Literature DB >> 26612985

Data standards can boost metabolomics research, and if there is a will, there is a way.

Philippe Rocca-Serra1, Reza M Salek2, Masanori Arita3,4, Elon Correa5,6, Saravanan Dayalan7, Alejandra Gonzalez-Beltran1, Tim Ebbels8, Royston Goodacre6, Janna Hastings2, Kenneth Haug2, Albert Koulman9, Macha Nikolski10,11, Matej Oresic12, Susanna-Assunta Sansone1, Daniel Schober13, James Smith9,14, Christoph Steinbeck2, Mark R Viant15, Steffen Neumann13.   

Abstract

Thousands of articles using metabolomics approaches are published every year. With the increasing amounts of data being produced, mere description of investigations as text in manuscripts is not sufficient to enable re-use anymore: the underlying data needs to be published together with the findings in the literature to maximise the benefit from public and private expenditure and to take advantage of an enormous opportunity to improve scientific reproducibility in metabolomics and cognate disciplines. Reporting recommendations in metabolomics started to emerge about a decade ago and were mostly concerned with inventories of the information that had to be reported in the literature for consistency. In recent years, metabolomics data standards have developed extensively, to include the primary research data, derived results and the experimental description and importantly the metadata in a machine-readable way. This includes vendor independent data standards such as mzML for mass spectrometry and nmrML for NMR raw data that have both enabled the development of advanced data processing algorithms by the scientific community. Standards such as ISA-Tab cover essential metadata, including the experimental design, the applied protocols, association between samples, data files and the experimental factors for further statistical analysis. Altogether, they pave the way for both reproducible research and data reuse, including meta-analyses. Further incentives to prepare standards compliant data sets include new opportunities to publish data sets, but also require a little "arm twisting" in the author guidelines of scientific journals to submit the data sets to public repositories such as the NIH Metabolomics Workbench or MetaboLights at EMBL-EBI. In the present article, we look at standards for data sharing, investigate their impact in metabolomics and give suggestions to improve their adoption.

Entities:  

Keywords:  Data sharing; Data standards; Experimental metadata; Mass spectrometry; Metabolomics; NMR

Year:  2015        PMID: 26612985      PMCID: PMC4648992          DOI: 10.1007/s11306-015-0879-3

Source DB:  PubMed          Journal:  Metabolomics        ISSN: 1573-3882            Impact factor:   4.290


  47 in total

1.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

2.  Summary recommendations for standardization and reporting of metabolic analyses.

Authors:  John C Lindon; Jeremy K Nicholson; Elaine Holmes; Hector C Keun; Andrew Craig; Jake T M Pearce; Stephen J Bruce; Nigel Hardy; Susanna-Assunta Sansone; Henrik Antti; Par Jonsson; Clare Daykin; Mahendra Navarange; Richard D Beger; Elwin R Verheij; Alexander Amberg; Dorrit Baunsgaard; Glenn H Cantor; Lois Lehman-McKeeman; Mark Earll; Svante Wold; Erik Johansson; John N Haselden; Kerstin Kramer; Craig Thomas; Johann Lindberg; Ina Schuppe-Koistinen; Ian D Wilson; Michael D Reily; Donald G Robertson; Hans Senn; Arno Krotzky; Sunil Kochhar; Jonathan Powell; Frans van der Ouderaa; Robert Plumb; Hartmut Schaefer; Manfred Spraul
Journal:  Nat Biotechnol       Date:  2005-07       Impact factor: 54.908

3.  MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

Authors:  Guillaume Robichaud; Kenneth P Garrard; Jeremy A Barry; David C Muddiman
Journal:  J Am Soc Mass Spectrom       Date:  2013-03-28       Impact factor: 3.109

4.  A cross-platform toolkit for mass spectrometry and proteomics.

Authors:  Matthew C Chambers; Brendan Maclean; Robert Burke; Dario Amodei; Daniel L Ruderman; Steffen Neumann; Laurent Gatto; Bernd Fischer; Brian Pratt; Jarrett Egertson; Katherine Hoff; Darren Kessner; Natalie Tasman; Nicholas Shulman; Barbara Frewen; Tahmina A Baker; Mi-Youn Brusniak; Christopher Paulse; David Creasy; Lisa Flashner; Kian Kani; Chris Moulding; Sean L Seymour; Lydia M Nuwaysir; Brent Lefebvre; Frank Kuhlmann; Joe Roark; Paape Rainer; Suckau Detlev; Tina Hemenway; Andreas Huhmer; James Langridge; Brian Connolly; Trey Chadick; Krisztina Holly; Josh Eckels; Eric W Deutsch; Robert L Moritz; Jonathan E Katz; David B Agus; Michael MacCoss; David L Tabb; Parag Mallick
Journal:  Nat Biotechnol       Date:  2012-10       Impact factor: 54.908

5.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Authors:  Jeremy Goecks; Anton Nekrutenko; James Taylor
Journal:  Genome Biol       Date:  2010-08-25       Impact factor: 13.583

6.  MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

Authors:  Stephan Beisken; Mark Earll; David Portwood; Mark Seymour; Christoph Steinbeck
Journal:  Mol Inform       Date:  2014-04-22       Impact factor: 3.353

7.  Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments.

Authors:  Kyle D Bemis; April Harry; Livia S Eberlin; Christina Ferreira; Stephanie M van de Ven; Parag Mallick; Mark Stolowitz; Olga Vitek
Journal:  Bioinformatics       Date:  2015-03-15       Impact factor: 6.937

8.  Financial costs and personal consequences of research misconduct resulting in retracted publications.

Authors:  Andrew M Stern; Arturo Casadevall; R Grant Steen; Ferric C Fang
Journal:  Elife       Date:  2014-08-14       Impact factor: 8.140

9.  Design and implementation of microarray gene expression markup language (MAGE-ML).

Authors:  Paul T Spellman; Michael Miller; Jason Stewart; Charles Troup; Ugis Sarkans; Steve Chervitz; Derek Bernhart; Gavin Sherlock; Catherine Ball; Marc Lepage; Marcin Swiatek; W L Marks; Jason Goncalves; Scott Markel; Daniel Iordan; Mohammadreza Shojatalab; Angel Pizarro; Joe White; Robert Hubley; Eric Deutsch; Martin Senger; Bruce J Aronow; Alan Robinson; Doug Bassett; Christian J Stoeckert; Alvis Brazma
Journal:  Genome Biol       Date:  2002-08-23       Impact factor: 13.583

10.  COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Authors:  Reza M Salek; Steffen Neumann; Daniel Schober; Jan Hummel; Kenny Billiau; Joachim Kopka; Elon Correa; Theo Reijmers; Antonio Rosato; Leonardo Tenori; Paola Turano; Silvia Marin; Catherine Deborde; Daniel Jacob; Dominique Rolin; Benjamin Dartigues; Pablo Conesa; Kenneth Haug; Philippe Rocca-Serra; Steve O'Hagan; Jie Hao; Michael van Vliet; Marko Sysi-Aho; Christian Ludwig; Jildau Bouwman; Marta Cascante; Timothy Ebbels; Julian L Griffin; Annick Moing; Macha Nikolski; Matej Oresic; Susanna-Assunta Sansone; Mark R Viant; Royston Goodacre; Ulrich L Günther; Thomas Hankemeier; Claudio Luchinat; Dirk Walther; Christoph Steinbeck
Journal:  Metabolomics       Date:  2015-05-26       Impact factor: 4.290

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  48 in total

1.  Untargeted LC-MS metabolomic studies of Asteraceae species to discover inhibitors of Leishmania major dihydroorotate dehydrogenase.

Authors:  Lucas A Chibli; Annylory L Rosa; Maria Cristina Nonato; Fernando B Da Costa
Journal:  Metabolomics       Date:  2019-04-04       Impact factor: 4.290

2.  rDolphin: a GUI R package for proficient automatic profiling of 1D 1H-NMR spectra of study datasets.

Authors:  Daniel Cañueto; Josep Gómez; Reza M Salek; Xavier Correig; Nicolau Cañellas
Journal:  Metabolomics       Date:  2018-01-31       Impact factor: 4.290

Review 3.  Mass spectrometry as a quantitative tool in plant metabolomics.

Authors:  Tiago F Jorge; Ana T Mata; Carla António
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2016-10-28       Impact factor: 4.226

Review 4.  Increasing rigor in NMR-based metabolomics through validated and open source tools.

Authors:  Hamid R Eghbalnia; Pedro R Romero; William M Westler; Kumaran Baskaran; Eldon L Ulrich; John L Markley
Journal:  Curr Opin Biotechnol       Date:  2016-09-16       Impact factor: 9.740

Review 5.  Pharmacognosy in the digital era: shifting to contextualized metabolomics.

Authors:  Pierre-Marie Allard; Jonathan Bisson; Antonio Azzollini; Guido F Pauli; Geoffrey A Cordell; Jean-Luc Wolfender
Journal:  Curr Opin Biotechnol       Date:  2018-02-27       Impact factor: 9.740

Review 6.  Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids.

Authors:  Joana Krämer; Rui Kang; Laura M Grimm; Luisa De Cola; Pierre Picchetti; Frank Biedermann
Journal:  Chem Rev       Date:  2022-01-07       Impact factor: 60.622

7.  The mwtab Python Library for RESTful Access and Enhanced Quality Control, Deposition, and Curation of the Metabolomics Workbench Data Repository.

Authors:  Christian D Powell; Hunter N B Moseley
Journal:  Metabolites       Date:  2021-03-12

8.  Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

Authors:  Jennifer E Van Eyk; Fernando J Corrales; Ruedi Aebersold; Ferdinando Cerciello; Eric W Deutsch; Paola Roncada; Jean-Charles Sanchez; Tadashi Yamamoto; Pengyuan Yang; Hui Zhang; Gilbert S Omenn
Journal:  J Proteome Res       Date:  2016-09-20       Impact factor: 4.466

9.  Metabolomics: beyond biomarkers and towards mechanisms.

Authors:  Caroline H Johnson; Julijana Ivanisevic; Gary Siuzdak
Journal:  Nat Rev Mol Cell Biol       Date:  2016-03-16       Impact factor: 94.444

Review 10.  The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Authors:  James B McAlpine; Shao-Nong Chen; Andrei Kutateladze; John B MacMillan; Giovanni Appendino; Andersson Barison; Mehdi A Beniddir; Maique W Biavatti; Stefan Bluml; Asmaa Boufridi; Mark S Butler; Robert J Capon; Young H Choi; David Coppage; Phillip Crews; Michael T Crimmins; Marie Csete; Pradeep Dewapriya; Joseph M Egan; Mary J Garson; Grégory Genta-Jouve; William H Gerwick; Harald Gross; Mary Kay Harper; Precilia Hermanto; James M Hook; Luke Hunter; Damien Jeannerat; Nai-Yun Ji; Tyler A Johnson; David G I Kingston; Hiroyuki Koshino; Hsiau-Wei Lee; Guy Lewin; Jie Li; Roger G Linington; Miaomiao Liu; Kerry L McPhail; Tadeusz F Molinski; Bradley S Moore; Joo-Won Nam; Ram P Neupane; Matthias Niemitz; Jean-Marc Nuzillard; Nicholas H Oberlies; Fernanda M M Ocampos; Guohui Pan; Ronald J Quinn; D Sai Reddy; Jean-Hugues Renault; José Rivera-Chávez; Wolfgang Robien; Carla M Saunders; Thomas J Schmidt; Christoph Seger; Ben Shen; Christoph Steinbeck; Hermann Stuppner; Sonja Sturm; Orazio Taglialatela-Scafati; Dean J Tantillo; Robert Verpoorte; Bin-Gui Wang; Craig M Williams; Philip G Williams; Julien Wist; Jian-Min Yue; Chen Zhang; Zhengren Xu; Charlotte Simmler; David C Lankin; Jonathan Bisson; Guido F Pauli
Journal:  Nat Prod Rep       Date:  2018-07-13       Impact factor: 13.423

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