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Bioinformatics Advance Access originally published online on June 29, 2009
Bioinformatics 2009 25(17):2263-2270; doi:10.1093/bioinformatics/btp391
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Biophysical annotation and representation of CellML models

S. M. Wimalaratne 1,*, M. D. B. Halstead 1, C. M. Lloyd 1, E. J. Crampin 1,2 and P. F. Nielsen 1,2

1 Auckland Bioengineering Institute and 2 Department of Engineering Science, The University of Auckland, 70 Symonds Street, Auckland, New Zealand

* To whom correspondence should be addressed.


  Abstract

Motivation: CellML is an implementation-independent model description language for specifying and exchanging biological processes. The focus of CellML is the representation of mathematical formulations of biological processes. The language captures the mathematical and model building constructs well, but does not lend itself to capturing the biology these models represent.

Results: This article describes the development of an ontological framework for annotating CellML models with biophysical concepts. We demonstrate that, by using these ontological mappings, in combination with a set of graph reduction rules, it is possible to represent the underlying biological process described in a CellML model.

Contact: sarala.dissanayake{at}auckland.ac.nz

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on February 23, 2009; revised on June 17, 2009; accepted on June 21, 2009

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