BioPortal as a dataset of linked biomedical ontologies and terminologies in RDF

Article type: Research Article

Authors: Salvadores, Manuel^; | Alexander, Paul R. | Musen, Mark A. | Noy, Natalya F.

Affiliations: Stanford Center for Biomedical Informatics Research, Stanford University, USA. E-mail: {manuelso,palexander,musen,noy}@stanford.edu

Note: [] Corresponding author.

Abstract: BioPortal is a repository of biomedical ontologies – the largest such repository, with more than 300 ontologies to date. This set includes ontologies that were developed in OWL, OBO and other formats, as well as a large number of medical terminologies that the US National Library of Medicine distributes in its own proprietary format. We have published the RDF version of all these ontologies at http://sparql.bioontology.org. This dataset contains 190M triples, representing both metadata and content for the 300 ontologies. We use the metadata that the ontology authors provide and simple RDFS reasoning in order to provide dataset users with uniform access to key properties of the ontologies, such as lexical properties for the class names and provenance data. The dataset also contains 9.8M cross-ontology mappings of different types, generated both manually and automatically, which come with their own metadata.

Keywords: Biomedical ontologies, BioPortal, RDF, linked data

DOI: 10.3233/SW-2012-0086

Journal: Semantic Web, vol. 4, no. 3, pp. 277-284, 2013