Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Laura Ann Slaughter (laurasla@ifi.uio.no), Eveliina Päivikki Kallioniemi (eveliina.p.kallioniemi@artsdatabanken.no)
Received: 24 Aug 2022 | Published: 24 Aug 2022
© 2022 Laura Slaughter, Leif Harald Karlsen, Eveliina Kallioniemi, Martin Skjæveland
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Slaughter LA, Karlsen LH, Kallioniemi EP, Skjæveland MG (2022) Reusable Ontology Modelling Patterns for Biodiversity Data with Reasonable Ontology Templates (OTTR). Biodiversity Information Science and Standards 6: e93939. https://doi.org/10.3897/biss.6.93939
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The Norwegian Biodiversity Information Centre (NBIC) is currently building a traitbank for Norwegian species. The purpose of the NBIC TraitBank is to enhance sharing of traits and other information about species to support conservation actions and ecological research. The traitbank will cover a subset of traits for all multicellular species and taxa that are found in Norway. Observations of traits, collected through citizen science as well as by experts, are connected to the NBIC TraitBank ontology, forming a knowledge base. We have modeled TraitBank’s ontology in accordance with NBIC’s data management requirements, focusing on the domain knowledge necessary for ontology-based data integration of internal databases and queries specified by use cases. Our initial steps in ontology construction included outlining competency questions, which are natural language sentences expressing the questions system users expect an ontology to answer (
We will present our experiences with implementing Reasonable Ontology Templates (OTTR) (
We argue that templates are an effective means to support the integration and use of digital biodiversity data in transparent ways, leading to successful collaboration and reuse of data. Following the "Don't repeat yourself" (DRY) principle of software development (
Example: Scientific Name
The NBIC uses Scientific Name as the main identifier and means to track a species. The OTTR template shown below captures the NBIC’s modelling pattern for Scientific Name. The signature of the template specifies the Internationalized Resource Identifier (IRI) of the template (adb-t:ScientificName), and six parameters (where ?iri is the 1st parameter). The parameters are used in the body of the template and define how instances of the template are expanded to Resource Description Framework (RDF) statements. Template instance expansion is done in a recursive manner, similar to many macro programming languages.
With the OTTR template definition given in Fig.
The benefits of using the OTTR framework is that modeling patterns are explicitly represented as an OTTR template, allowing for instances of patterns to be compactly and consistently captured. The format of template instances lends itself to instantiation from tabular data sources like spreadsheets and databases.
ontology patterns, FAIR principles, Reasonable Ontology Templates (OTTR)
Laura A. Slaughter
TDWG 2022