» Articles » PMID: 29043062

The Future of Metabolomics in ELIXIR

Abstract

Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.

Citing Articles

ELIXIR and Toxicology: a community in development.

Martens M, Stierum R, Schymanski E, Evelo C, Aalizadeh R, Aladjov H F1000Res. 2023; 10.

PMID: 37842337 PMC: 10568213. DOI: 10.12688/f1000research.74502.2.


Emerging technologies and their impact on regulatory science.

Anklam E, Bahl M, Ball R, Beger R, Cohen J, Fitzpatrick S Exp Biol Med (Maywood). 2021; 247(1):1-75.

PMID: 34783606 PMC: 8749227. DOI: 10.1177/15353702211052280.


The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform.

Bray S, Lucas X, Kumar A, Gruning B J Cheminform. 2021; 12(1):40.

PMID: 33431029 PMC: 7268608. DOI: 10.1186/s13321-020-00442-7.


Capillary Electrophoresis-Mass Spectrometry at Trial by Metabo-Ring: Effective Electrophoretic Mobility for Reproducible and Robust Compound Annotation.

Drouin N, van Mever M, Zhang W, Tobolkina E, Ferre S, Servais A Anal Chem. 2020; 92(20):14103-14112.

PMID: 32961048 PMC: 7581015. DOI: 10.1021/acs.analchem.0c03129.


Metabolic Fingerprint of Chronic Obstructive Lung Diseases: A New Diagnostic Perspective.

Tsoukalas D, Sarandi E, Thanasoula M, Docea A, Tsilimidos G, Calina D Metabolites. 2019; 9(12).

PMID: 31779131 PMC: 6949962. DOI: 10.3390/metabo9120290.


References
1.
Afendi F, Okada T, Yamazaki M, Hirai-Morita A, Nakamura Y, Nakamura K . KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol. 2011; 53(2):e1. DOI: 10.1093/pcp/pcr165. View

2.
Salek R, Neumann S, Schober D, Hummel J, Billiau K, Kopka J . COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics. 2015; 11(6):1587-1597. PMC: 4605977. DOI: 10.1007/s11306-015-0810-y. View

3.
Kell D, Oliver S . The metabolome 18 years on: a concept comes of age. Metabolomics. 2016; 12(9):148. PMC: 5009154. DOI: 10.1007/s11306-016-1108-4. View

4.
Goecks J, Nekrutenko A, Taylor J . Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010; 11(8):R86. PMC: 2945788. DOI: 10.1186/gb-2010-11-8-r86. View

5.
Rocca-Serra P, Salek R, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A . Data standards can boost metabolomics research, and if there is a will, there is a way. Metabolomics. 2015; 12:14. PMC: 4648992. DOI: 10.1007/s11306-015-0879-3. View