Representing and analysing molecular and cellular function using the computer.

TitleRepresenting and analysing molecular and cellular function using the computer.
Publication TypeJournal Article
Year of Publication2000
Authorsvan Helden, J., Naim A., Mancuso R., Eldridge M., Wernisch L., Gilbert D., and Wodak S. J.
JournalBiol Chem
Date Published2000 Sep-Oct
KeywordsCell Physiological Phenomena, Computer Simulation, Databases, Factual

Determining the biological function of a myriad of genes, and understanding how they interact to yield a living cell, is the major challenge of the post genome-sequencing era. The complexity of biological systems is such that this cannot be envisaged without the help of powerful computer systems capable of representing and analysing the intricate networks of physical and functional interactions between the different cellular components. In this review we try to provide the reader with an appreciation of where we stand in this regard. We discuss some of the inherent problems in describing the different facets of biological function, give an overview of how information on function is currently represented in the major biological databases, and describe different systems for organising and categorising the functions of gene products. In a second part, we present a new general data model, currently under development, which describes information on molecular function and cellular processes in a rigorous manner. The model is capable of representing a large variety of biochemical processes, including metabolic pathways, regulation of gene expression and signal transduction. It also incorporates taxonomies for categorising molecular entities, interactions and processes, and it offers means of viewing the information at different levels of resolution, and dealing with incomplete knowledge. The data model has been implemented in the database on protein function and cellular processes 'aMAZE' (, which presently covers metabolic pathways and their regulation. Several tools for querying, displaying, and performing analyses on such pathways are briefly described in order to illustrate the practical applications enabled by the model.

Alternate JournalBiol. Chem.
PubMed ID11076023