Summary
An ontology captures knowledge of a domain in a structured and well-defined way. Anatomy provides a conceptual framework for the parts and tissues of an organism including structural (parts and sub-parts), functional (system elements), developmental (change of structure during embryogenesis) and derivation. Anatomy is also used to define place or spatial location. This can be in the form of topological relationships, e.g. adjacency or connectedness, or geometric, e.g. distance and direction. Atlases provide a direct or iconic framework to describe the spatial organisation of an organism with no reference to the conceptual anatomical framework. In this chapter we discuss how anatomical and atlas frameworks can be used to provide a rich ontology encompassing both conceptual, topological and geometric spaces. We also introduce the notion of a natural coordinate system both as a robust tool for navigation within an organism (e.g. the mouse embryo) and as a mechanism for cross-atlas interoperability.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
R.A. Baldock, J. Bard, M.H. Kaufman, and D Davidson. A real mouse for your computer.BioEssays, 14:501–502, 1992.
Richard Baldock, Jonathan Bard, Albert Burger, Nicolas Burton, Jeff Christiansen,Guangjie Feng, Bill Hill, Derek Houghton, Mathew Kaufman, Jianguo Rao, JamesSharpe, Allyson Ross, Peter Stevenson, Shanmugasundaram Venkataraman, AndrewWaterhouse,Yiya Yang, and Duncan Davidson. Emap and emage: A framework for understandingspatially organised data. Neuroinformatics, pages 309–325, 2003.
W. W. Ballard. Comparative Anatomy and Embryology. Ronald Press, USA, 1964.
Tim Berners-Lee, James Hendler, and Ora Lassila. The semantic web. Scientific American,May 2002.
Albert Burger, Duncan Davidson, and Richard Baldock. Formalization of mouse embryoanatomy. Bioinformatics, 20:259–267, 2004.
R. Casati and A.C. Varzi. Parts and Places, The Structures of Spatial Representation. TheMIT Press, Cambridge, Massachusetts, 1999.
Duncan Davidson and Richard Baldock. Bioinformatics beyond sequence: Mapping genefunction in the embryo. Nature Reviews Genetics, 2:409–418, 2001.
D. de Roure, N.R. Jennings, and N. Shadbolt. The semantic grid: A future e-scienceinfrastructure. In F. Berman, G. Fox, and A.J.G. Hey, editors, Grid Computing - Making the Global Infrastructure a Reality, pages 437–470. John Wiley and Sons Ltd., 2003.
T.R. Gruber. A translation approach to portable ontology specifications. Knowledge Acquisition, 5:199–220, 1993.
Isam Hilal, Serge van Sint Jan, Alberto Leardini, and Ugo Della Croce. D3.2 final reporton data collection procedure - annex 1. Technical report, University of Brussels, 2002.Report from EU project 10954 Virtual Animation of the Kinematics of the Human forIndustrial Educational and Research Purposes.
Janet Kerwin, Mark Scott, James Sharpe, Luis Puelles, Stephen C Robson, Margaret Martinezde-la Torre, Jose Luis Ferran, Guangjie Feng, Richard Baldock, Tom Strachan, DuncanDavidson, and Susan Lindsay. 3 dimensional modelling of early human brain developmentusing optical projection tomography. BMC Neuroscience, 5:27, 2004.
Anderson Maciel, Luciana Porcher Nedel, and Carla Maria Dal Sasso Freitas. Anatomybasedjoint models for virtual human skeletons. In Computer Animation 2002 (CA 2002), 19-21 June 2002, Geneva, Switzerland, pages 220–224. IEEE Computer Society, 2002.
Allan MacKenzie-Graham, Erh-Fang Lee, Ivo D Dinov, Mihail Bota, David W Shattuck,Seth Ruffins, Heng Yuan, Fotios Konstantinidis, Alain Pitiot, Yi Ding, Guogang Hu, RussellE Jacobs, and Arthur W Toga. A multimodal, multidimensional atlas of the c57bl/6jmouse brain. J Anat, 204(2):93–102, 2004.
George Paxinos and Keith B. J. Franklin. The Mouse Brain in Stereotaxic Coordinates.Academic Press, San Diego, 2nd edition, 2001.
C. Rosse and J.L.V. Mejino. A reference ontology for biomedical informatics: the foundationalmodel of anatomy. Biomedical Informatics, 36:478–500, 2003.
S.J. Surma, J.T. Srzednicki, D.I. Barnett, and F.V. Rickey, editors. Stanislaw Le’sniewski: Collected Works. Kluwer Academic Press, 1992.
Karl Theiler. The House Mouse. Springer-Verlag, New York, 1989.
P. L. Williams, R. Warwick, M. Dyson, and L. H. Bannister, editors. Gray’s Anatomy.Churchill Livingstone, London, 37 edition, 1995.
Morton E. Winston, Roger Chaffin, and Douglas Herrmann. A taxonomy of part-wholerelations. Cognitive Science, 11:417–444, 1987.
Editor information
Rights and permissions
Copyright information
© 2008 Albert Burger, Duncan Davidson, Richard Baldock
About this chapter
Cite this chapter
Baldock, R.A., Burger, A. (2008). Anatomical Ontologies: Linking Names to Places in Biology. In: Burger, A., Davidson, D., Baldock, R. (eds) Anatomy Ontologies for Bioinformatics. Computational Biology, vol 6. Springer, London. https://doi.org/10.1007/978-1-84628-885-2_10
Download citation
DOI: https://doi.org/10.1007/978-1-84628-885-2_10
Publisher Name: Springer, London
Print ISBN: 978-1-84628-884-5
Online ISBN: 978-1-84628-885-2
eBook Packages: Computer ScienceComputer Science (R0)