Journal Article

Biophysical annotation and representation of CellML models

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

in Bioinformatics

Volume 25, issue 17, pages 2263-2270
Published in print September 2009 | ISSN: 1367-4803
Published online June 2009 | e-ISSN: 1460-2059 | DOI:
Biophysical annotation and representation of CellML models

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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.


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5954 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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