Metabolic pathway databases and model repositories

Abstract

Background: The number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly. These resources are diverse in the type of information/data, the analytical tools, and objectives. 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. 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.

Results: Four pathways databases and three model repositories were selected on the basis of popularity and diversity. Our review showed that the pathway resources vary in many aspects, such as their scope, content, access to data and the tools. In addition, inconsistencies have been observed in nomenclature and representation of database entities. The three model repositories reviewed do not offer a brief description of the models’ characteristics such as simulation conditions.

Conclusions: 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. 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. 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.

Author summary

Four metabolic pathway databases and three model repositories were reviewed with regard to their scope, content, and applicability. Despite their innumerable use in the fields of systems biology and metabolic engineering, these pathway databases and model repositories are not in harmony with each other due to the inconsistencies in the way they represent their contents. Besides, the automatically generated metabolic models that can be obtained from the model repositories are not accurate enough for further scientific usage without additional manual curation. Therefore, international standards such as IUBMB principles should be strictly obeyed in creating such metabolic pathway resources.

Graphical abstract

Keywords

metabolic pathway / database / model repository

References

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ACKNOWLEDGEMENTS

This work was supported by the National Natural Science Foundation of China (No. 31470068), Sichuan Youth Science and Technology Foundation of China (No. 2014JQ0051) and the Fundamental Research Funds for the Central Universities of China (Nos. ZYGX2015Z006 and ZYGX2015J144). The funders had no role in study design, data collection and analysis, decision to publish, and preparation of the manuscript.

COMPLIANCE WITH ETHICAL GUIDELINES

The authors Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua and Feng-Biao Guo declare that they have no conflict of interest.ƒ

This article is a review article and does not contain any studies with human or animal subjects performed by any of the authors.

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