OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system

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: Biodiversity; Biodiversity informatics; Biological systematics; Concept taxonomy; Data modeling; Knowledge management; Linked open data; OWL; Ontology; RDF; Semantic publishing; Semantic web; Taxonomy.

Fig. 1

Taxonomic article diagram. A graphical representation of the relationships between instances of the publishing-related classes that OpenBiodiv introduces

Fig. 2

Example article metadata. This example shows how to express the metadata of a taxonomic article with the SPAR Ontologies’ model and the classes that OpenBiodiv defines. The code is in Turtle

Fig. 3

Example article structure. This examples shows how to express the article structure with the help of :contains. The code is in Turtle

Fig. 4

Taxonomic name class hierarchy diagram. We created this class hierarchy to accommodate both traditional taxonomic name usages and the usage of taxonomic concept labels and operational taxonomic units

Fig. 5

Scientific name patterns diagram. Chains of replacement names can be followed to find the currently used name. Related name indicates that two names are related somehow, but not which one is preferable

Fig. 6

Example taxonomic name usage. This examples shows how taxonomic name usages link document components to taxonomic names. The code is in Turtle

Fig. 7

Taxonomic concept diagram. A taxonomic concept is a skos:Concept, a frbr:Work, a dwc:Taxon and has at least one taxonomic concept label

Fig. 8

Taxonomic name property hierarchy diagram. Property hierarchy is aligned with the taxonomic name class hierarchy and with DarwinCore

Fig. 9

Taxonomic concept relationships diagram. In order to express an RCC-5 relationship between concepts, create an :RCC5Sgtatement and use the corresponding properties to link two taxonomic concepts via it. Further, taxonomic concepts are linked to traits (e.g. ecology in ENVO), occurrences (e.g. Darwin-SW) and realize treatments

Fig. 10

Example simple taxonomic concept relationships. We can use SKOS semantic properties to illustrate simple relationships between taxonomic concepts

Fig. 11

Example of RCC-5 taxonomic concept relationships. In order to express an RCC-5 relationship between concepts, create an :RCC5Sgtatement and use the corresponding properties to link two taxonomic concepts via it. SKOS relations relate concepts directly

Fig. 12

Example of combining ENVO with OpenBiodiv-O. We create a shortcut for has habitat and instance of the “forest biome” and link them to our taxonomic concept in order to express the fact that specimens of it have been found to live in Casuarina trees

Fig. 13

Example connection between a treatment and a taxonomic concept. A treatment is the realization of a taxonomic concept