ReDU: a framework to find and reanalyze public mass spectrometry data View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2020-08-17

AUTHORS

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

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. More... »

PAGES

901-904

Journal

TITLE

Nature Methods

ISSUE

9

VOLUME

17

Author Affiliations

  • Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
  • Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA
  • Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
  • Department of Medicine, University of California, San Diego, La Jolla, CA, USA
  • Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
  • Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK
  • Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic
  • TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
  • Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
  • Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
  • Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
  • Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
  • Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
  • Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA
  • Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
  • Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
  • Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
  • Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
  • Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
  • Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41592-020-0916-7

    DOI

    http://dx.doi.org/10.1038/s41592-020-0916-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1130146038

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/32807955


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