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J Mol Biol. 2004 May 21;339(1):77-88.

A description scheme of biological processes based on elementary bricks of action.

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CNRS UMR 5160, Center for Pharmacology and Health Biotechnology, Faculté de Pharmacie, 15 Av. Charles Flahault, B.P. 14491, 34093 Montpellier Cedex 5, France.


With the fast growth of high-throughput strategies in Biology, there is a strong need to accelerate knowledge acquisition and organization of molecular functions. Unfortunately, although we know that there is a correlation between protein molecules and their functions, we are unable to clearly identify this link. Here, we revisit the current views of protein functions as well as their annotation, and we show that they are incompatible with unambiguous interpretations and the use of this knowledge. We describe herein a description scheme for biological processes based on elementary bricks of action that may be associated with biological molecules. To retrieve the descriptive quality found in annotations of other kinds of biological data, it was decided to develop a scheme involving four levels of abstraction: Basic Elements of Action, Biological Activities, Biological Functionalities and Biological Roles. This multi-level organization is a generic method; it allows for a description of biological processes by using a limited number of elementary bricks of action. Moreover, by using this description of biological processes, it should now be possible to clearly identify unambiguous relationships between the organization of biological processes and the structural or functional organizations of biological molecules.

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