Biophysical annotation and representation of CellML models.
BACKGROUND
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.
Wimalaratne
S M
SM
Auckland Bioengineering Institute, The University of Auckland, 70 Symonds Street, Auckland, New Zealand. sarala.dissanayake@auckland.ac.nz
Halstead
M D B
MD
Lloyd
C M
CM
Crampin
E J
EJ
Nielsen
P F
PF
D055592:Biophysical Phenomena; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D008954:Models, Biological; D011381:Programming Languages; D012984:Software