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

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, 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 journal › Article › Academic › peer-review

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
Article number	14
Journal	Journal of biomedical semantics
Volume	5
DOIs	https://doi.org/10.1186/2041-1480-5-14
Publication status	Published - 6 Mar 2014
Externally published	Yes

Access to Document

10.1186/2041-1480-5-14Licence: CC BY

Cite this

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, 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 Jose 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 Nuria Queralt-Rosinach and Matthias Samwald and Natalia Villanueva-Rosales and Wilkinson, {Mark D.} and Robert Hoehndorf",

year = "2014",

month = mar,

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doi = "10.1186/2041-1480-5-14",

language = "English",

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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, 14. https://doi.org/10.1186/2041-1480-5-14

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T1 - The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

AU - Dumontier, Michel

AU - Baker, Christopher J. O.

AU - Baran, Joachim

AU - Callahan, Alison

AU - Chepelev, Leonid

AU - Cruz-Toledo, Jose

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, Nuria

AU - Samwald, Matthias

AU - Villanueva-Rosales, Natalia

AU - Wilkinson, Mark D.

AU - Hoehndorf, Robert

PY - 2014/3/6

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