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Focused Review ARTICLE

Ontologies for neuroscience: what are they and what are they good for?

Stephen D. Larson and Maryann E. Martone*

Department of Neurosciences, University of California, San Diego, CA, USA

Current information technology practices in neuroscience make it difficult to understand the organization of the brain across spatial scales. Subcellular junctional connectivity, cytoarchitectural local connectivity, and long-range topographical connectivity are just a few of the relevant data domains that must be synthesized in order to make sense of the brain. However, due to the heterogeneity of the data produced within these domains, the landscape of multiscale neuroscience data is fragmented. A standard framework for neuroscience data is needed to bridge existing digital data resources and to help in the conceptual unification of the multiple disciplines of neuroscience. Using our efforts in building ontologies for neuroscience as an example, we examine the benefits and limits of ontologies as a solution for this data integration problem. We provide several examples of their application to problems of image annotation, content-based retrieval of structural data, and integration of data across scales and researchers.

Keywords:

neuroinformatics, neuroanatomy, databases, subcellular anatomy, data integration

Citation:

Larson SD and Martone ME (2009). Ontologies for neuroscience: what are they and what are they good for? Front. Neurosci. 3:1. doi: 10.3389/neuro.01.007.2009

Received:

23 September 2008;

Paper pending published:

04 November 2008;

Accepted:

22 March 2009;

Published online:

01 May 2009.

Edited by:

Jan G. Bjaalie, International Neuroinformatics Coordination Facility, Sweden; University of Oslo, Norway

Reviewed by:

Mihail Bota, University of Southern California, USA
Raphael Ritz, INCF, Sweden

© 2009 Larson and Martone. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.

*Correspondence:

Dr. Maryann E. Martone, Department of Neurosciences University of California, San Diego San Diego, CA 92093-0446 USA 9500 Gilman Drive San Diego, CA, 92093-0446, USA. email: mmartone@ucsd.edu