ReDU: a framework to find and reanalyze public mass spectrometry data.,Nature Methods

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ReDU: a framework to find and reanalyze public mass spectrometry data.
Nature Methods ( IF 48.0 ) Pub Date : 2020-08-17 , DOI: 10.1038/s41592-020-0916-7
Alan K Jarmusch _{1,

2} , Mingxun Wang _{1,

2} , Christine M Aceves _{1,

2} , Rohit S Advani _{1,

2} , Shaden Aguirre _{1,

2} , Alexander A Aksenov _{1,

2} , Gajender Aleti ₃ , Allegra T Aron _{1,

2} , Anelize Bauermeister _{1,

4} , Sanjana Bolleddu _{1,

2} , Amina Bouslimani _{1,

2} , Andres Mauricio Caraballo Rodriguez _{1,

2} , Rama Chaar _{1,

2} , Roxana Coras ₅ , Emmanuel O Elijah _{1,

2} , Madeleine Ernst _{1,

2,

6} , Julia M Gauglitz _{1,

2} , Emily C Gentry _{1,

2} , Makhai Husband _{1,

2} , Scott A Jarmusch ₇ , Kenneth L Jones _{1,

2} , Zdenek Kamenik ₈ , Audrey Le Gouellec ₉ , Aileen Lu _{1,

2} , Laura-Isobel McCall ₁₀ , Kerry L McPhail ₁₁ , Michael J Meehan _{1,

2} , Alexey V Melnik _{1,

2} , Riya C Menezes ₁₂ , Yessica Alejandra Montoya Giraldo ₁₃ , Ngoc Hung Nguyen _{1,

2} , Louis Felix Nothias _{1,

2} , Mélissa Nothias-Esposito _{1,

2} , Morgan Panitchpakdi _{1,

2} , Daniel Petras _{1,

2,

14} , Robert A Quinn ₁₅ , Nicole Sikora _{1,

2} , Justin J J van der Hooft _{1,

16} , Fernando Vargas _{1,

2,

17} , Alison Vrbanac ₁₈ , Kelly C Weldon _{1,

2,

19} , Rob Knight _{18,

19,

20,

21} , Nuno Bandeira _{2,

19,

20} , Pieter C Dorrestein _{1,

2,

18,

19}

Affiliation

Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
Department of Psychiatry, Stein Clinical Research, University of California, San Diego, La Jolla, CA, USA.
Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
Center for Newborn Screening, Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.
Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, UK.
Institute of Microbiology, Czech Academy of Sciences, Videnska, Czech Republic.
TIMC-IMAG, Univ. Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, Grenoble, France.
Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, and Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA.
Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA.
Research Group Mass Spectrometry, Max Planck Institute for Chemical Ecology, Jena, Germany.
Grupo de Investigación en Ciencias Biológicas y Bioprocesos (CIBIOP), Department of Biological Sciences, Universidad EAFIT, Medellín, Colombia.
Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
Department of Biochemistry and Molecular Biology, Michigan State University, Lansing, MI, USA.
Bioinformatics Group, Wageningen University, Wageningen, the Netherlands.
Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.

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.

中文翻译：

ReDU：查找和重新分析公共质谱数据的框架。

我们介绍了ReDU（https://redu.ucsd.edu/），这是一个基于公共质谱的代谢组学数据元数据捕获的系统，具有经过验证的受控词汇表。系统地获取知识可以重新分析公共数据和/或对自己的数据进行共同分析。ReDU支持多种类型的分析，包括查找化学物质和相关的元数据，比较样品组之间共享和不同的化学物质以及元数据过滤的存储库规模的分子网络。

更新日期：2020-08-17

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