Original Research ARTICLE

Front. Neuroinform., 02 November 2007 | doi: 10.3389/neuro.11.003.2007

A formal ontology of subcellular neuroanatomy

  • 1 National Center for Microscopy and Imaging Research, University of California, USA
  • 2 San Diego Supercomputer Center, University of California, USA
  • 3 Laboratory for Bioimaging and Anatomical Informatics, Drexel University College of Medicine, USA

The complexity of the nervous system requires high-resolution microscopy to resolve the detailed 3D structure of nerve cells and supracellular domains. The analysis of such imaging data to extract cellular surfaces and cell components often requires the combination of expert human knowledge with carefully engineered software tools. In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational models, we have created a core of formalized knowledge about the structure of the nervous system and have integrated that core into several software applications. In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between these parts. Many applications of this ontology to image annotation, content-based retrieval of structural data, and integration of shared data across scales and researchers are also described.

Keywords: neuroanatomy, neuronal cell types, electron microscopy, subcellular anatomy, data integration

Citation: Stephen D. Larson, Lisa L. Fong, Amarnath Gupta, Christopher Condit, William J. Bug and Maryann E. Martone (2007). A formal ontology of subcellular neuroanatomy. Front. neuroinform. 1:3. doi: 10.3389/neuro.11/003.2007

Received: 1 September 2007; Paper pending published: 24 September 2007;
Accepted: 7 October 2007; Published online: 2 November 2007.

Edited by:

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

Reviewed by:

Jose L. Mejino, Structural Informatics Group, University of Washington, USA
Jan G. Bjaalie, International Neuroinformatics Coordination Facility, Stockholm, Sweden; University of Oslo, Norway

Copyright: © 2007 Larson, Fong, Gupta, Condit, Bug, Martone. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

*Correspondence: Maryann E. Martone, National Center for Microscopy and Imaging Research, Center for Research in Biological Structure and Development of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA. e-mail: mmartone@ucsd.edu

Back to top