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. 2017 Aug 1;6(8):1-4.
doi: 10.1093/gigascience/gix062.

Automated assembly of species metabolomes through data submission into a public repository

Reza M Salek  1 , Pablo Conesa  1 , Keeva Cochrane  1 , Kenneth Haug  1 , Mark Williams  1 , Namrata Kale  1 , Pablo Moreno  1 , Kalai Vanii Jayaseelan  1 , Jose Ramon Macias  1 , Venkata Chandrasekhar Nainala  1 , Robert D Hall  2 , Laura K Reed  3 , Mark R Viant  4 , Claire O'Donovan  1 , Christoph Steinbeck  1   5
Affiliations

Automated assembly of species metabolomes through data submission into a public repository

Reza M Salek et al. Gigascience. .

Abstract

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.

Keywords: curation; databases; metabolomics; species metabolomes.

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Figures

Figure 1:
Figure 1:
Growth in data repositories at the EMBL-EBI. The graph shows the data volume in each of the repositories over time on a logarithmic scale. Shown are repositories for controlled access human data, raw sequencing data, microarray, proteomics, and metabolomics data. Archives were started at different moments in history. Metabolomics shows the steepest growth of all repositories at the EMBL-EBI.
Figure 2:
Figure 2:
Bar chart distribution of the number of studies in MetaboLights by species. The distribution reflects the most used model species in biological and biomedical research.
Figure 3:
Figure 3:
Long-tail distribution of metabolites per species in the MetaboLights reference layer. A few model species are covered very well, while for the majority of more than 1600 species, only a few metabolites were reported. These data cover both metabolites reported in studies and those manually added from the literature by MetaboLights and ChEBI curators. a) Truncated version with the 30 most annotated species. b) Full graph.
See this image and copyright information in PMC

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