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

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

in 631/114/129 / 631/114/2398 / 631/1647/296 / 631/45/320 / Analysis / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical and Life Sciences / Biomedical Engineering/Biotechnology / Biotechnology / Brief Communication / Databases, Chemical / Life Sciences / Mass Spectrometry / Mass spectroscopy / Metabolomics / Metabolomics - methods / Metadata / Models, Chemical / Proteomics / Repositories / Scientific imaging / Software / Spectroscopy / Vocabularies & taxonomies

2020

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2020

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2020

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Journal Article

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

McCall, Laura-Isobel,

Montoya Giraldo, Yessica Alejandra,

Sikora, Nicole,

Aguirre, Shaden,

Husband, Makhai,

Bauermeister, Anelize,

Bolleddu, Sanjana,

Menezes, Riya C.,

Elijah, Emmanuel O.,

Gauglitz, Julia M.,

Melnik, Alexey V.,

Knight, Rob,

Caraballo Rodriguez, Andres Mauricio,

Bandeira, Nuno,

Le Gouellec, Audrey,

Meehan, Michael J.,

Petras, Daniel,

Nothias-Esposito, Mélissa,

Vrbanac, Alison,

Quinn, Robert A.,

Weldon, Kelly C.,

Gentry, Emily C.,

Jarmusch, Scott A.,

van der Hooft, Justin J. J.,

Bouslimani, Amina,

Ernst, Madeleine,

McPhail, Kerry L.,

Dorrestein, Pieter C.,

Aksenov, Alexander A.,

Jarmusch, Alan K.,

Aron, Allegra T.,

Aceves, Christine M.,

Nothias, Louis Felix,

Chaar, Rama,

Coras, Roxana,

Nguyen, Ngoc Hung,

Lu, Aileen,

Jones, Kenneth L.,

Advani, Rohit S.,

Wang, Mingxun,

Panitchpakdi, Morgan,

Aleti, Gajender,

Vargas, Fernando,

Kamenik, Zdenek

2020

Overview

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.

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Publisher

Nature Publishing Group US,Nature Publishing Group

Subject

/ Biological Microscopy