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'''MetaboLights'''<ref>{{Cite journal | doi = 10.1093/nar/gks1004| title = Metabo ''Lights''--an open-access general-purpose repository for metabolomics studies and associated meta-data| journal = Nucleic Acids Research| volume = 41| issue = Database issue| pages = D781–D786| year = 2012| last1 = Haug | first1 = K.| last2 = Salek | first2 = R. M.| last3 = Conesa | first3 = P.| last4 = Hastings | first4 = J.| last5 = De Matos | first5 = P.| last6 = Rijnbeek | first6 = M.| last7 = Mahendraker | first7 = T.| last8 = Williams | first8 = M.| last9 = Neumann | first9 = S.| last10 = Rocca-Serra | first10 = P.| last11 = Maguire | first11 = E.| last12 = Gonzalez-Beltran | first12 = A.| last13 = Sansone | first13 = S. -A. | last14 = Griffin | first14 = J. L.| last15 = Steinbeck | first15 = C. | pmid=23109552 | pmc=3531110}}</ref> is a data repository founded in 2012 for cross-[[species]] and cross-platform [[Metabolomics|metabolomic]] studies that provides primary research data and meta data for metabolomic studies as well as a knowledge base for properties of individual [[metabolites]].<ref>{{cite journal|last1=Sansone|first1=Susanna-Assunta|last2=Rocca-Serra|first2=Philippe|last3=Field|first3=Dawn|last4=Maguire|first4=Eamonn|last5=Taylor|first5=Chris|last6=Hofmann|first6=Oliver|last7=Fang|first7=Hong|last8=Neumann|first8=Steffen|last9=Tong|first9=Weida|last10=Amaral-Zettler|first10=Linda|title=Toward interoperable bioscience data|journal=Nature Genetics|date=27 January 2012|volume=44|issue=2|pages=121–126|doi=10.1038/ng.1054|pmid=22281772|display-authors=etal|pmc=3428019}}</ref><ref>{{cite news|last1=Haug|first1=Kenneth|last2=Salek|first2=Reza M.|last3=Conesa|first3=Pablo|last4=Mahendraker|first4=Tejasvi|last5=Williams|first5=Mark|last6=Griffin|first6=Julian L.|last7=Steinbeck|first7=Christoph|title=MetaboLights - The new EBI Metabolomics database|url=http://www.metabonews.ca/Mar2013/MetaboNews_Mar2013.htm|access-date=5 May 2015|issue=19|publisher=MetaboNews}}</ref><ref>{{cite journal|last1=Salek|first1=Reza M|last2=Haug|first2=Kenneth|last3=Conesa|first3=Pablo|last4=Hastings|first4=Janna|last5=Williams|first5=Mark|last6=Mahendraker|first6=Tejasvi|last7=Maguire|first7=Eamonn|last8=GonzÌÁlez-BeltrÌÁn|first8=Alejandra N|last9=Rocca-Serra|first9=Philippe|last10=Sansone|first10=Susanna-Assunta|title=The MetaboLights repository: curation challenges in metabolomics|journal=Database|date=29 April 2013|doi=10.1093/database/bat029|pmid=23630246|volume=2013|pages=bat029|pmc=3638156}}</ref>
'''MetaboLights'''<ref name=metabolights>{{cite q|Q27818909}}</ref> is a data repository founded in 2012 for cross-[[species]] and cross-platform [[Metabolomics|metabolomic]] studies that provides primary research data and meta data for metabolomic studies as well as a knowledge base for properties of individual [[metabolites]].<ref name=towards>{{cite q|Q28090939}}</ref><ref>{{cite news|last1=Haug|first1=Kenneth|last2=Salek|first2=Reza M.|last3=Conesa|first3=Pablo|last4=Mahendraker|first4=Tejasvi|last5=Williams|first5=Mark|last6=Griffin|first6=Julian L.|last7=Steinbeck|first7=Christoph|title=MetaboLights - The new EBI Metabolomics database|url=http://www.metabonews.ca/Mar2013/MetaboNews_Mar2013.htm|access-date=5 May 2015|issue=19|publisher=MetaboNews}}</ref><ref name=challenges>{{cite q|Q28707581}}</ref>
The database is maintained by the [[European Bioinformatics Institute|European Bioinformatics Institute (EMBL-EBI)]] and the development is funded by [[Biotechnology and Biological Sciences Research Council]] (BBSRC).<ref>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</ref><ref>{{Citation |year=2015 |title=£30,000 Boost For UK-China Metabolomics Data Sharing |publisher=Asian Scientist Newsroom |url=http://www.asianscientist.com/2015/05/academia/30000-boost-uk-china-metabolomics-data-sharing/ |access-date=2015-06-11 }}</ref> As of July 2018, the MetaboLights browse functionality consists of 383 studies, two analytical platforms, [[NMR spectroscopy]] and [[mass spectrometry]].<ref>{{Cite web|url=http://www.ebi.ac.uk/metabolights/browse|title = Browse}}</ref>
The database is maintained by the [[European Bioinformatics Institute|European Bioinformatics Institute (EMBL-EBI)]] and the development is funded by [[Biotechnology and Biological Sciences Research Council]] (BBSRC).<ref>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</ref><ref>{{Citation |year=2015 |title=£30,000 Boost For UK-China Metabolomics Data Sharing |publisher=Asian Scientist Newsroom |url=http://www.asianscientist.com/2015/05/academia/30000-boost-uk-china-metabolomics-data-sharing/ |access-date=2015-06-11 }}</ref> As of July 2018, the MetaboLights browse functionality consists of 383 studies, two analytical platforms, [[NMR spectroscopy]] and [[mass spectrometry]].<ref>{{Cite web|url=http://www.ebi.ac.uk/metabolights/browse|title = Browse}}</ref>


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==Scope and access==
==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]].<ref name=pmid23683662>{{cite journal|last1=Salek|first1=R. M.|last2=Haug|first2=K.|last3=Steinbeck|first3=C.|title=Dissemination of Metabolomics results: Role of MetaboLights and COSMOS|journal=GigaScience|date=17 May 2013|volume=2|issue=1|pages=8|doi=10.1186/2047-217X-2-8|pmid=23683662|pmc=3658998}}</ref> Copyright and license information, however, is not easily identifiable.
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]].<ref name=pmid23683662>{{cite q|Q21195826}}</ref> 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.<ref>{{cite journal|last1=Rocca-Serra|first1=Philippe|last2=Brandizi|first2=Marco|last3=Maguire|first3=Eamonn|last4=Sklyar|first4=Nataliya|last5=Taylor|first5=Chris|last6=Begley|first6=Kimberly|last7=Field|first7=Dawn|last8=Harris|first8=Stephen|last9=Hide|first9=Winston|last10=Hofmann|first10=Oliver|last11=Neumann|first11=Steffen|last12=Sterk|first12=Peter|last13=Tong|first13=Weida|last14=Sansone|first14=Susanna-Assunta|title=ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level|journal=Bioinformatics|date=August 2, 2010|volume=26|issue=18|pages=2354–2356|doi=10.1093/bioinformatics/btq415|pmid=20679334|pmc=2935443}}</ref> 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 journal]]s, including [[EMBO Journal]]<ref>Author Guidelines, http://emboj.embopress.org/authorguide</ref> and [[Nature Publishing Group|Nature]]'s [[Scientific Data (journal)|Scientific Data]].<ref>Recommended Data Repositories, http://www.nature.com/sdata/data-policies/repositories</ref> 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.<ref>{{cite journal|last1=Sansone|first1=Susanna-Assunta|last2=Fan|first2=Teresa|last3=Goodacre|first3=Royston|last4=Griffin|first4=Julian L|last5=Hardy|first5=Nigel W|last6=Kaddurah-Daouk|first6=Rima|last7=Kristal|first7=Bruce S|last8=Lindon|first8=John|last9=Mendes|first9=Pedro|display-authors=etal|title=The Metabolomics Standards Initiative|journal=Nature Biotechnology|date=August 2007|volume=25|issue=8|pages=846–848|doi=10.1038/nbt0807-846b|pmid=17687353|doi-access=free}}</ref>
MetaboLights includes user tools for submission of experiments using the [[ISA-TAB]] format for [[metadata]] tagging of all submissions.<ref name=isa>{{cite q|Q28749402}}</ref> 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 journal]]s, including [[EMBO Journal]]<ref>Author Guidelines, http://emboj.embopress.org/authorguide</ref> and [[Nature Publishing Group|Nature]]'s [[Scientific Data (journal)|Scientific Data]].<ref>Recommended Data Repositories, http://www.nature.com/sdata/data-policies/repositories</ref> 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.<ref name=init>{{cite q|Q56982425}}</ref>


==References==
==References==
{{reflist}}
{{reflist}}


==External links==
* [http://www.ebi.ac.uk/metabolights/ Official website]
* [https://www.ebi.ac.uk/training/online/course/metabolights-quick-tour-0 MetaboLights Tutorial]-MetaboLights Train On-Line
* [http://www.bmrb.wisc.edu/ Biological Magnetic Resonance Data Bank]- A repository for NMR spectroscopy
* http://isa-tools.org/ - The Investigation/Study/Assay format for reporting metadata
* [http://www.nature.com/nbt/journal/v25/n8/full/nbt0807-846b.html Metabolites Standard Initiative]- (Correspondence) ''Nature Biotechnology'' '''25''': 2007. [[Digital object identifier|doi]][http://www.nature.com/nbt/journal/v25/n8/full/nbt0807-846b.html 10.1038/nbt0807-846b].
* Nature [http://www.nature.com/sdata/about Scientific Data]- Open access, online-only publication for descriptions of scientifically valuable datasets.
* http://metabolomexchange.org/- International collaboration of metabolomics data repositories.
* http://services.cbib.u-bordeaux2.fr/MERYB/ - Plant metabolomics knowledgebase.
* http://www.metabolomicsworkbench.org/ - National and International repository for metabolomic data and metadata.


[[Category:Biological databases]]
[[Category:Biological databases]]

Revision as of 21:12, 20 February 2022

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
LaboratoryUnited Kingdom 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

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:

  • 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. ^ 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 (Database issue): D781-6. doi:10.1093/NAR/GKS1004. ISSN 0305-1048. PMC 3531110. PMID 23109552. Wikidata Q27818909.
  2. ^ Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; et al. (27 January 2012). "Toward interoperable bioscience data". Nature Genetics. 44 (2): 121–6. doi:10.1038/NG.1054. ISSN 1061-4036. PMC 3428019. PMID 22281772. Wikidata Q28090939.
  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 (0): bat029. doi:10.1093/DATABASE/BAT029. ISSN 1758-0463. PMC 3638156. PMID 23630246. Wikidata Q28707581.
  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. Wikidata Q21195826.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  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): 2354–6. doi:10.1093/BIOINFORMATICS/BTQ415. ISSN 1367-4803. PMC 2935443. PMID 20679334. Wikidata Q28749402.
  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. Wikidata Q56982425.
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