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The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

Michel Dumontier14*, Christopher JO Baker2, Joachim Baran3, Alison Callahan4, Leonid Chepelev4, José Cruz-Toledo4, Nicholas R Del Rio5, Geraint Duck6, Laura I Furlong7, Nichealla Keath4, Dana Klassen8, James P McCusker9, Núria Queralt-Rosinach7, Matthias Samwald10, Natalia Villanueva-Rosales5, Mark D Wilkinson11 and Robert Hoehndorf12

Author Affiliations

1 Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA

2 Department of Computer Science and Applied Statistics, University of New Brunswick, Saint John, New Brunswick, Canada

3 Ontario Institute for Cancer Research, Toronto, Ontario, Canada

4 Department of Biology, Carleton University, Ottawa, Ontario, Canada

5 Cyber-ShARE Center of Excellence, University of Texas at El Paso, El Paso, Texas, USA

6 School of Computer Science, University of Manchester, Manchester, UK

7 Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain

8 Digital Enterprise Research Institute, National University of Ireland, Galway, Ireland

9 Department of Computer Science, Rensselaer Polytechnic Institute, Troy, New York, USA

10 Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria

11 Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Madrid, Spain

12 Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK

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Journal of Biomedical Semantics 2014, 5:14  doi:10.1186/2041-1480-5-14

Published: 6 March 2014

Abstract

The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and associate qualities, capabilities, functions, quantities, and informational entities including textual, geometrical, and mathematical entities, and provides specific extensions in the domains of chemistry, biology, biochemistry, and bioinformatics. SIO provides an ontological foundation for the Bio2RDF linked data for the life sciences project and is used for semantic integration and discovery for SADI-based semantic web services. SIO is freely available to all users under a creative commons by attribution license. See website for further information: http://sio.semanticscience.org webcite.