Content area
Abstract
We present ReDU (
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.
Details
Title
ReDU: a framework to find and reanalyze public mass spectrometry data
Author
Jarmusch, Alan K 1
; Wang Mingxun 1
; Aceves, Christine M 1 ; Advani, Rohit S 1
; Aguirre Shaden 1 ; Aksenov, Alexander A 1
; Gajender, Aleti 2 ; Aron, Allegra T 1 ; Bauermeister Anelize 3 ; Bolleddu Sanjana 1 ; Bouslimani Amina 1 ; Caraballo Rodriguez Andres Mauricio 1 ; Chaar Rama 1 ; Coras Roxana 4 ; Elijah, Emmanuel O 1 ; Ernst, Madeleine 5 ; Gauglitz, Julia M 1 ; Gentry, Emily C 1 ; Husband Makhai 1 ; Jarmusch Scott A 6 ; Jones, Kenneth L, II 1 ; Kamenik Zdenek 7
; Le Gouellec Audrey 8
; Lu, Aileen 1 ; McCall Laura-Isobel 9 ; McPhail, Kerry L 10
; Meehan, Michael J 1 ; Melnik, Alexey V 1 ; Menezes, Riya C 11 ; Montoya Giraldo Yessica Alejandra 12 ; Nguyen Ngoc Hung 1 ; Nothias Louis Felix 1
; Nothias-Esposito Mélissa 1 ; Morgan, Panitchpakdi 1 ; Petras, Daniel 13
; Quinn, Robert A 14
; Sikora, Nicole 1 ; van der Hooft Justin J J 15
; Vargas, Fernando 16 ; Vrbanac Alison 17 ; Weldon, Kelly C 18
; Knight, Rob 19
; Bandeira Nuno 20
; Dorrestein, Pieter C 21
1 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
2 University of California, San Diego, Department of Psychiatry, Stein Clinical Research, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
3 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); Universidade de São Paulo, Institute of Biomedical Sciences, São Paulo, Brazil (GRID:grid.11899.38) (ISNI:0000 0004 1937 0722)
4 University of California, San Diego, Department of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
5 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); Statens Serum Institut, Center for Newborn Screening, Department of Congenital Disorders, Copenhagen, Denmark (GRID:grid.6203.7) (ISNI:0000 0004 0417 4147)
6 University of Aberdeen, Marine Biodiscovery Centre, Department of Chemistry, Old Aberdeen, UK (GRID:grid.7107.1) (ISNI:0000 0004 1936 7291)
7 Czech Academy of Sciences, Institute of Microbiology, Videnska, Czech Republic (GRID:grid.418095.1) (ISNI:0000 0001 1015 3316)
8 Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France (GRID:grid.5676.2) (ISNI:0000000417654326)
9 University of Oklahoma, Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018)
10 College of Pharmacy, Oregon State University, Department of Pharmaceutical Sciences, Corvallis, USA (GRID:grid.4391.f) (ISNI:0000 0001 2112 1969)
11 Max Planck Institute for Chemical Ecology, Research Group Mass Spectrometry, Jena, Germany (GRID:grid.418160.a) (ISNI:0000 0004 0491 7131)
12 Universidad EAFIT, Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Medellín, Colombia (GRID:grid.448637.a) (ISNI:0000 0000 9989 4956)
13 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Scripps Institution of Oceanography, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
14 Michigan State University, Department of Biochemistry and Molecular Biology, Lansing, USA (GRID:grid.17088.36) (ISNI:0000 0001 2150 1785)
15 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); Wageningen University, Bioinformatics Group, Wageningen, the Netherlands (GRID:grid.4818.5) (ISNI:0000 0001 0791 5666)
16 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Division of Biological Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
17 University of California, San Diego, Department of Pediatrics, School of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
18 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
19 University of California, San Diego, Department of Pediatrics, School of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Computer Science and Engineering, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Bioengineering, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
20 University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Computer Science and Engineering, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
21 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Pediatrics, School of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
; Wang Mingxun 1
; Aceves, Christine M 1 ; Advani, Rohit S 1
; Aguirre Shaden 1 ; Aksenov, Alexander A 1
; Gajender, Aleti 2 ; Aron, Allegra T 1 ; Bauermeister Anelize 3 ; Bolleddu Sanjana 1 ; Bouslimani Amina 1 ; Caraballo Rodriguez Andres Mauricio 1 ; Chaar Rama 1 ; Coras Roxana 4 ; Elijah, Emmanuel O 1 ; Ernst, Madeleine 5 ; Gauglitz, Julia M 1 ; Gentry, Emily C 1 ; Husband Makhai 1 ; Jarmusch Scott A 6 ; Jones, Kenneth L, II 1 ; Kamenik Zdenek 7
; Le Gouellec Audrey 8
; Lu, Aileen 1 ; McCall Laura-Isobel 9 ; McPhail, Kerry L 10
; Meehan, Michael J 1 ; Melnik, Alexey V 1 ; Menezes, Riya C 11 ; Montoya Giraldo Yessica Alejandra 12 ; Nguyen Ngoc Hung 1 ; Nothias Louis Felix 1
; Nothias-Esposito Mélissa 1 ; Morgan, Panitchpakdi 1 ; Petras, Daniel 13
; Quinn, Robert A 14
; Sikora, Nicole 1 ; van der Hooft Justin J J 15
; Vargas, Fernando 16 ; Vrbanac Alison 17 ; Weldon, Kelly C 18
; Knight, Rob 19
; Bandeira Nuno 20
; Dorrestein, Pieter C 21
1 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
2 University of California, San Diego, Department of Psychiatry, Stein Clinical Research, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
3 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); Universidade de São Paulo, Institute of Biomedical Sciences, São Paulo, Brazil (GRID:grid.11899.38) (ISNI:0000 0004 1937 0722)
4 University of California, San Diego, Department of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
5 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); Statens Serum Institut, Center for Newborn Screening, Department of Congenital Disorders, Copenhagen, Denmark (GRID:grid.6203.7) (ISNI:0000 0004 0417 4147)
6 University of Aberdeen, Marine Biodiscovery Centre, Department of Chemistry, Old Aberdeen, UK (GRID:grid.7107.1) (ISNI:0000 0004 1936 7291)
7 Czech Academy of Sciences, Institute of Microbiology, Videnska, Czech Republic (GRID:grid.418095.1) (ISNI:0000 0001 1015 3316)
8 Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, Grenoble, France (GRID:grid.5676.2) (ISNI:0000000417654326)
9 University of Oklahoma, Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, Norman, USA (GRID:grid.266900.b) (ISNI:0000 0004 0447 0018)
10 College of Pharmacy, Oregon State University, Department of Pharmaceutical Sciences, Corvallis, USA (GRID:grid.4391.f) (ISNI:0000 0001 2112 1969)
11 Max Planck Institute for Chemical Ecology, Research Group Mass Spectrometry, Jena, Germany (GRID:grid.418160.a) (ISNI:0000 0004 0491 7131)
12 Universidad EAFIT, Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Medellín, Colombia (GRID:grid.448637.a) (ISNI:0000 0000 9989 4956)
13 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Scripps Institution of Oceanography, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
14 Michigan State University, Department of Biochemistry and Molecular Biology, Lansing, USA (GRID:grid.17088.36) (ISNI:0000 0001 2150 1785)
15 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); Wageningen University, Bioinformatics Group, Wageningen, the Netherlands (GRID:grid.4818.5) (ISNI:0000 0001 0791 5666)
16 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Division of Biological Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
17 University of California, San Diego, Department of Pediatrics, School of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
18 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
19 University of California, San Diego, Department of Pediatrics, School of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Computer Science and Engineering, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Bioengineering, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
20 University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Computer Science and Engineering, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
21 University of California, San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Department of Pediatrics, School of Medicine, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242); University of California, San Diego, Center for Microbiome Innovation, La Jolla, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242)
Pages
901-904
Publication year
2020
Publication date
Sep 2020
ISSN
15487091
e-ISSN
15487105
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2439185121
Copyright
© The Author(s), under exclusive licence to Springer Nature America, Inc. 2020.