Article (Scientific journals)
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
Noronha, Alberto; Modamio Chamarro, Jennifer; Jarosz, Yohan et al.
2018In Nucleic Acids Research
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Abstract :
[en] 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, www.vmh.life) database encapsulating current knowledge of human metabolism within five interlinked resources ‘Human metabolism’, ‘Gut microbiome’, ‘Disease’, ‘Nutrition’, and ‘ReconMaps’. The VMH captures 5180 unique metabolites, 17 730 unique reactions, 3695 human genes, 255 Mendelian diseases, 818 microbes, 632 685 microbial genes and 8790 food items. The VMH’s unique features are (i) the hosting of 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; (v) user feedback option for community engagement and (vi) the connection of its entities to 57 other web resources. The VMH represents a novel, interdisciplinary database for data interpretation and hypothesis generation to the biomedical community.
Disciplines :
Biotechnology
Biochemistry, biophysics & molecular biology
Author, co-author :
Noronha, Alberto ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Modamio Chamarro, Jennifer ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Jarosz, Yohan ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Guerard, Elisabeth ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Sompairac, Nicolas;  PSL Research University INSERM U900F > Institut Curie ; MINES ParisTech > CBIO-Centre for Computational Biology, PSL Research University
Preciat Gonzalez, German Andres ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Danielsdottir, Anna Dröfn ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Krecke, Max ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Merten, Diane ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Haraldsdottir, Hulda ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Heinken, Almut Katrin ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Heirendt, Laurent  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Magnusdottir, Stefania ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Ravcheev, Dmitry ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Sahoo, Swagatika ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Gawron, Piotr ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Friscioni, Lucia ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Garcia Santa Cruz, Beatriz ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Prendergast, Mabel
Puente, Alberto ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Rodrigues, Mariana
Roy, Akansha ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Mouss, Rouquaya ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Wiltgen, Luca ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Zagare, Alise ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
John, Elisabeth ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Krüger, Maren ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Kuperstein, Inna;  PSL Research University, INSERM U900 > Institut Curie ; MINES ParisTech, PSL Research University > CBIO-Centre for Computational Biology
Zinovyev, Andrei;  PSL Research University, INSERM U900 > Institut Curie ; MINES ParisTech, PSL Research University > CBIO-Centre for Computational Biology
Schneider, Reinhard ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Fleming, Ronan MT ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Thiele, Ines ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
More authors (22 more) Less
External co-authors :
yes
Language :
English
Title :
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
Publication date :
29 October 2018
Journal title :
Nucleic Acids Research
ISSN :
1362-4962
Publisher :
Oxford University Press, Oxford, United Kingdom
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
Luxembourg National Research Fund (FNR) through the ATTRACT program [FNR/A12/01]
FNR CORE program [C16/BM/11332722]; FNR OPEN grant [FNR/O16/11402054]
FNR National Centre of Excellence in Research (NCER) on Parkinson's disease
European Union's Horizon 2020 research and innovation program under grant agreement [668738]
European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [757922]
Art2Cure ASBL
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