MetaboLights

MetaboLights[1] is a data repository founded in 2012 for cross-species and cross-platform metabolomic studies that provides primary research data and meta data for metabolomic studies as well as a knowledge base for properties of individual metabolites.[2][3][4] The database is maintained by the European Bioinformatics Institute (EMBL-EBI) and the development is funded by Biotechnology and Biological Sciences Research Council (BBSRC).[5][6] As of July 2018, the MetaboLights browse functionality consists of 383 studies, two analytical platforms, NMR spectroscopy and mass spectrometry.[7]

MetaboLights
Content
DescriptionMetabolomics database
Data types
captured		metabolites from different species, metabolite structure, chemical properties, synonyms, experimental protocols, taxonomy, reactions, pathways, NMR spectra, mass spectra
Contact
Research centerEuropean Molecular Biology Laboratory
Laboratory European Bioinformatics Institute
Primary citationPMID 23109552
Access
Websitehttp://www.ebi.ac.uk/metabolights/
Download URLhttp://www.ebi.ac.uk/metabolights/download
Tools
WebMetaboLights Website
Miscellaneous
Data release
frequency		live
Curation policyManually curated

Semantic annotation is based on various ontologies and controlled vocabularies, including the BRENDA tissue ontology and the NCBI taxonomy. The metabolite structure data is linked to chemical databases, including ChemSpider, PubChem, and ChEBI. Links to metabolite databases, however, seem to be missing.

MetaboLights consists of two components:

  • a repository, that enables the metabolomic community to share experimental findings, data and protocols for any metabolomic study. (Fig. 1-2)
Fig.2 MetaboLights Study Protocol
  • a reference layer of individual metabolite compounds and their reference spectra including additional information on their biological roles, locations, concentrations and raw data from metabolomic experiments. (Fig. 3)
Fig.3 Metabolite Page

Scope and access

The data stored in MetaboLights is available for download from an FTP site and can be reused by the scientific community, where data sharing is considered an integral part of the scientific method.[8] Copyright and license information, however, is not easily identifiable.

MetaboLights includes user tools for submission of experiments using the ISA-TAB format for metadata tagging of all submissions.[9] Submitted studies are automatically assigned a stable unique accession number (e.g. MTBLS1) that can be used as a publication reference; MetaboLights is one of the repositories recommended by several scientific journals, including EMBO Journal[10] and Nature's Scientific Data.[11] There is also a guided submission process to help meet the Metabolomics Standards Initiative (MSI) recommendations for high quality data submissions for NMR and MS experiments.[12]

References
  1. Haug, K.; Salek, R. M.; Conesa, P.; Hastings, J.; De Matos, P.; Rijnbeek, M.; Mahendraker, T.; Williams, M.; Neumann, S.; Rocca-Serra, P.; Maguire, E.; Gonzalez-Beltran, A.; Sansone, S. -A.; Griffin, J. L.; Steinbeck, C. (2012). "Metabo Lights--an open-access general-purpose repository for metabolomics studies and associated meta-data". Nucleic Acids Research. 41 (Database issue): D781–D786. doi:10.1093/nar/gks1004. PMC 3531110. PMID 23109552.
  2. Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn; Maguire, Eamonn; Taylor, Chris; Hofmann, Oliver; Fang, Hong; Neumann, Steffen; Tong, Weida; Amaral-Zettler, Linda; et al. (27 January 2012). "Toward interoperable bioscience data". Nature Genetics. 44 (2): 121–126. doi:10.1038/ng.1054. PMC 3428019. PMID 22281772.
  3. Haug, Kenneth; Salek, Reza M.; Conesa, Pablo; Mahendraker, Tejasvi; Williams, Mark; Griffin, Julian L.; Steinbeck, Christoph. "MetaboLights - The new EBI Metabolomics database" (19). MetaboNews. Retrieved 5 May 2015.
  4. Salek, Reza M; Haug, Kenneth; Conesa, Pablo; Hastings, Janna; Williams, Mark; Mahendraker, Tejasvi; Maguire, Eamonn; GonzÌÁlez-BeltrÌÁn, Alejandra N; Rocca-Serra, Philippe; Sansone, Susanna-Assunta (29 April 2013). "The MetaboLights repository: curation challenges in metabolomics". Database. 2013: bat029. doi:10.1093/database/bat029. PMC 3638156. PMID 23630246.
  5. BBSRC Grant BB/I000933/1 "MetaboLights: Creating the missing Metabolomics community resource", http://www.bbsrc.ac.uk/research/grants/grants/AwardDetails.aspx?FundingReference=BB/I000933/1
  6. £30,000 Boost For UK-China Metabolomics Data Sharing, Asian Scientist Newsroom, 2015, retrieved 2015-06-11
  7. http://www.ebi.ac.uk/metabolights/browse
  8. Salek, R. M.; Haug, K.; Steinbeck, C. (17 May 2013). "Dissemination of Metabolomics results: Role of MetaboLights and COSMOS". Gigascience. 2 (1): 8. doi:10.1186/2047-217X-2-8. PMC 3658998. PMID 23683662.
  9. Rocca-Serra, Philippe; Brandizi, Marco; Maguire, Eamonn; Sklyar, Nataliya; Taylor, Chris; Begley, Kimberly; Field, Dawn; Harris, Stephen; Hide, Winston; Hofmann, Oliver; Neumann, Steffen; Sterk, Peter; Tong, Weida; Sansone, Susanna-Assunta (August 2, 2010). "ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level". Bioinformatics. 26 (18): 2354–2356. doi:10.1093/bioinformatics/btq415. PMC 2935443. PMID 20679334.
  10. Author Guidelines, http://emboj.embopress.org/authorguide
  11. Recommended Data Repositories, http://www.nature.com/sdata/data-policies/repositories
  12. Sansone, Susanna-Assunta; Fan, Teresa; Goodacre, Royston; Griffin, Julian L; Hardy, Nigel W; Kaddurah-Daouk, Rima; Kristal, Bruce S; Lindon, John; Mendes, Pedro; et al. (August 2007). "The Metabolomics Standards Initiative". Nature Biotechnology. 25 (8): 846–848. doi:10.1038/nbt0807-846b. PMID 17687353.
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