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

被引：128

作者：

Dumontier, Michel ^{[1
,4
]}

Baker, Christopher J. O. ^{[2
]}

Baran, Joachim ^{[3
]}

Callahan, Alison ^{[4
]}

Chepelev, Leonid ^{[4
]}

Cruz-Toledo, Jose ^{[4
]}

Del Rio, Nicholas R. ^{[5
]}

Duck, Geraint ^{[6
]}

Furlong, Laura I. ^{[7
]}

Keath, Nichealla ^{[4
]}

Klassen, Dana ^{[8
]}

McCusker, James P. ^{[9
]}

Queralt-Rosinach, Nuria ^{[7
]}

Samwald, Matthias ^{[10
]}

Villanueva-Rosales, Natalia ^{[5
]}

Wilkinson, Mark D. ^{[11
]}

Hoehndorf, Robert ^{[12
]}

机构：

[1] Stanford Univ, Ctr Biomed Informat Res, Stanford, CA 94305 USA

[2] Univ New Brunswick, Dept Comp Sci & Appl Stat, St John, NB E2L 4L5, Canada

[3] Ontario Inst Canc Res, Toronto, ON, Canada

[4] Carleton Univ, Dept Biol, Ottawa, ON K1S 5B6, Canada

[5] Univ Texas El Paso, Cyber ShARE Ctr Excellence, El Paso, TX 79968 USA

[6] Univ Manchester, Sch Comp Sci, Manchester, Lancs, England

[7] Univ Pompeu Fabra, Hosp del Mar, Med Res Inst, Barcelona, Spain

[8] Natl Univ Ireland, Digital Enterprise Res Inst, Galway, Ireland

[9] Rensselaer Polytech Inst, Dept Comp Sci, Troy, NY 12180 USA

[10] Med Univ Vienna, Ctr Med Stat Informat & Intelligent Syst, Vienna, Austria

[11] Univ Politecn Madrid, Ctr Biotecnol & Genom Plantas, Madrid, Spain

[12] Univ Cambridge, Dept Physiol Dev & Neurosci, Cambridge, England

来源：

JOURNAL OF BIOMEDICAL SEMANTICS | 2014年 / 5卷

基金：

加拿大自然科学与工程研究理事会; 美国国家科学基金会;

关键词：

DESIGN PATTERNS; COORDINATED EVOLUTION; BIO-ONTOLOGIES; SADI; METHODOLOGY; MASHUP; DOMAIN; GENE;

D O I：

10.1186/2041-1480-5-14

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：11

共 43 条

[1]

[Anonymous], 2001, Proceedings of the International Joint Conference on Artificial Intelligence-01 Workshop: Ontologies and Information Sharing

[2]

[Anonymous], RESOURCE DESCRIPTION

[3]

[Anonymous], 2004, RDF Vocabulary Description Language 1.0: RDF Schema

[4]

[Anonymous], 2009, W3C RECOMM

[5]

Antony G, 2010, FORMAL ONTOLOGY INFO, P387

[6] Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology [J].

Aranguren, Mikel Egana ;

Antezana, Erick ;

Kuiper, Martin ;

Stevens, Robert .

BMC BIOINFORMATICS, 2008, 9 (Suppl 5)

[7] Bio2RDF: Towards a mashup to build bioinformatics knowledge systems [J].

Belleau, Francois ;

Nolin, Marc-Alexandre ;

Tourigny, Nicole ;

Rigault, Philippe ;

Morissette, Jean .

JOURNAL OF BIOMEDICAL INFORMATICS, 2008, 41 (05) :706-716

[8] Bio-ontologies: current trends and future directions [J].

Bodenreider, Olivier ;

Stevens, Robert .

BRIEFINGS IN BIOINFORMATICS, 2006, 7 (03) :256-274

[9] Modeling biomedical experimental processes with OBI [J].

Brinkman R.R. ;

Courtot M. ;

Derom D. ;

Fostel J.M. ;

He Y. ;

Lord P. ;

Malone J. ;

Parkinson H. ;

Peters B. ;

Rocca-Serra P. ;

Ruttenberg A. ;

Sansone S.-A. ;

Soldatova L.N. ;

Stoeckert C.J., Jr. ;

Turner J.A. ;

Zheng J. ;

Grethe J. ;

Rubin D. ;

Bug B. ;

Wiemann S. ;

Hernandez-Boussard T. ;

Scheuermann R. ;

Bruskiewich R. ;

Gibson F. ;

Morrison N. ;

Field D. ;

Gray T. ;

Deutsch E. ;

Schober D. ;

Montecchi L. ;

Taylor C. ;

Whetzel T. ;

Westbrook J. ;

Fragoso G. ;

White J. ;

Heiskanen M. ;

Fan L. ;

Causton H. ;

Lister A. ;

Clancy K. ;

Cocos C. ;

Greenbaum J. ;

Grenon P. ;

Mungall C. ;

Pocock M. ;

Stenzhorn H. ;

Hunter L. ;

Mc Gee M. ;

Smith B. ;

Stevens R. .

Journal of Biomedical Semantics, 1 (Suppl 1)

[10] Ontology-Based Querying with Bio2RDF's Linked Open Data [J].

Callahan A. ;

Cruz-Toledo J. ;

Dumontier M. .

Journal of Biomedical Semantics, 4 (Suppl 1)

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