Publications

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; Gouellec, Audrey Le; 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; Hooft, Justin J.J. van der; Vargas, Fernando; Vrbanac, Alison; Weldon, Kelly C.; Knight, Rob; Bandeira, Nuno; Dorrestein, Pieter C.

Summary

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.