Biophysical annotation and representation of CellML models

Auckland Bioengineering Institute, The University of Auckland, 70 Symonds Street, Auckland, New Zealand.
Bioinformatics (Impact Factor: 4.98). 07/2009; 25(17):2263-70. DOI: 10.1093/bioinformatics/btp391
Source: PubMed


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}

Supplementary information: Supplementary data are available at Bioinformatics online.

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Available from: Matt D. B. Halstead, Nov 05, 2015
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