The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
By Alberto Noronha, J. Modamio, Y. Jarosz, Nicolas Sompairac, German A. Preciat Gonzalez, A. D. Daníelsdóttir, Max Krecké, D. Merten, Hulda S. Haraldsdóttir, Almut Heinken and 22 more. bioRxiv, 2018
365 citations recorded by the source corpus.
A multitude of factors contribute to complex diseases and can be measured with “omics” methods. Databases facilitate data interpretation for underlying mechanisms. Here, we describe the Virtual Metabolic Human (VMH, http://vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources “Human metabolism”, “Gut microbiome”, “Disease”, “Nutrition”, and “ReconMaps”. The VMH captures 5,180 unique metabolites, 17,730 unique reactions, 3,288 human genes, 255 Mendelian diseases, 818 microbes, 632,685 microbial genes, and 8,790 food items. The VMH’s unique features are i) the hosting the metabolic reconstructions of human and gut microbes amenable for metabolic modeling; ii) seven human metabolic maps for data visualization; iii) a nutrition designer; iv) a user-friendly webpage and application-programming interface to access its content; and v) user feedback option for community engagement. We demonstrate with four examples the VMH’s utility. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.
Subfields: Molecular Biology, Physiology
View Paper: https://www.semanticscholar.org/paper/44b3f52d707edbcc92d78863085c6c8660250d95
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Citations in the corpus
- Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community (2019, methodology): “COBRA has also been used as a tool to develop models in order to subsequently predict dietary supplements for treating Crohn’s disease [81] and to integrate human and gut microbiome metabolism with nutrition and disease in the Virtual Metabolic Human database [82].”