Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience

Samwald, Matthias; Chen, Huajun; Ruttenberg, Alan; Lim, Ernest; Marenco, Luis; Miller, Perry; Shepherd, Gordon; Cheung, Kei-Hoi

doi:10.1016/j.artmed.2009.11.003

« Previous Next »Artificial Intelligence in Medicine
Volume 48, Issue 1 , Pages 21-28, January 2010

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience

Matthias Samwald
- Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
- Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland
- Konrad Lorenz Institute for Evolution and Cognition Research, Adolf Lorenz Gasse 2, A-3422 Altenberg, Austria
- Section on Medical Expert and Knowledge-Based Systems, Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
- Corresponding author at: Konrad Lorenz Institute for Evolution and Cognition Research, Adolf Lorenz Gasse 2, A-3422 Altenberg, Austria. Tel.: +43 2242 32390x19; fax: +43 2242 323904.
Huajun Chen
- Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
- College of Computer Science, Zhejiang University, 310027 Hangzhou, China
Alan Ruttenberg
- Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, MA 02139, USA
Ernest Lim
- Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
Luis Marenco
- Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
- Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
Perry Miller
- Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
- Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8009, USA
Gordon Shepherd
- Department of Neurobiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
Kei-Hoi Cheung
- Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA
- Department of Anesthesiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8005, USA
- Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT 06511, USA

Received 24 August 2007; received in revised form 6 October 2009; accepted 16 November 2009.

Abstract

Objective

Integrative neuroscience research needs a scalable informatics framework that enables semantic integration of diverse types of neuroscience data. This paper describes the use of the Web Ontology Language (OWL) and other Semantic Web technologies for the representation and integration of molecular-level data provided by several of SenseLab suite of neuroscience databases.

Methods

Based on the original database structure, we semi-automatically translated the databases into OWL ontologies with manual addition of semantic enrichment. The SenseLab ontologies are extensively linked to other biomedical Semantic Web resources, including the Subcellular Anatomy Ontology, Brain Architecture Management System, the Gene Ontology, BIRNLex and UniProt. The SenseLab ontologies have also been mapped to the Basic Formal Ontology and Relation Ontology, which helps ease interoperability with many other existing and future biomedical ontologies for the Semantic Web. In addition, approaches to representing contradictory research statements are described. The SenseLab ontologies are designed for use on the Semantic Web that enables their integration into a growing collection of biomedical information resources.

Conclusion

We demonstrate that our approach can yield significant potential benefits and that the Semantic Web is rapidly becoming mature enough to realize its anticipated promises. The ontologies are available online at http://neuroweb.med.yale.edu/senselab/.

Keywords: Semantic Web, Neuroscience, Description logic, Ontology mapping, Web Ontology Language, Integration