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

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

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


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
Article number14
JournalJournal of biomedical semantics
Publication statusPublished - 6 Mar 2014
Externally publishedYes


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