Metabolic pathway databases and model repositories

• DOI: 10.1007/s40484-017-0108-3
• Publication Date: 2017-09-14T13:36:25Z
• Authors: Abraham A. Labena; Yi‐Zhou Gao; Chuan Dong; Hong‐li Hua; Feng‐Biao Guo
• Keywords: Scope (computer science); Popularity; Representation; Biological database

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 information/data, analytical tools, objectives. Here we present a review most popular databases model repositories, focusing on their scope, content including reactions, enzymes, compounds, genes, applicability. aims to help researchers choose suitable database or repository according data required, by providing an insight look each resource. Results Four pathways three repositories were selected basis popularity diversity. Our showed that vary many aspects, such as content, access tools. In addition, inconsistencies have observed nomenclature representation entities. reviewed do not offer brief description models’ characteristics simulation conditions. Conclusions among representing contents may hamper maximal use knowledge accumulated these particular area systems biology at large. Therefore, it is strongly recommended creators network developers should follow international standards for reactions metabolites. Besides, computationally generated could be obtained from utilized with manual curations they lack some important components necessary full functionality models.