The relational modeling of hierarchical data in biodiversity databases

The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures using R packages provided by inspected platforms. If neither of these was available, we used the public interface of individual databases. For almost half (12) of the databases analyzed, we did not find any formalized taxa hierarchy data structure, providing only biological information about taxon membership in higher ranks, which is not fully formalizable and thus not generally usable. The least effective Adjacency List model (storing parentId of a taxon) dominates among the remaining providers. This study demonstrates the lack of attention paid by current biodiversity databases to modeling taxon hierarchy, particularly to making it available to researchers in the form of a hierarchical data structure within the data provided. For biodiversity relational databases, the Closure Table type is the most suitable of the known data models, which also corresponds to the ontology concept. However, its use is rather sporadic within the biodiversity databases ecosystem.