MetaboLights

Last updated
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 center European Molecular Biology Laboratory
Laboratory Flag of the United Kingdom.svg European Bioinformatics Institute
Primary citation PMID   23109552
Access
Website http://www.ebi.ac.uk/metabolights/
Download URL http://www.ebi.ac.uk/metabolights/download
Tools
Web MetaboLights Website
Miscellaneous
Data release
frequency		live
Curation policyManually curated

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]

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:

Fig.2 MetaboLights Study Protocol Protocol.png
Fig.2 MetaboLights Study Protocol
Fig.3 Metabolite Page Metabolite Page.png
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. ↑ Kenneth Haug; Reza M. Salek; Pablo Conesa; et al. (January 2013). "MetaboLights--an open-access general-purpose repository for metabolomics studies and associated meta-data". Nucleic Acids Research . 41 (D1): D781 –D786. doi: 10.1093/NAR/GKS1004 . ISSN   0305-1048. PMC   3531110 . PMID   23109552.
  2. ↑ Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; et al. (27 January 2012). "Toward interoperable bioscience data". Nature Genetics . 44 (2): 121–126. doi:10.1038/NG.1054. ISSN   1061-4036. 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". No. 19. MetaboNews. Retrieved 5 May 2015.
  4. ↑ Reza M. Salek; Kenneth Haug; Pablo Conesa; et al. (2013). "The MetaboLights repository: curation challenges in metabolomics". Database . 2013 bat029. doi: 10.1093/DATABASE/BAT029 . ISSN   1758-0463. 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. ↑ "Browse".
  8. ↑ Reza M Salek; Kenneth Haug; Christoph Steinbeck (2013). "Dissemination of metabolomics results: role of MetaboLights and COSMOS". GigaScience . 2 (1) 8. doi: 10.1186/2047-217X-2-8 . ISSN   2047-217X. PMC   3658998 . PMID   23683662.
  9. ↑ Philippe Rocca-Serra; Marco Brandizi; Eamonn Maguire; et al. (15 September 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 . ISSN   1367-4803. 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. ↑ "The Metabolomics Standards Initiative". Nature Biotechnology . 25 (8): 846–848. August 2007. doi:10.1038/NBT0807-846B. ISSN   1087-0156. PMID   17687353.
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