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1. ReDU: a framework to find and reanalyze public mass spectrometry data

Author

Zdenek Kamenik, Alexey V. Melnik, Robert A. Quinn, Aileen Lu, Rohit S. Advani, Rama Chaar, Laura-Isobel McCall, Kerry L. McPhail, Ngoc Hung Nguyen, Alexander A. Aksenov, Emily C. Gentry, Pieter C. Dorrestein, Yessica Alejandra Montoya Giraldo, Makhai Husband, Rob Knight, Sanjana Bolleddu, Morgan Panitchpakdi, Julia M. Gauglitz, Nicole Sikora, Fernando Vargas, Shaden Aguirre, Mélissa Nothias-Esposito, Allegra T. Aron, Andrés M. C. Rodríguez, Emmanuel O. Elijah, Anelize Bauermeister, Nuno Bandeira, Audrey Le Gouellec, Gajender Aleti, Scott A. Jarmusch, Madeleine Ernst, Justin J. J. van der Hooft, Christine M. Aceves, Michael J. Meehan, Amina Bouslimani, Alison Vrbanac, Mingxun Wang, Kelly C. Weldon, Louis-Félix Nothias, Alan K. Jarmusch, Kenneth L. Jones, Riya Christina Menezes, Roxana Coras, Daniel Petras, Université Grenoble Alpes - UFR Médecine (UGA UFRM), Université Grenoble Alpes (UGA), and Centre Hospitalier Universitaire [Grenoble] (CHU)

Subjects
Technology, Interface (Java), Computer science, Bioinformatics, Chemical, Mass spectrometry, Biochemistry, Medical and Health Sciences, Article, Mass Spectrometry, 03 medical and health sciences, Disk formatting, Databases, Models, Controlled vocabulary, Bioinformatica, Metabolomics, Life Science, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Metadata, Information retrieval, Cell Biology, Biological Sciences, Metabolomics data, Models, Chemical, Molecular networking, Databases, Chemical, Software, Biotechnology, Developmental Biology
Abstract

We present ReDU ( https://redu.ucsd.edu/ ), a system for metadata capture of public mass spectrometry-based metabolomics data, with validated controlled vocabularies. Systematic capture of knowledge enables the reanalysis of public data and/or co-analysis of one’s own data. ReDU enables multiple types of analyses, including finding chemicals and associated metadata, comparing the shared and different chemicals between groups of samples, and metadata-filtered, repository-scale molecular networking. Repository-scale reanalysis of public mass spectrometry-based metabolomics data is facilitated by the Reanalysis of Data User (ReDU) interface, a system that uses consistent formatting and controlled vocabularies for metadata capture.

Published
2020
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2. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Jingqui Dai, Alexey V. Melnik, Jenan J. Kharbush, Kenji L. Kurita, Robert A. Keyzers, Katrina M. Waters, Mario Sandoval-Calderón, Ajit Jadhav, Clifford A. Kapono, Charles B. Larson, Evgenia Glukhov, Danielle VanLeer, Daniel P. Demarque, Lars Jelsbak, Yi Zeng, Eve A. Granatosky, Kit Pogliano, Maryam Elfeki, Marcelino Gutiérrez, Jeramie D. Watrous, Katherine R. Duncan, Laura M. Sanchez, Jeremy Carver, Brendan M. Duggan, Thomas O. Metz, Julia A. Vorholt, Pep Charusanti, Paul Shinn, Nuno Bandeira, Pavel A. Pevzner, Amy C. Sims, Nobuhiro Koyama, David Gonzalez, Xueting Liu, Denise Brentan Silva, Venkat R. Macherla, Pieter C. Dorrestein, Andrew R. Johnson, Jörn Piel, Michael J. Meehan, Delphine Parrot, Jehad Almaliti, Don D. Nguyen, Louis-Félix Nothias, Wenyuan Shi, Max Crüsemann, Cristopher A. Boya P., Philip G. Williams, Erin E. Carlson, Ronnie G. Gavilan, Yao Peng, Roland D. Kersten, Jennifer E. Kyle, Bertrand Aigle, Yu-Liang Yang, Mingxun Wang, Amina Bouslimani, Lixin Zhang, Ram P. Neupane, Chih-Chuang Liaw, Tyler Peryea, Eric J. N. Helfrich, Kristian Fog Nielsen, Hans-Ulrich Humpf, Robert A. Quinn, Rolf Müller, Paul R. Jensen, Hailey Houson, Eduardo Esquenazi, Kathleen Dorrestein, Vanessa V. Phelan, Bernhard O. Palsson, Lisa Vuong, Cheng-Chih Hsu, Sophie Tomasi, Trent R. Northen, Laura A. Pace, Marc Litaudon, Samantha J. Mascuch, Chen Zhang, Maria Maansson, Ashley M. Sidebottom, Vinayak Agarwal, Ricardo Pianta Rodrigues da Silva, Ellis C. O’Neill, Tal Luzzatto-Knaan, Florian Ryffel, Oliver B. Vining, Andrés M. C. Rodríguez, Andreas Klitgaard, Enora Briand, Brian T. Murphy, Neha Garg, Norberto Peporine Lopes, Ralph S. Baric, William H. Gerwick, Pierre-Marie Allard, Daniel Torres-Mendoza, Jeffrey S. McLean, Stefan Jenkins, Lena Gerwick, Theodore Alexandrov, Roger G. Linington, Egle Pociute, Christian Sohlenkamp, Joshua R. Gurr, Matthew F. Traxler, Wei-Ting Liu, Rob Knight, Anne Lamsa, Anna Edlund, Bradley S. Moore, Prasad Phapale, Hosein Mohimani, Karin Kleigrewe, Charlotte Frydenlund Michelsen, Lucas Miranda Marques, Niclas Engene, Jean-Luc Wolfender, Thomas Hoffman, Rachel J. Dutton, Dac-Trung Nguyen, Paul D. Boudreau, Dimitrios J. Floros, Kerry L. McPhail, Carla Porto, Brian E. Sedio, Computer Science and Engineering, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Collaborative Mass Spectrometry Innovation Center, KDDI R&D Laboratories Inc. [Saitama], Shandong University of Science and Technology, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Metacohorts Consortium, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Unité mixte de physique CNRS/Thales (UMPhy CNRS/THALES), THALES [France]-Centre National de la Recherche Scientifique (CNRS), Department of Civil Engineering, University of Siegen, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de recherches sur la catalyse et l'environnement de Lyon (IRCELYON), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, 2014/01884-2, FAPESP, São Paulo Research Foundation, DAAD, German Academic Exchange Service, K12 GM068524, NIH, National Institutes of Health, RCSA, Research Corporation for Science Advancement, K99DE024543, NIH, National Institutes of Health, PQ 480 306385/2011-2, CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, T32 GM075762, NIH, National Institutes of Health, U01TW006634-06, NIH, National Institutes of Health, U19-AI106772, NIAID, National Institute of Allergy and Infectious Diseases, U19-AI106772, NIH, National Institutes of Health, DFG, Deutsche Forschungsgemeinschaft, 2013/16496-5, FAPESP, São Paulo Research Foundation, 2014/50265-3, FAPESP, São Paulo Research Foundation, 1F32GM089044, NIH, National Institutes of Health, 1R01DE023810-01, NIH, National Institutes of Health, 1R01GM095373, NIH, National Institutes of Health, 200020-146200, FNS, French Norwegian Foundation, 2012/18031-7, FAPESP, São Paulo Research Foundation, NIAID, National Institute of Allergy and Infectious Diseases, K01 GM103809, NIH, National Institutes of Health, 31125002, NSFC, National Natural Science Foundation of China, 5R21AI085540, NIH, National Institutes of Health, 81102369, NSFC, National Natural Science Foundation of China, CN-12-552, CONACYT, Consejo Nacional de Ciencia y Tecnología, DEB 1010816, NSF, National Science Foundation, Wolfender, Jean-Luc, University of California-University of California, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Campinas [Campinas] (UNICAMP), Centre National de la Recherche Scientifique (CNRS)-THALES, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de physique CNRS/Thalès (UMP CNRS/THALES), THALES-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS),Saarland Universitätscampus E8.1, 66123 Saarbrücken, Germany.

Subjects
0301 basic medicine, Internationality, Computer science, Information Dissemination/methods, Information Storage and Retrieval, Bioinformatics, Mass spectrometry data, 01 natural sciences, Applied Microbiology and Biotechnology, Knowledge base, Data driven, Ms libraries, Data Curation, Data Curation/methods, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, ddc:615, Natural products, 3. Good health, Identification (information), Molecular networking, Molecular Medicine, Knowledge based systems, Raw data, Biotechnology, Biological Products/chemistry/classification, Biomedical Engineering, Chemical, Bioengineering, Mass spectrometry, Article, Databases, Open Access, 03 medical and health sciences, Knowledge-based systems, Computational platforms and environments, TA164, MEDICINA, Tandem mass, High through-put characterization, Mass Spectrometry/statistics & numerical data, Biological Products, Data curation, Information Dissemination, Information Storage and Retrieval/methods, Spectrometry, 010405 organic chemistry, business.industry, Data science, 0104 chemical sciences, Data sharing, 030104 developmental biology, ZA, Database Management Systems, business, Databases, Chemical
Abstract

International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
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