MetabolomeXchange - An international data aggregation and notification service for metabolomics, with access to 160+ publicly available datasets

Although Metabolomics is considered a fairly young player in the world of –omics we have seen an impressive increase of both general- and special- purpose databases for storing and sharing Metabolomics data. The first steps were made back in 2005 when the Metabolomics Standards Initiative (MSI) drafted the first standards enabling the Metabolomics community to share their insights.  Together with some of the original people behind the MSI, a new effort was started in 2012 called COSMOS [2]. The aim of COSMOS is to build on the foundational work by PSI [3] and MSI and further develop and contribute to data exchange formats, including open formats in MS and NMR, the reporting of metabolite quantification and metabolite identification, and the experimental metadata.

At the beginning of 2014, we started to develop a platform that links existing Metabolomics databases at metadata level.  This allows the Metabolomics community to search all publicly available datasets in one place. In addition to the search engine it is used to host additional services like RSS feeds, an API and in the near future RDF output.

The initial release of the platform was June 1st 2014 and it was officially announced as “MetabolomeXchange” [4] at the Metabolomics2014 conference in Japan later that month. Now, only 6 months later, we have four providers connected that together share over 160 datasets with more being added every month.

To create a sustainable infrastructure and encourage the re-use of our work we share all software through GitHub [5] under an Apache 2.0 license.

[1] http://msi-workgroups.sourceforge.net/
[2] http://www.cosmos-fp7.eu/
[3] http://www.psidev.info/
[4] http://metabolomexchange.org/
[5] https://github.com/leidenuniv-lacdr-abs/metabolomexchange


Screenshots

fig 1. Homepage - with latest 5 datasets, search option and tag-cloud.

 

 

fig 2. Search page - showing datasets found when searching for Valine.

 

 

fig 3. RSS - example of rss output based on search.

 

 

fig 4. Stats - overview of datasets added over time.

 

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