I claim no originality for this, it's very close to how uBio models classification concepts:
The trick here is going to be ensuring that I can do sensible queries, such as linking a node in a classification to alternative names.
The other entity that I need to think carefully about are OTUs (Operational Taxonomic Units). By OTUs I mean the taxa that appear in phylogenetic trees. In the TbMap project I mapped TreeBASE taxa to names in external databases, but noted that TreeBASE taxa are better thought of as OTUs:
...many taxon names in TreeBASE are best though of as Operational Taxonomy Units (OTUs) rather than taxonomic names. They identify a set of observations for a particular specimen, set of specimens, or a taxon. For instance, "Eleutherodactylus crassidigitus FMNH257676 Panama" (TaxonID T51971) refers to a 1200 base pair stretch of mitochondrial DNA (AY273113) obtained from Field Museum Natural History specimen FMNH 257676, which has been identified as Eleutherodactylus crassidigitus. [see doi:10.1186/1471-2105-8-158.
Taxa in phylogenetic trees may be single sequences, multiple sequences (from one or more specimens), or aggregates of information from multiple taxa. The challenge is to model these in the simplest way that reflects this, but also makes queries feasible. What I'm aiming for is for the user to click on a node in a phylogeny, and be taken to a page that best corresponds to the entity in the tree, but at the same time enable queries that will list all phylogenies that contain a given taxon.