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

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

doi:10.1038/s41592-020-0916-7

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

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

^*Corresponding author for this work

Bioinformatics

Research output: Contribution to journal › Article › Academic › peer-review

66 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	901-904
Number of pages	4
Journal	Nature Methods
Volume	17
Issue number	9
DOIs	https://doi.org/10.1038/s41592-020-0916-7
Publication status	Published - Sept 2020

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Jarmusch, A. K., Wang, M., Aceves, C. M., Advani, R. S., Aguirre, S., Aksenov, A. A., Aleti, G., Aron, A. T., Bauermeister, A., Bolleddu, S., Bouslimani, A., Caraballo Rodriguez, A. M., Chaar, R., Coras, R., Elijah, E. O., Ernst, M., Gauglitz, J. M., Gentry, E. C., Husband, M., ... Dorrestein, P. C. (2020). ReDU: a framework to find and reanalyze public mass spectrometry data. Nature Methods, 17(9), 901-904. https://doi.org/10.1038/s41592-020-0916-7

@article{b11729705ece494b8a5b177bf765459a,

title = "ReDU: a framework to find and reanalyze public mass spectrometry data",

abstract = "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{\textquoteright}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.",

author = "Jarmusch, {Alan K.} and Mingxun Wang and Aceves, {Christine M.} and Advani, {Rohit S.} and Shaden Aguirre and Aksenov, {Alexander A.} and Gajender Aleti and Aron, {Allegra T.} and Anelize Bauermeister and Sanjana Bolleddu and Amina Bouslimani and {Caraballo Rodriguez}, {Andres Mauricio} and Rama Chaar and Roxana Coras and Elijah, {Emmanuel O.} and Madeleine Ernst and Gauglitz, {Julia M.} and Gentry, {Emily C.} and Makhai Husband and Jarmusch, {Scott A.} and Jones, {Kenneth L.} and Zdenek Kamenik and {Le Gouellec}, Audrey and Aileen Lu and McCall, {Laura Isobel} and McPhail, {Kerry L.} and Meehan, {Michael J.} and Melnik, {Alexey V.} and Menezes, {Riya C.} and {Montoya Giraldo}, {Yessica Alejandra} and Nguyen, {Ngoc Hung} and Nothias, {Louis Felix} and M{\'e}lissa Nothias-Esposito and Morgan Panitchpakdi and Daniel Petras and Quinn, {Robert A.} and Nicole Sikora and {van der Hooft}, {Justin J.J.} and Fernando Vargas and Alison Vrbanac and Weldon, {Kelly C.} and Rob Knight and Nuno Bandeira and Dorrestein, {Pieter C.}",

year = "2020",

month = sep,

doi = "10.1038/s41592-020-0916-7",

language = "English",

volume = "17",

pages = "901--904",

journal = "Nature Methods",

issn = "1548-7091",

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Jarmusch, AK, Wang, M, Aceves, CM, Advani, RS, Aguirre, S, Aksenov, AA, Aleti, G, Aron, AT, Bauermeister, A, Bolleddu, S, Bouslimani, A, Caraballo Rodriguez, AM, Chaar, R, Coras, R, Elijah, EO, Ernst, M, Gauglitz, JM, Gentry, EC, Husband, M, Jarmusch, SA, Jones, KL, Kamenik, Z, Le Gouellec, A, Lu, A, McCall, LI, McPhail, KL, Meehan, MJ, Melnik, AV, Menezes, RC, Montoya Giraldo, YA, Nguyen, NH, Nothias, LF, Nothias-Esposito, M, Panitchpakdi, M, Petras, D, Quinn, RA, Sikora, N, van der Hooft, JJJ, Vargas, F, Vrbanac, A, Weldon, KC, Knight, R, Bandeira, N & Dorrestein, PC 2020, 'ReDU: a framework to find and reanalyze public mass spectrometry data', Nature Methods, vol. 17, no. 9, pp. 901-904. https://doi.org/10.1038/s41592-020-0916-7

TY - JOUR

T1 - ReDU: a framework to find and reanalyze public mass spectrometry data

AU - Jarmusch, Alan K.

AU - Wang, Mingxun

AU - Aceves, Christine M.

AU - Advani, Rohit S.

AU - Aguirre, Shaden

AU - Aksenov, Alexander A.

AU - Aleti, Gajender

AU - Aron, Allegra T.

AU - Bauermeister, Anelize

AU - Bolleddu, Sanjana

AU - Bouslimani, Amina

AU - Caraballo Rodriguez, Andres Mauricio

AU - Chaar, Rama

AU - Coras, Roxana

AU - Elijah, Emmanuel O.

AU - Ernst, Madeleine

AU - Gauglitz, Julia M.

AU - Gentry, Emily C.

AU - Husband, Makhai

AU - Jarmusch, Scott A.

AU - Jones, Kenneth L.

AU - Kamenik, Zdenek

AU - Le Gouellec, Audrey

AU - Lu, Aileen

AU - McCall, Laura Isobel

AU - McPhail, Kerry L.

AU - Meehan, Michael J.

AU - Melnik, Alexey V.

AU - Menezes, Riya C.

AU - Montoya Giraldo, Yessica Alejandra

AU - Nguyen, Ngoc Hung

AU - Nothias, Louis Felix

AU - Nothias-Esposito, Mélissa

AU - Panitchpakdi, Morgan

AU - Petras, Daniel

AU - Quinn, Robert A.

AU - Sikora, Nicole

AU - van der Hooft, Justin J.J.

AU - Vargas, Fernando

AU - Vrbanac, Alison

AU - Weldon, Kelly C.

AU - Knight, Rob

AU - Bandeira, Nuno

AU - Dorrestein, Pieter C.

PY - 2020/9

Y1 - 2020/9

N2 - 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.

AB - 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.

U2 - 10.1038/s41592-020-0916-7

DO - 10.1038/s41592-020-0916-7

M3 - Article

C2 - 32807955

AN - SCOPUS:85089870197

SN - 1548-7091

VL - 17

SP - 901

EP - 904

JO - Nature Methods

JF - Nature Methods

IS - 9

ER -

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

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