(2002) Metabolism Is Composed of Many Coupled, Interconnecting Reactions. Besides, computationally generated models that could be obtained from model repositories should be utilized with manual curations as they lack some important components that are necessary for full functionality of the models.īerg, J. Therefore, it is strongly recommended that the database creators and the metabolic network models developers should follow international standards for the nomenclature of reactions and metabolites. The inconsistencies among the databases in representing their contents may hamper the maximal use of the knowledge accumulated in these databases in particular and the area of systems biology at large. The three model repositories reviewed do not offer a brief description of the models’ characteristics such as simulation conditions. In addition, inconsistencies have been observed in nomenclature and representation of database entities. Our review showed that the pathway resources vary in many aspects, such as their scope, content, access to data and the tools. Resultsįour pathways databases and three model repositories were selected on the basis of popularity and diversity. The review aims to help researchers choose a suitable database or model repository according to the information and data required, by providing an insight look of each pathway resource. Here we present a review of the most popular metabolic pathway databases and model repositories, focusing on their scope, content including reactions, enzymes, compounds, and genes, and applicability. These resources are diverse in the type of information/data, the analytical tools, and objectives. The number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly.
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