Automated assembly of species metabolomes through data submission into a public repository
Salek, Reza ; Conesa, Pablo ; Cochrane, Keeva ; Haug, Kenneth ; Williams, M. ; Kale, Namrata ; Moreno, P. ; Jayaseelan, Kalai Vanii ; Macias, Jose Ramon ; Nainala, Venkata Chandrasekhar ; Hall, R.D. ; Reed, Laura ; Viant, Mark ; Donovan, C. ; Steinbeck, Christoph - \ 2017
GigaScience 6 (2017)8. - ISSN 2047-217X - 4 p.
Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions.
The Time Is Right to Focus on Model Organism Metabolomes
Edison, Arthur ; Hall, Robert ; Junot, Christophe ; Karp, Peter ; Kurland, Irwin ; Mistrik, Robert ; Reed, Laura ; Saito, Kazuki ; Salek, Reza ; Steinbeck, Christoph ; Sumner, Lloyd ; Viant, Mark - \ 2016
Metabolites 6 (2016)1. - ISSN 2218-1989
Model organisms are an essential component of biological and biomedical research that can be used to study specific biological processes. These organisms are in part selected for facile experimental study. However, just as importantly, intensive study of a small number of model organisms yields important synergies as discoveries in one area of science for a given organism shed light on biological processes in other areas, even for other organisms. Furthermore, the extensive knowledge bases compiled for each model organism enable systems-level understandings of these species, which enhance the overall biological and biomedical knowledge for all organisms, including humans. Building upon extensive genomics research, we argue that the time is now right to focus intensively on model organism metabolomes. We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of evolutionary metabolomics, i.e., phylometabolomics. These efforts should focus on a series of established model organisms in microbial, animal and plant research.