ReDU: a framework to find and reanalyze public mass spectrometry data
| Autor: | Zdenek Kamenik, Alexey V. Melnik, Robert A. Quinn, Aileen Lu, Rohit S. Advani, Rama Chaar, Laura-Isobel McCall, Kerry L. McPhail, Ngoc Hung Nguyen, Alexander A. Aksenov, Emily C. Gentry, Pieter C. Dorrestein, Yessica Alejandra Montoya Giraldo, Makhai Husband, Rob Knight, Sanjana Bolleddu, Morgan Panitchpakdi, Julia M. Gauglitz, Nicole Sikora, Fernando Vargas, Shaden Aguirre, Mélissa Nothias-Esposito, Allegra T. Aron, Andrés M. C. Rodríguez, Emmanuel O. Elijah, Anelize Bauermeister, Nuno Bandeira, Audrey Le Gouellec, Gajender Aleti, Scott A. Jarmusch, Madeleine Ernst, Justin J. J. van der Hooft, Christine M. Aceves, Michael J. Meehan, Amina Bouslimani, Alison Vrbanac, Mingxun Wang, Kelly C. Weldon, Louis-Félix Nothias, Alan K. Jarmusch, Kenneth L. Jones, Riya Christina Menezes, Roxana Coras, Daniel Petras |
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| Přispěvatelé: | Université Grenoble Alpes - UFR Médecine (UGA UFRM), Université Grenoble Alpes (UGA), Centre Hospitalier Universitaire [Grenoble] (CHU) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Technology
Interface (Java) Computer science Bioinformatics Chemical Mass spectrometry Biochemistry Medical and Health Sciences Article Mass Spectrometry 03 medical and health sciences Disk formatting Databases Models Controlled vocabulary Bioinformatica Metabolomics Life Science [SDV.BBM]Life Sciences [q-bio]/Biochemistry Molecular Biology Molecular Biology ComputingMilieux_MISCELLANEOUS 030304 developmental biology 0303 health sciences Metadata Information retrieval Cell Biology Biological Sciences Metabolomics data Models Chemical Molecular networking Databases Chemical Software Biotechnology Developmental Biology |
| Zdroj: | Nature Methods 17 (2020) 9 Nature methods, vol 17, iss 9 Nat Methods Nature Methods, 17(9), 901-904 Nature Methods Nature Methods, Nature Publishing Group, 2020, 17 (9), pp.901-904. ⟨10.1038/s41592-020-0916-7⟩ |
| ISSN: | 1548-7091 1548-7105 |
| DOI: | 10.1038/s41592-020-0916-7⟩ |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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