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Updated: Aug 23, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems
Magali Roux-Rouquié1, Nicolas Caritey, Laurent Gaubert
1BSMI, Institut PASTEUR, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France. magil.roux@lip6.fr
Abstract:
One of the main issues in Systems Biology is to deal with semantic data integration. Previously, we examined the requirements for a reference conceptual model to guide semantic integration based on the systemic principles. In the present paper, we examine the usefulness of the Unified Modelling Language (UML) to describe and specify biological systems and processes. This makes unambiguous representations of biological systems, which would be suitable for translation into mathematical and computational formalisms, enabling analysis, simulation and prediction of these systems behaviours.
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