MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data
Kenneth Haug,Reza M. Salek,Pablo Conesa,Janna Hastings,Paula de Matos,Mark L Rijnbeek,Tejasvi Mahendraker,Mark Williams,Steffen Neumann,Philippe Rocca-Serra,Eamonn Maguire,Alejandra Gonzalez-Beltran,Susanna-Assunta Sansone,Julian L. Griffin,Christoph Steinbeck +14 more
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TLDR
The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique and will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments.Abstract:
MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.read more
Citations
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Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Mingxun Wang,Jeremy Carver,Vanessa V. Phelan,Laura M. Sanchez,Neha Garg,Yao Peng,Don D. Nguyen,Jeramie D. Watrous,Clifford A. Kapono,Tal Luzzatto-Knaan,Carla Porto,Amina Bouslimani,Alexey V. Melnik,Michael J. Meehan,Wei-Ting Liu,Max Crüsemann,Paul D. Boudreau,Eduardo Esquenazi,Mario Sandoval-Calderón,Roland D. Kersten,Laura A. Pace,Robert A. Quinn,Katherine R. Duncan,Cheng-Chih Hsu,Dimitrios J. Floros,Ronnie G. Gavilan,Karin Kleigrewe,Trent R. Northen,Rachel J. Dutton,Delphine Parrot,Erin E. Carlson,Bertrand Aigle,Charlotte Frydenlund Michelsen,Lars Jelsbak,Christian Sohlenkamp,Pavel A. Pevzner,Anna Edlund,Anna Edlund,Jeffrey S. McLean,Jeffrey S. McLean,Jörn Piel,Brian T. Murphy,Lena Gerwick,Chih-Chuang Liaw,Yu-Liang Yang,Hans-Ulrich Humpf,Maria Maansson,Robert A. Keyzers,Amy C. Sims,Andrew R. Johnson,Ashley M. Sidebottom,Brian E. Sedio,Andreas Klitgaard,Charles B. Larson,Charles B. Larson,Cristopher A. Boya P.,Daniel Torres-Mendoza,David Gonzalez,Denise Brentan Silva,Denise Brentan Silva,Lucas Miranda Marques,Daniel P. Demarque,Egle Pociute,Ellis C. O’Neill,Enora Briand,Enora Briand,Eric J. N. Helfrich,Eve A. Granatosky,Evgenia Glukhov,Florian Ryffel,Hailey Houson,Hosein Mohimani,Jenan J. Kharbush,Yi Zeng,Julia A. Vorholt,Kenji L. Kurita,Pep Charusanti,Kerry L. McPhail,Kristian Fog Nielsen,Lisa Vuong,Maryam Elfeki,Matthew F. Traxler,Niclas Engene,Nobuhiro Koyama,Oliver B. Vining,Ralph S. Baric,Ricardo Pianta Rodrigues da Silva,Samantha J. Mascuch,Sophie Tomasi,Stefan Jenkins,Venkat R. Macherla,Thomas Hoffman,Vinayak Agarwal,Philip G. Williams,Jingqui Dai,Ram P. Neupane,Joshua R. Gurr,Andrés M. C. Rodríguez,Anne Lamsa,Chen Zhang,Kathleen Dorrestein,Brendan M. Duggan,Jehad Almaliti,Pierre-Marie Allard,Prasad Phapale,Louis-Félix Nothias,Theodore Alexandrov,Marc Litaudon,Jean-Luc Wolfender,Jennifer E. Kyle,Thomas O. Metz,Tyler Peryea,Dac-Trung Nguyen,Danielle VanLeer,Paul Shinn,Ajit Jadhav,Rolf Müller,Katrina M. Waters,Wenyuan Shi,Xueting Liu,Lixin Zhang,Rob Knight,Paul R. Jensen,Bernhard O. Palsson,Kit Pogliano,Roger G. Linington,Marcelino Gutiérrez,Norberto Peporine Lopes,William H. Gerwick,William H. Gerwick,Bradley S. Moore,Bradley S. Moore,Pieter C. Dorrestein,Pieter C. Dorrestein,Nuno Bandeira,Nuno Bandeira +135 more
TL;DR: In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations and data-driven social-networking should facilitate identification of spectra and foster collaborations.
Journal ArticleDOI
Emerging applications of metabolomics in drug discovery and precision medicine
TL;DR: This Review discusses some of the latest technological advances in metabolomics, focusing on the application of metabolomics towards uncovering the underlying causes of complex diseases, the growing role of metabolites in drug discovery and its potential effect on precision medicine.
Journal ArticleDOI
ChEBI in 2016: Improved services and an expanding collection of metabolites.
Janna Hastings,Gareth Owen,Adriano Dekker,Marcus Ennis,Namrata Kale,Venkatesh Muthukrishnan,Steve Turner,Neil Swainston,Pedro Mendes,Christoph Steinbeck +9 more
TL;DR: This update paper has substantially extended the collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast and added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery.
Journal ArticleDOI
WikiPathways : a multifaceted pathway database bridging metabolomics to other omics research
Denise Slenter,Martina Kutmon,Kristina Hanspers,Anders Riutta,Jacob Windsor,Nuno Nunes,Jonathan Mélius,Elisa Cirillo,Susan L. Coort,Daniela Digles,Friederike Ehrhart,Pieter Giesbertz,Marianthi Kalafati,Marvin Martens,Ryan A. Miller,Kozo Nishida,Linda Rieswijk,Andra Waagmeester,Lars M. T. Eijssen,Lars M. T. Eijssen,Chris T. Evelo,Alexander R. Pico,Egon Willighagen +22 more
TL;DR: There is a doubling of the number of annotated metabolite nodes in WikiPathways and an OpenAPI documentation of the authors' web services and the FAIR annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data.
Journal ArticleDOI
Predicting Network Activity from High Throughput Metabolomics
Shuzhao Li,Youngja Park,Youngja Park,Sai Duraisingham,Sai Duraisingham,Fred Strobel,Nooruddin Khan,Nooruddin Khan,Quinlyn A. Soltow,Dean P. Jones,Bali Pulendran,Bali Pulendran +11 more
TL;DR: A set of computational algorithms are presented which, by leveraging the collective power of metabolic pathways and networks, predict functional activity directly from spectral feature tables without a priori identification of metabolites.
References
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Journal ArticleDOI
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
TL;DR: An LC/MS-based data analysis approach, XCMS, which incorporates novel nonlinear retention time alignment, matched filtration, peak detection, and peak matching, and is demonstrated using data sets from a previously reported enzyme knockout study and a large-scale study of plasma samples.
Journal ArticleDOI
Metabolomics - the link between genotypes and phenotypes
TL;DR: In this review, the differences among metabolite target analysis, metabolite profiling, and metabolic fingerprinting are clarified, and terms are defined.
Journal ArticleDOI
HMDB: The human metabolome database
David S. Wishart,Dan Tzur,Craig Knox,Roman Eisner,An Chi Guo,Nelson Young,Dean Cheng,Kevin Jewell,David Arndt,Summit Sawhney,Chris Fung,Lisa Nikolai,Michael J. Lewis,Marie-Aude Coutouly,Ian D. Forsythe,Peter Tang,Savita Shrivastava,Kevin Jeroncic,Paul Stothard,Godwin Amegbey,David Block,David Hau,James Wagner,Jessica Miniaci,Melisa Clements,Mulu Gebremedhin,Natalie Guo,Ying Wen Zhang,Gavin E. Duggan,Glen D. MacInnis,Alim M. Weljie,Reza Dowlatabadi,Fiona Bamforth,Derrick L. J. Clive,Russell Greiner,Liang Li,Thomas J. Marrie,Brian D. Sykes,Hans J. Vogel,Lori M.M. Querengesser +39 more
TL;DR: The Human Metabolome Database is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community.
Journal ArticleDOI
METLIN: a metabolite mass spectral database.
Colin A. Smith,Grace O'Maille,Elizabeth J. Want,Chuan Qin,Sunia A. Trauger,Theodore R. Brandon,Darlene E. Custodio,Ruben Abagyan,Gary Siuzdak +8 more
TL;DR: METLIN includes an annotated list of known metabolite structural information that is easily cross-correlated with its catalogue of high-resolution Fourier transform mass spectrometry (FTMS) spectra, tandem mass spectrumetry (MS/MS) Spectra, and LC/MS data.
Journal ArticleDOI
Metabolomics by numbers: acquiring and understanding global metabolite data.
Royston Goodacre,Seetharaman Vaidyanathan,Warwick B. Dunn,George G. Harrigan,Douglas B. Kell +4 more
TL;DR: In this postgenomic era, there is a specific need to assign function to orphan genes in order to validate potential targets for drug therapy and to discover new biomarkers of disease.
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