ABSTRACT
MOTIVATION: The Physiome Project was established in 1997 to develop tools to facilitate international collaboration in the physiological sciences and the sharing of biological models and experimental data. The CellML language was developed to represent and exchange mathematical models of biological processes. CellML models can be very complicated, making it difficult to interpret the underlying physical and biological concepts and relationships captured/described in the mathematical model. RESULTS: To address this issue a set of ontologies was developed to explicitly annotate the biophysical concepts represented in the CellML models. This article presents a framework that combines a visual language, together with CellML ontologies, to support the visualization of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model. Automated CellML model visualization assists in the interpretation of model concepts and facilitates model communication and exchange between different communities.
Subject(s)
Computational Biology/methods , Models, Theoretical , Algorithms , Databases, Factual , Models, BiologicalABSTRACT
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.
Subject(s)
Biophysical Phenomena , Computational Biology/methods , Models, Biological , Software , Internet , Programming LanguagesABSTRACT
The CellML language was developed in response to the need for a high-level language to represent and exchange mathematical models of biological processes. The flexible structure of CellML allows modellers to construct mathematical models of the same biological system in many different ways. However, some modelling styles do not naturally lead to clear abstractions of the biophysical concepts and produce CellML models that are hard to understand and from which it is difficult to isolate parts that may be useful for constructing other models. In this article, we advocate building CellML models which isolate common biophysical concepts and, using these, to build mathematical models of biological processes that provide a close correspondence between the CellML model and the underlying biological process. Subsequently, models of higher complexity can be constructed by reusing these modularized CellML models in part or in whole. Development of CellML models that best describe the underlying biophysical concepts thus avoids the need to code models from scratch and enhances the extensibility, reusability, consistency and interpretation of the models.
Subject(s)
Biophysical Phenomena , Models, Biological , Animals , Computer Simulation , GTP-Binding Proteins/physiology , Humans , Ligands , Models, Statistical , Receptors, G-Protein-Coupled/physiologyABSTRACT
CellML is an open XML-based markup language for describing and exchanging mathematical models of biological processes. While CellML was originally designed to describe and exchange models of cellular and subcellular processes, the design principles that were applied to the construction of a language with this relatively narrow focus are equally applicable to the specification of a language with a much wider scope. In this paper we describe the structure of CellML, how the language is evolving to broaden its scope, and what tools are being developed to facilitate its use.
