MetaboLights: An Open‐Access Database Repository for Metabolomics Data

Namrata S. Kale1, Kenneth Haug1, Pablo Conesa1, Kalaivani Jayseelan1, Pablo Moreno1, Philippe Rocca‐Serra2, Venkata Chandrasekhar Nainala1, Rachel A. Spicer1, Mark Williams1, Xuefei Li3, Reza M. Salek1, Julian L. Griffin3, Christoph Steinbeck1

1 European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, 2 Oxford e‐Research Centre, University of Oxford, Oxford, 3 MRC HNR, Elsie Widdowson Laboratory, Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 14.13
DOI:  10.1002/0471250953.bi1413s53
Online Posting Date:  March, 2016
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

MetaboLights is the first general purpose, open‐access database repository for cross‐platform and cross‐species metabolomics research at the European Bioinformatics Institute (EMBL‐EBI). Based upon the open‐source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user‐friendly submission tools. © 2016 by John Wiley & Sons, Inc.

Keywords: metabolomics; open‐access; cross‐species; cross‐platform; raw data; metadata; metabolites

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Basic Protocol 1: Querying the Metabolights Repository for Metabolomics Studies
  • Basic Protocol 2: Querying Metabolights Reference Layer for Metabolites
  • Basic Protocol 3: Querying the Metabolights Repository for Target Organism
  • Basic Protocol 4: Submitting Private Metabolomics Studies to the Metabolights Repository
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
  Gremse, M., Chang, A., Schomburg, I., Grote, A., Scheer, M., Ebeling, C., and Schomburg, D. 2011. The BRENDA Tissue Ontology (BTO): The first all‐integrating ontology of all organisms for enzyme sources. Nucl. Acids Res. 39:D507‐D513. doi: 10.1093/nar/gkq968.
  Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. 2013. The ChEBI reference database and ontology for biologically relevant chemistry: Enhancements for 2013. Nucl. Acids Res. 41:D456‐D463. doi: 10.1093/nar/gks1146.
  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., González‐Beltrán, A., Sansone, S.A., Griffin, J.L., and Steinbeck, C. 2013. MetaboLights–an open‐access general‐purpose repository for metabolomics studies and associated meta‐data. Nucl. Acids Res. 41:D781‐D786. doi: 10.1093/nar/gks1004.
  Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., Oda, Y, Kakazu, Y., Kusano, M., Tohge, T., Matsuda, F., Sawada, Y., Hirai, M.Y., Nakanishi, H., Ikeda, K., Akimoto, N., Maoka, T., Takahashi, H., Ara, T., Sakurai, N., Suzuki, H., Shibata, D., Neumann, S., Iida, T., Tanaka, K., Funatsu, K., Matsuura, F., Soga, T., Taguchi, R., Saito, K., and Nishioka, T. 2010. MassBank: A public repository for sharing mass spectral data for life sciences. J. Mass Spectrom. 45:703‐714. doi: 10.1002/jms.1777.
  Ludwig, C., Easton, J.M., Lodi, A., Tiziani, S., Manzoor, S.E, Southam, A.D., Byrne, J.J., Bishop, L.M., He, S., Arvanitis, T.N., Günther, U.L., and Viant, M.R. 2012. Birmingham Metabolite Library: A publicly accessible database of 1‐D 1H and 2‐D 1H J‐resolved NMR spectra of authentic metabolite standards (BML‐NMR). Metabolomics 8:8‐18. doi: 10.1007/s11306-011-0347-7.
  Morgat, A., Axelsen, K.B., Lombardot, T., Alcántara, R., Aimo, L., Zerara, M., Niknejad, A., Belda, E., Hyka‐Nouspikel, N., Coudert, E., Redaschi, N., Bougueleret, L., Steinbeck, C., Xenarios, I., and Bridge, A. 2015. Updates in Rhea‐a manually curated resource of biochemical reactions. Nucl. Acids Res. 43:D459‐D64. doi: 10.1093/nar/gku961.
  Patti, G.J., Yanes O., and Siuzdak G. 2012. Innovation: Metabolomics: The apogee of the omics trilogy. Nat. Rev. Mol. Cell Biol. 13:263‐269. doi: 10.1038/nrm3314.
  Rocca‐Serra, P., Brandizi, M., Maguire, E., Sklyar, N., Taylor, C., Begley, K., Field, D., Harris, S., Hide, W., Hofmann, O., Neumann, S., Sterk, P., Tong, W., and Sansone, S.A. 2010. ISA software suite: Supporting standards‐compliant experimental annotation and enabling curation at the community level. Bioinformatics 26:2354‐2356. doi: 10.1093/bioinformatics/btq415.
  Salek, R.M., Haug, K., Conesa, P., Hastings, J., Williams, M., Mahendraker, T., Maguire, E., González‐Beltrán, A.N., Rocca‐Serra, P., Sansone, S.A., and Steinbeck, C. 2013. The MetaboLights repository: Curation challenges in metabolomics. Database 2013:bat029. doi: 10.1093/database/bat029.
  Sansone, S.A., Fan, T., Goodacre, R., Griffin, J.L., Hardy, N.W., Kaddurah‐Daouk, R., Kristal, B.S., Lindon, J., Mendes, P., Morrison, N., Nikolau, B., Robertson, D., Sumner, L.W., Taylor, C., van der Werf, M., van Ommen, B., and Fiehn, O. 2007. The metabolomics standards initiative. Nat. Biotechnol. 25:846‐848. doi: 10.1038/nbt0807-846b.
  Smith, C.A., O'Maille, G., Want, E.J., Qin, C., Trauger, S.A., Brandon, T.R., Custodio, D.E., Abagyan R., and Siuzdak, G. 2005. METLIN: A metabolite mass spectral database. Ther. Drug Monit. 27:747‐751. doi: 10.1097/01.ftd.0000179845.53213.39.
  Ulrich, E.L., Akutsu, H., Doreleijers, J.F., Harano, Y., Ioannidis, Y.E., Lin, J., Livny, M., Mading, S., Maziuk, D., Miller, Z., Nakatani, E., Schulte, C.F., Tolmie, D.E., Kent Wenger, R., Yao, H., and Markley J.L. 2008. BioMagResBank. Nucl. Acids Res. 36:D402‐D408. doi: 10.1093/nar/gkm957.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library