ReDU: a framework to find and reanalyze public mass spectrometry data
Por:
Jarmusch A.K., Wang M., Aceves C.M., Advani R.S., Aguirre S., Aksenov A.A., Aleti G., Aron A.T., Bauermeister A., Bolleddu S., Bouslimani A., Caraballo Rodriguez A.M., Chaar R., Coras R., Elijah E.O., Ernst M., Gauglitz J.M., Gentry E.C., Husband M., Jarmusch S.A., Jones K.L., II, Kamenik Z., Le Gouellec A., Lu A., McCall L.-I., McPhail K.L., Meehan M.J., Melnik A.V., Menezes R.C., Montoya Giraldo Y.A., Nguyen N.H., Nothias L.F., Nothias-Esposito M., Panitchpakdi M., Petras D., Quinn R.A., Sikora N., van der Hooft J.J.J., Vargas F., Vrbanac A., Weldon K.C., Knight R., Bandeira N., Dorrestein P.C.
Publicada:
1 ene 2020
Ahead of Print:
1 ago 2020
Resumen:
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. © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.
Filiaciones:
Jarmusch A.K.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Wang M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Aceves C.M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Advani R.S.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Aguirre S.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Aksenov A.A.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Aleti G.:
Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, United States
Aron A.T.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Bauermeister A.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
Bolleddu S.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Bouslimani A.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Caraballo Rodriguez A.M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Chaar R.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Coras R.:
Department of Medicine, University of California, San Diego, La Jolla, CA, United States
Elijah E.O.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Ernst M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
Gauglitz J.M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Gentry E.C.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Husband M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Jarmusch S.A.:
Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, United Kingdom
Jones K.L.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
II:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Kamenik Z.:
Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic
Le Gouellec A.:
TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France
Lu A.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
McCall L.-I.:
Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, United States
McPhail K.L.:
Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
Meehan M.J.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Melnik A.V.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Menezes R.C.:
Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany
Montoya Giraldo Y.A.:
Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia
Nguyen N.H.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Nothias L.F.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Nothias-Esposito M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Panitchpakdi M.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Petras D.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
Quinn R.A.:
Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, United States
Sikora N.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
van der Hooft J.J.J.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Bioinformatics Group, Wageningen University, Wageningen, Netherlands
Vargas F.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
Vrbanac A.:
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
Weldon K.C.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
Knight R.:
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States
Bandeira N.:
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, United States
Dorrestein P.C.:
Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, United States
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, United States
Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
Green Accepted, Green Submitted, Green
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