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

Year: 2014

Venue: Journal of Biomedical Semantics

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

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.