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

doi:10.1186/2041-1480-5-14

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 journal › Article › peer-review

180 Scopus citations

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.

Original language	English (US)
Article number	14
Journal	Journal of biomedical semantics
Volume	5
Issue number	1
DOIs	https://doi.org/10.1186/2041-1480-5-14
State	Published - Mar 6 2014
Externally published	Yes

ASJC Scopus subject areas

Information Systems
Computer Science Applications
Health Informatics
Computer Networks and Communications

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10.1186/2041-1480-5-14

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Dumontier, M., Baker, C. J. O., Baran, J., Callahan, A., Chepelev, L., Cruz-Toledo, J., Del Rio, N. R., Duck, G., Furlong, L. I., Keath, N., Klassen, D., McCusker, J. P., Queralt-Rosinach, N., Samwald, M., Villanueva-Rosales, N., Wilkinson, M. D., & Hoehndorf, R. (2014). The semanticscience integrated ontology (SIO) for biomedical research and knowledge discovery. Journal of biomedical semantics, 5(1), Article 14. https://doi.org/10.1186/2041-1480-5-14

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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.",

author = "Michel Dumontier and Baker, {Christopher J.O.} and Joachim Baran and Alison Callahan and Leonid Chepelev and Jos{\'e} Cruz-Toledo and {Del Rio}, {Nicholas R.} and Geraint Duck and Furlong, {Laura I.} and Nichealla Keath and Dana Klassen and McCusker, {James P.} and N{\'u}ria Queralt-Rosinach and Matthias Samwald and Natalia Villanueva-Rosales and Wilkinson, {Mark D.} and Robert Hoehndorf",

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Dumontier, M, Baker, CJO, Baran, J, Callahan, A, Chepelev, L, Cruz-Toledo, J, Del Rio, NR, Duck, G, Furlong, LI, Keath, N, Klassen, D, McCusker, JP, Queralt-Rosinach, N, Samwald, M, Villanueva-Rosales, N, Wilkinson, MD & Hoehndorf, R 2014, 'The semanticscience integrated ontology (SIO) for biomedical research and knowledge discovery', Journal of biomedical semantics, vol. 5, no. 1, 14. https://doi.org/10.1186/2041-1480-5-14

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AU - Baker, Christopher J.O.

AU - Baran, Joachim

AU - Callahan, Alison

AU - Chepelev, Leonid

AU - Cruz-Toledo, José

AU - Del Rio, Nicholas R.

AU - Duck, Geraint

AU - Furlong, Laura I.

AU - Keath, Nichealla

AU - Klassen, Dana

AU - McCusker, James P.

AU - Queralt-Rosinach, Núria

AU - Samwald, Matthias

AU - Villanueva-Rosales, Natalia

AU - Wilkinson, Mark D.

AU - Hoehndorf, Robert

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

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