Proliferation of Terms
A major concern for the PSO is the proliferation of terms. Thenumber of terms needs to be large enough for precise annotationof genes and phenotypes, but small enough for curators and endusers to navigate the ontology easily. The terminology for describingplants is rich and complex and is often species or family specific.Available visualization and editing software portrays the ontologiesas strictly hierarchical, whereas plant structure is not. Rather,it is modular in nature, with a relatively small number of tissueand cell types recurring, often with slight modification, indifferent organ systems at different times during development.Converting a modular structure to a formal hierarchy requiresextensive redundancy in the ontology. For example, a flowermight be a part of a cyme, a raceme, or any other inflorescencetypes. To maintain the appropriate upward flow of informationthrough the hierarchy, we would need to create a term specifyinga distinct type of flower within each inflorescence type. Thus,we faced the possibility of creating the terms flower of cyme,flower of raceme, flower of panicle, etc., followed by stamenof flower of cyme, gynoecium of flower of cyme, etc. With inflorescenceand fruit types, we solved the problem by placing all of thedifferent inflorescence and fruit types as synonyms of inflorescenceand fruit, respectively. This effectively removed one hierarchicallevel from the ontology at these positions (Supplemental Fig.S3).
Synonymy was not appropriate to account for staminate and pistillateinflorescences of Zea, which are physically separate and morphologicallydistinct (monoecious) from each other. The two types of inflorescenceoften have different phenotypes in single-gene mutants and identicalgenes are often deployed differently in each. Maize geneticiststhus often want to be able to distinguish these two. Therefore,the maize ear and tassel are the only two inflorescence typesthat are treated as a type of inflorescence.
The solution by synonymy does not fully eliminate the problemswith proliferation of terms. Users of the ontology will findextensive residual redundancy in some areas. Ultimately, newvisualization and ontology editing software and a differentapproach to creating ontologies will be needed to reflect themodularity of biological reality more precisely and intuitively.
Homology Assessment and Taxon-Specific Forms
The PSO is designed to be a practical tool for annotating genesand germplasms and to be, as far as possible, neutral on questionsof homology. Thus, for example, the terms cotyledon and scutellumare not treated as synonyms, even though there is a body ofthought that suggests that they might be derived from the samesort of ancestral structure. As our knowledge of plant structurecontinues to develop, however, some of these terms may be merged.
More problematic, but also perhaps more interesting, are structures
that are unique to particular clades of plants. These are currently
accommodated by the sensu designation, but as major groups are
added, the number of such terms is likely to increase. For example,
stipules are considered to have arisen independently in multiple
lineages and they may prove to be developmentally and genetically
distinct. If true, in addition to a common term stipule
the PO could be faced with multiple terms such as stipule sensu
Rubiaceae, stipule sensu Fabaceae, stipule sensu Brassicaceae,
etc. Handling a phylogenetic relationship is beyond the scope
of the PSO currently, but it is an important topic to address
in the long run. As more genes are annotated from more species,
the PSO may help to discover whether similar structures that
have evolved independently are produced by very distinct underlying