The semanticscience integrated ontology (SIO) for biomedical research and knowledge discovery

Michel Dumontier*, Christopher J.O. Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura I. Furlong, Nichealla Keath, Dana Klassen, James P. McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D. Wilkinson, Robert Hoehndorf

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

157 Scopus citations


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:

Original languageEnglish (US)
Article number14
JournalJournal of Biomedical Semantics
Issue number1
StatePublished - Mar 6 2014
Externally publishedYes

Bibliographical note

Funding Information:
This work was funded, in part, by NSERC Discovery Grant to MD, Ontario Early Researcher Award to MD and CANARIE NEP-2 grant to MD, CB and MW. This work has received support from the IMI Joint Undertaking under grant agreement no. 115191, Open PHACTS, resources of which comprise financial contribution from the EU FP7 (FP7/2007-2013) and EFPIA companies’ in kind contribution; and Instituto de Salud Carlos III FEDER [CP10/00524]. The Research Programme on Biomedical Informatics (GRIB) is a node of the Spanish National Institute of Bioinformatics (INB). ELSEWeb is funded by NASA ACCESS grant NNX12AF49A (UTEP) and used resources from Cyber-ShARE Center of Excellence supported by NSF grant HRD-1242122. We would like to thank the following individuals for thoughtful discussions and contributions on and off the mailing list: Jerven Bolleman, Kevin Cohen, Melanie Courtot, Simon Jupp, Jin-Dong Kim, James Malone, Luke McCarthy, Chris Mungall, David Osumi-Sutherland, Alexandre Riazanov and Robert Stevens.

Publisher Copyright:
© 2014 Dumontier et al.; licensee BioMed Central Ltd.

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Health Informatics
  • Computer Networks and Communications


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