Biological Taxonomy and Ontology Development: Scope and Limitations

 The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. Traditionally ontological representations of taxonomy have adopted the model of a single and static hierarchy. This model is contrasted with a more realistic situation involving dynamic revisions of particular groups and alignments among alternative taxonomic perspectives. Taxonomic practice is bound by a range of epistemological constraints and linguistic conventions that run orthogonal to the logical background from which ontological entities and relationships originate, resulting in severe challenges for ontological representation and reasoning. In particular, the purported existence of a single hierarchy in nature forces taxonomists to gradually approximate this hierarchy and make frequent rearrangements in light of new evidence. The evolvability of taxa implies that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life. As a result, many terms for phenotypic properties are phylogenetically underdetermined and have limited hierarchical transitivity. The standard approach of defining taxa both in reference to properties (intensional) and members (ostensive) undermines the individual/class dichotomy that sustains conventional ontologies, and compromises the reasoning capabilities associated with this distinction. Neither the use of Linnaean ranks in taxonomy nor the 250-year legacy of nomenclatural adjustments have obvious analogues in the ontological realm. Lastly, the piece-meal appearance of full-blown taxonomic information makes it necessary to use expert alignments to obtain a comprehensive static perspective. In light of these limitations, research along the taxonomy/ontology interface should focus either on strictly nomenclatural entities and relationships or on ontology-driven strategies for aligning multiple taxonomies, but not on building static networks for large portions of the tree of life. The prospects of using ontology-based services in taxonomy will largely depend on the ability of the taxonomic expert community to present its products in ways that are more compatible with ontological principles than concurrent practice.