sup></sup>article]) in the PSO. Besides this main criterion for creating<sup></sup>a term, in some cases (following annotation requirements), we<sup></sup>have considered derivation (i.e. origin of plant parts and cell<sup></sup>lineages, as well as spatial/positional organization of tissues,<sup></sup>organs, and organ systems of a flowering plant (e.g. <em>leaf abaxial<sup></sup>epidermis</em> and <em>leaf adaxial epidermis</em>).<sup></sup></p> <p> We established general rules for deciding when not to add terms<sup></sup>to the ontology. To a great extent, qualifiers (or attributes)<sup></sup>of the terms are avoided, and the ontology makes only very limited<sup></sup>use of attributes. Thus, the term <em>corolla</em> is included, but the<sup></sup>terms "sympetalous corolla" and "apopetalous corolla" are not.<sup></sup>Attributes that are specific for describing mutant plants (e.g.<sup></sup>wrinkled seed) are also excluded. Because it does not include<sup></sup>attributes, the PSO is insufficient as, nor is it intended to<sup></sup>be, a taxonomic vocabulary on its own and does not address phylogeny<sup></sup>of angiosperms. Moreover, the most granular terminology in the<sup></sup>PSO is at the cell-type level. Therefore, terms for subcellular<sup></sup>compartments are not included in the PSO. These terms are handled<sup></sup>by the GO Cellular Component ontology. In addition, temporal<sup></sup>landmarks (i.e. morphological and anatomical changes that occur<sup></sup>via developmental progression of organs and organ systems) are<sup></sup>excluded from the PSO; this aspect is a part of the Plant Growth<sup></sup>and Developmental Stages Ontology (Pujar et al., 2006<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&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>). Nonetheless,<sup></sup>some temporal aspects are indirectly present in the PSO. Unlike<sup></sup>in animal systems, most plant organs are developed in the postembryonic<sup></sup>phase of the life cycle. Many plant structures develop continually,<sup></sup>whereas others exist only temporarily; that is, at a particular<sup></sup>time during the life cycle. Structures that exist even in a<sup></sup>very short period of time, such as a leaf primordium, are included<sup></sup>as terms in the PSO. For example, terms such as <em>apical hook</em><sup></sup>(defined as a hook-like structure that develops at the apical<sup></sup>part of the hypocotyl in dark-grown seedlings in dicots) and<sup></sup><em>leaf primordium</em> (defined as an organized group of cells that<sup></sup>will differentiate into a leaf that emerges as an outgrowth<sup></sup>in the shoot apex) exist in the PSO. A leaf primordium is merely<sup></sup>the first visible appearance of a leaf and, therefore, both<sup></sup>terms, <em>leaf</em> and <em>leaf primordium</em>, describe the same entity (leaf)<sup></sup>at different time points in development. There are genes that<sup></sup>are expressed in organ primordia, such as <em>JAGGED</em> and <em>FILAMENTOUS<sup></sup>FLOWER</em> genes in Arabidopsis (both expressed in leaf, sepal,<sup></sup>petal, stamen, and carpel primordia) with expression levels<sup></sup>declining in the developing or adult organs (Dinneny et al.,<sup></sup>2004<a href="http://www.plantphysiol.org/cgi/content/full/143/2/587?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&andorexactfulltext=and&searchid=1&FIRSTINDEX=0&sortspec=relevance&volume=143&firstpage=587&resourcetype=HWCIT#BIB9"><img src="http://www.plantphysiol.org/icons/fig-down.gif" alt="Go"></a>). To accurately annotate expression patterns of such genes,<sup></sup>we created separate terms for each primordium structure. Currently,<sup></sup>the PSO has 11 such terms.<sup></sup></p> To integrate terms from different species, we extensively used<sup></sup>synonymy wherever feasible. This allows users to search existing<sup></sup>plant databases using either a generic term or its taxon-specific<sup></sup>synonyms. For example, <em>silique</em>, <em>caryopsis</em>, and <em>kernel</em> are listed<sup></sup>as synonyms of the term <em>fruit</em>. Therefore, a search for <em>fruit</em><sup></sup>in the PO database would retrieve all genes expressed in the<sup></sup>silique of Arabidopsis, caryopsis of rice, and kernel of maize.<sup></sup>In reality, silique, caryopsis, and kernel are types (classes)<sup></sup>of fruit, rather than strict synonyms. However, for the purpose<sup></sup>of this ontology, specific types of a few high-level terms (e.g.<sup></sup><em>fruit</em>, <em>inflorescence</em>, and <em>stem</em>) are included only as synonyms.<sup></sup>Thus, we intentionally overlooked an enormous morphological<sup></sup>diversity of flowering plants in favor of cross species comparisons,<sup></sup>generic searches, and intuitive ontology browsing. Therefore,<sup></sup>synonyms in the PSO can be taxon-specific morphological forms<sup></sup>of a generic structure. Also, an entity in the PSO can either<sup></sup>be a term or a synonym, but not both. In a few cases where synonymy<sup></sup>was not a suitable option, we created new terms as specific<sup></sup>classes. Typical examples are the terms <em>tassel</em> and <em>ear</em>, staminate<sup></sup>and pistilate inflorescences specific to the genus Zea, respectively.<sup></sup>In addition to the synonyms described above, the PSO contains<sup></sup>a number of terms that have authentic (exact) synonyms. Examples<sup></sup>include the terms <em>male gametophyte</em> (synonym: <em>pollen grain</em>),<sup></sup><em>female gametophyte</em> (synonym: <em>embryo sac</em>), or <em>perisperm</em> (synonym:<sup></sup><em>seed nucellus</em>). Extensive use of synonymy in the PSO resulted<sup></sup>in reduced granularity (i.e. the degree of detail in the ontology)<sup></sup>and emphasized generic aspects of the ontology. As a rule, a<sup></sup>high level of granularity was limited in the PSO because we<sup></sup>strove to keep the ontology relatively simple, yet sufficiently<sup></sup>broad and generic to encompass a number of flowering plants.
Confirmation code: Enter the code exactly as it appears. All letters are case insensitive, there is no zero.