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ReDU: a framework to find and reanalyze public mass spectrometry data.
Jarmusch, Alan K; Wang, Mingxun; Aceves, Christine M; Advani, Rohit S; Aguirre, Shaden; Aksenov, Alexander A; Aleti, Gajender; Aron, Allegra T; Bauermeister, Anelize; Bolleddu, Sanjana; Bouslimani, Amina; Caraballo Rodriguez, Andres Mauricio; Chaar, Rama; Coras, Roxana; Elijah, Emmanuel O; Ernst, Madeleine; Gauglitz, Julia M; Gentry, Emily C; Husband, Makhai; Jarmusch, Scott A; Jones, Kenneth L; Kamenik, Zdenek; Le Gouellec, Audrey; Lu, Aileen; McCall, Laura-Isobel; McPhail, Kerry L; Meehan, Michael J; Melnik, Alexey V; Menezes, Riya C; Montoya Giraldo, Yessica Alejandra; Nguyen, Ngoc Hung; Nothias, Louis Felix; Nothias-Esposito, Mélissa; Panitchpakdi, Morgan; Petras, Daniel; Quinn, Robert A; Sikora, Nicole; van der Hooft, Justin J J; Vargas, Fernando; Vrbanac, Alison; Weldon, Kelly C; Knight, Rob; Bandeira, Nuno; Dorrestein, Pieter C.
Afiliação
  • Jarmusch AK; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Wang M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Aceves CM; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Advani RS; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Aguirre S; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Aksenov AA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Aleti G; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Aron AT; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Bauermeister A; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Bolleddu S; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Bouslimani A; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Caraballo Rodriguez AM; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Chaar R; Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA.
  • Coras R; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Elijah EO; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Ernst M; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Gauglitz JM; Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
  • Gentry EC; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Husband M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Jarmusch SA; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Jones KL; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Kamenik Z; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Le Gouellec A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Lu A; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • McCall LI; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • McPhail KL; Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
  • Meehan MJ; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Melnik AV; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Menezes RC; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Montoya Giraldo YA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Nguyen NH; Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
  • Nothias LF; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Nothias-Esposito M; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Panitchpakdi M; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Petras D; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Quinn RA; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Sikora N; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • van der Hooft JJJ; Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK.
  • Vargas F; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Vrbanac A; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
  • Weldon KC; Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic.
  • Knight R; TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France.
  • Bandeira N; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
  • Dorrestein PC; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Nat Methods ; 17(9): 901-904, 2020 09.
Article em En | MEDLINE | ID: mdl-32807955
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Espectrometria de Massas / Software / Metabolômica / Bases de Dados de Compostos Químicos Tipo de estudo: Prognostic_studies Idioma: En Revista: Nat Methods Assunto da revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Espectrometria de Massas / Software / Metabolômica / Bases de Dados de Compostos Químicos Tipo de estudo: Prognostic_studies Idioma: En Revista: Nat Methods Assunto da revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Ano de publicação: 2020 Tipo de documento: Article País de afiliação: Estados Unidos