BIOREALM—An ontology of comparative biogeography: New insights into the semantics of biodiversity conservation

Abstract

Aim: We aimed to apply 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 present BIOREALM, the first informatic ontology for comparative biogeography. Location: Global. Taxon: Any taxon can be integrated in BIOREALM. Methods: 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. In all, 20 subregions which are part of the Austral Bioregionalisation Atlas have been selected for the study and integrated in BIOREALM. Results: We have created an ontology—formatted in the Web Ontology Language 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. One main class and 20 individuals per class were implemented. Main Conclusions: 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.