OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system

Viktor SenderovEmail author View ORCID ID profile,
Kiril Simov,
Nico Franz,
Pavel Stoev,
Terry Catapano,
Donat Agosti,
Guido Sautter,
Robert A. Morris and
Lyubomir Penev

Journal of Biomedical Semantics20189:5

https://doi.org/10.1186/s13326-017-0174-5

Received: 18 August 2017

Accepted: 28 December 2017

Published: 18 January 2018

Abstract

Background

The biodiversity domain, and in particular biological taxonomy, is moving in the direction of semantization of its research outputs. The present work introduces OpenBiodiv-O, the ontology that serves as the basis of the OpenBiodiv Knowledge Management System. Our intent is to provide an ontology that fills the gaps between ontologies for biodiversity resources, such as DarwinCore-based ontologies, and semantic publishing ontologies, such as the SPAR Ontologies. We bridge this gap by providing an ontology focusing on biological taxonomy.

Results

OpenBiodiv-O introduces classes, properties, and axioms in the domains of scholarly biodiversity publishing and biological taxonomy and aligns them with several important domain ontologies (FaBiO, DoCO, DwC, Darwin-SW, NOMEN, ENVO). By doing so, it bridges the ontological gap across scholarly biodiversity publishing and biological taxonomy and allows for the creation of a Linked Open Dataset (LOD) of biodiversity information (a biodiversity knowledge graph) and enables the creation of the OpenBiodiv Knowledge Management System.

A key feature of the ontology is that it is an ontology of the scientific process of biological taxonomy and not of any particular state of knowledge. This feature allows it to express a multiplicity of scientific opinions. The resulting OpenBiodiv knowledge system may gain a high level of trust in the scientific community as it does not force a scientific opinion on its users (e.g. practicing taxonomists, library researchers, etc.), but rather provides the tools for experts to encode different views as science progresses.

Conclusions

OpenBiodiv-O provides a conceptual model of the structure of a biodiversity publication and the development of related taxonomic concepts. It also serves as the basis for the OpenBiodiv Knowledge Management System.

Keywords

BiodiversityBiodiversity informaticsSemantic webSemantic publishingOntologyKnowledge managementLinked open dataRDFOWLTaxonomyConcept taxonomyBiological systematicsData modeling