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<strong>Proliferation of Terms</strong> <p> A major concern for the PSO is the proliferation of terms. The<sup></sup>number of terms needs to be large enough for precise annotation<sup></sup>of genes and phenotypes, but small enough for curators and end<sup></sup>users to navigate the ontology easily. The terminology for describing<sup></sup>plants is rich and complex and is often species or family specific.<sup></sup>Available visualization and editing software portrays the ontologies<sup></sup>as strictly hierarchical, whereas plant structure is not. Rather,<sup></sup>it is modular in nature, with a relatively small number of tissue<sup></sup>and cell types recurring, often with slight modification, in<sup></sup>different organ systems at different times during development.<sup></sup>Converting a modular structure to a formal hierarchy requires<sup></sup>extensive redundancy in the ontology. For example, a flower<sup></sup>might be a part of a cyme, a raceme, or any other inflorescence<sup></sup>types. To maintain the appropriate upward flow of information<sup></sup>through the hierarchy, we would need to create a term specifying<sup></sup>a distinct type of flower within each inflorescence type. Thus,<sup></sup>we faced the possibility of creating the terms flower of cyme,<sup></sup>flower of raceme, flower of panicle, etc., followed by stamen<sup></sup>of flower of cyme, gynoecium of flower of cyme, etc. With inflorescence<sup></sup>and fruit types, we solved the problem by placing all of the<sup></sup>different inflorescence and fruit types as synonyms of <em>inflorescence</em><sup></sup>and <em>fruit</em>, respectively. This effectively removed one hierarchical<sup></sup>level from the ontology at these positions (Supplemental Fig.<sup></sup>S3).<sup></sup></p> <p> Synonymy was not appropriate to account for staminate and pistillate<sup></sup>inflorescences of Zea, which are physically separate and morphologically<sup></sup>distinct (monoecious) from each other. The two types of inflorescence<sup></sup>often have different phenotypes in single-gene mutants and identical<sup></sup>genes are often deployed differently in each. Maize geneticists<sup></sup>thus often want to be able to distinguish these two. Therefore,<sup></sup>the maize ear and tassel are the only two inflorescence types<sup></sup>that are treated as a type of <em>inflorescence</em>.<sup></sup></p> <p> The solution by synonymy does not fully eliminate the problems<sup></sup>with proliferation of terms. Users of the ontology will find<sup></sup>extensive residual redundancy in some areas. Ultimately, new<sup></sup>visualization and ontology editing software and a different<sup></sup>approach to creating ontologies will be needed to reflect the<sup></sup>modularity of biological reality more precisely and intuitively.<sup></sup></p> <p> <br><strong>Homology Assessment and Taxon-Specific Forms</strong> </p> <p> The PSO is designed to be a practical tool for annotating genes<sup></sup>and germplasms and to be, as far as possible, neutral on questions<sup></sup>of homology. Thus, for example, the terms <em>cotyledon</em> and <em>scutellum</em><sup></sup>are not treated as synonyms, even though there is a body of<sup></sup>thought that suggests that they might be derived from the same<sup></sup>sort of ancestral structure. As our knowledge of plant structure<sup></sup>continues to develop, however, some of these terms may be merged.<sup></sup></p> More problematic, but also perhaps more interesting, are structures<sup></sup>that are unique to particular clades of plants. These are currently<sup></sup>accommodated by the sensu designation, but as major groups are<sup></sup>added, the number of such terms is likely to increase. For example,<sup></sup>stipules are considered to have arisen independently in multiple<sup></sup>lineages and they may prove to be developmentally and genetically<sup></sup>distinct. If true, in addition to a common term <em>stipule</em> (PO:0020041),<sup></sup>the PO could be faced with multiple terms such as stipule sensu<sup></sup>Rubiaceae, stipule sensu Fabaceae, stipule sensu Brassicaceae,<sup></sup>etc. Handling a phylogenetic relationship is beyond the scope<sup></sup>of the PSO currently, but it is an important topic to address<sup></sup>in the long run. As more genes are annotated from more species,<sup></sup>the PSO may help to discover whether similar structures that<sup></sup>have evolved independently are produced by very distinct underlying<sup></sup>genetic mechanisms.
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