COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access

Abstract

Metabolomics has become a crucial phenotyping technique in a range of research fields including medicine, the life sciences, biotechnology and the environmental sciences. This necessitates the transfer of experimental information between research groups, as well as potentially to publishers and funders. After the initial efforts of the metabolomics standards initiative, minimum reporting standards were proposed which included the concepts for metabolomics databases. Built by the community, standards and infrastructure for metabolomics are still needed to allow storage, exchange, comparison and re-utilization of metabolomics data. The Framework Programme 7 EU Initiative ‘coordination of standards in metabolomics’ (COSMOS) is developing a robust data infrastructure and exchange standards for metabolomics data and metadata. This is to support workflows for a broad range of metabolomics applications within the European metabolomics community and the wider metabolomics and biomedical communities’ participation. Here we announce our concepts and efforts asking for re-engagement of the metabolomics community, academics and industry, journal publishers, software and hardware vendors, as well as those interested in standardisation worldwide (addressing missing metabolomics ontologies, complex-metadata capturing and XML based open source data exchange format), to join and work towards updating and implementing metabolomics standards.

Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy

“…Considering that mzXML (Lin et al 2005) is the precursor to mzML, adoption at this level is very encouraging. However, more community efforts are required to further reinforce the benefits of using established data standards (Salek et al 2015; Rocca-Serra et al 2016). The majority of respondents (91%) produce datasets that comprise of 50–500 samples.…”

Metabolomics: beyond biomarkers and towards mechanisms

“…This programme funds six regional comprehensive metabolomic resource cores, a data repository and a coordination centre, to enable hands–on and online training in a range of areas, including data processing and interpretation. Another initiative, the Coordination of Standards in Metabolomics (COSMOS), is also helping to promote the standardization of metabolomics, by providing both experimental and data sharing, thus aiding new researchers in the field 40 (see Supplementary information S1 (box)). There are several tools, including the workflows mentioned, that are user-friendly but have advanced parameters for expert users, thus providing a resource for all levels of expertise 41,42 .…”

The future of metabolomics in ELIXIR

“…Since then, several initiatives have been set up to address elements of standardisation, particularly on data standards, building on the work of the MSI. The COSMOS project (COordination Of Standards In MetabOlomicS, http://www.cosmos-fp7.eu) 7 , coordinated data standards efforts amongst database providers, ontologists, software engineers and instrument vendors working towards open access data standardization and agreements. A Metabolomics Society Data Standards Task Group was subsequently established to foster and coordinate efforts in enabling efficient storage, compression, terminological annotation, exchange and verification of information within metabolomics datasets.…”

“…Following the formation of national infrastructures for metabolomics, for example with the French infrastructure in Metabolomics and Fluxomics MetaboHUB and the Netherlands Metabolomics Centre Foundation (NMC), the COSMOS initiative 7 for the coordination of standards in metabolomics provided the first coordination action between all relevant efforts in metabolomics in Europe. Leading to the establishment of the worldwide metabolomeXchange network, COSMOS paved the way for PhenoMeNal.…”