BIOREALM: an ontology for biogeographic areas
Résumé
We would like to present BIOREALM, the first informatic ontology for comparative biogeography. We applied ontological techniques to address semantic ambiguities in protected area and conservation informatics. By doing so, we aimed to create a coherent, machine-actionable semantic representation of the biogeographic areas (which often overlap protected areas) to support more efficient and standardized informatics, supporting research, and decision-making. We convert a cladogram of biogeographic areas – generated by a process known as bioregionalization – into a series of ontological classes. Areas of endemism are treated as formal objects related by hierarchical relationships and constrained by a condition of monophyly. We use semantic web approaches to extend the Environment Ontology (ENVO) with classes for (often semantically confounded) biogeographic entities, including biogeographic areas, areas of endemism, and endemic areas. We applied this approach to a bioregionalization of Australia as a case study. We have created an ontology – formatted in the Web Ontology Language (OWL) and adhering to the practices of the Open Biomedical and Biological Ontology Foundry – which provides a rigorous, extensible, and machine-actionable framework that can improve biogeographic analyses and interoperability between systems. BIOREALM encodes a model-theoretic view of endemism using semantic web approaches, offering new avenues to express and analyse biogeographic units. This approach offers a means to identify monophyletic biogeographic areas for conservation, based on specific combinations of monophyletic endemic taxa. Such an ontology provides knowledge representation solutions which supports interoperability along the FAIR (Findable, Accessible, Interoperable, Reusable) principles, thus fostering more consistent ecological informatics.