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.

Keywords: Coordination and data sharing community; Data exchange; Data standards; Metabolomics; Metabonomics; e-Infrastructure.

Fig. 1

Initial model for the COSMOS data deposition workflow system. The data deposition cycle is initiated when a Submitter (who has generated or owns the study material) submits his/her metabolomics study to a specific associated database (1). Once the data submission has been completed, fulfilling the requirement of the associated repository submission guideline, a unique COSMOS accession number will be generated. The COSMOS engine will then properly annotate, format and store the minimum agreed metadata according to proposed reporting standards suggested by COSMOS partners (2, 3). COSMOS will bring together publishers and other metabolomics repositories to come to final agreement on a data workflow specifying minimum metadata exchange, associated raw data, source code and any additional information that can be shared (4, 5). Open access to the system will ensure that any interested party can benefit from the standardized resources

Fig. 2

COSMOS initiative workflow. Overview of COSMOS initiative role in metabolomics standards, databases, data exchange and dissemination of metabolomics experiments. Green metabolomics labs experimental workflow from lab based data generation, metadata collection to interaction with LIMS systems. Pink standardisation initiative and minimum information reporting agreement involved or used within the COSMOS project. Blue Dissemination and role of journal and link to other e-infrastructures. White databases and tools used to capture experimental data and metadata (Color figure online)