MetaboLights

MetaboLights
Content
Description Metabolomics 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 United Kingdom 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 policy Manually 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 June 2015, the MetaboLights browse functionality consists of 99 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
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: D781. doi:10.1093/nar/gks1004. PMC 3531110Freely accessible. 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 3428019Freely accessible. 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 March 2013. Check date values in: |access-date= (help)
  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. 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.
  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.
  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.

External links

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