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

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dc.contributor.authorDumontier, Michel
dc.contributor.authorBaker, Christopher JO
dc.contributor.authorBaran, Joachim
dc.contributor.authorCallahan, Alison
dc.contributor.authorChepelev, Leonid
dc.contributor.authorCruz-Toledo, José
dc.contributor.authorDel Rio, Nicholas R.
dc.contributor.authorDuck, Geraint
dc.contributor.authorFurlong, Laura I., 1971-
dc.contributor.authorKeath, Nichealla
dc.contributor.authorKlassen, Dana
dc.contributor.authorMcCusker, Jamie P.
dc.contributor.authorQueralt Rosinach, Núria
dc.contributor.authorSamwald, Matthias
dc.contributor.authorVillanueva-Rosales, Natalia
dc.contributor.authorWilkinson, Mark
dc.contributor.authorHoehndorf, Robert
dc.date.accessioned2023-12-18T06:50:52Z
dc.date.available2023-12-18T06:50:52Z
dc.date.issued2014
dc.description.abstractThe 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.
dc.description.sponsorshipThis 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.
dc.format.mimetypeapplication/pdf
dc.identifier.citationDumontier M, Baker CJO, Baran J, Callahan A, Chepelev L, Cruz-Toledo J, et al. The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. J Biomed Semant. 2014 Mar 6;5(1):14. DOI: 10.1186/2041-1480-5-14
dc.identifier.doihttp://dx.doi.org/10.1186/2041-1480-5-14
dc.identifier.issn2041-1480
dc.identifier.urihttp://hdl.handle.net/10230/58541
dc.language.isoeng
dc.publisherBioMed Central
dc.relation.ispartofJournal of Biomedical Semantics. 2014 Mar 6;5(1):14
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/FP7/115191
dc.rightsThis article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
dc.rights.accessRightsinfo:eu-repo/semantics/openAccess
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.subject.keywordResource description framework
dc.subject.keywordSPARQL query
dc.subject.keywordRelation ontology
dc.subject.keywordOpen biomedical ontology
dc.subject.keywordResource description framework data
dc.titleThe Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
dc.typeinfo:eu-repo/semantics/article
dc.type.versioninfo:eu-repo/semantics/publishedVersion

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