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

  • Authors:

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

  • Affiliations:

  • Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA and Digital Enterprise Research Institute, National University of Ireland Galwa ...;Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA and College of Computer Science, Zhejiang University, 310027 Hangzhou, China;Science Commons, c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory, Building 32-386D, 32 Vassar Street, Cambridge, MA 02139, USA;Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA;Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA and Department of Anesthesiology, Yale University School of Medicine, 333 Cedar ...;Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA and Department of Anesthesiology, Yale University School of Medicine, 333 Cedar ...;Department of Neurobiology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8051, USA;Center for Medical Informatics, Yale University School of Medicine, 300 George Street, New Haven, CT 06520-8009, USA and Department of Anesthesiology, Yale University School of Medicine, 333 Cedar ...

  • Venue:
  • Artificial Intelligence in Medicine
  • Year:
  • 2010

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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/.