Nature Communications

Enabling pan-repository reanalysis for big data science of public metabolomics data

Y Yasin El Abiead M Michael Strobel T Thomas Payne E Eoin Fahy C Claire O’Donovan S Shankar Subramamiam J Juan Antonio Vizcaíno O Ozgur Yurekten V Victoria Deleray S Simone Zuffa S Shipei Xing H Helena Mannochio-Russo I Ipsita Mohanty H Haoqi Nina Zhao A Andres M. Caraballo-Rodriguez P Paulo Wender P. Gomes N Nicole E. Avalon (Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography) T Trent R. Northen (Joint BioEnergy Institute) B Benjamin P. Bowen K Katherine B. Louie P Pieter C. Dorrestein (Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego) M Mingxun Wang

Abstract

Abstract Public untargeted metabolomics data is a growing resource for metabolite and phenotype discovery; however, accessing and utilizing these data across repositories pose significant challenges. Therefore, here we develop pan-repository universal identifiers and harmonized cross-repository metadata. This ecosystem facilitates discovery by integrating diverse data sources from public repositories including MetaboLights, Metabolomics Workbench, and GNPS/MassIVE. Our approach simplified data handling and unlocks previously inaccessible reanalysis workflows, fostering unmatched research opportunities.

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Article Details

Volume / Issue Vol. 16, Issue 1
Published May 24, 2025
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio
ISSN: 2041-1723 Open Access Life Sciences

Authors (22)

Y

Yasin El Abiead

M

Michael Strobel

T

Thomas Payne

E

Eoin Fahy

C

Claire O’Donovan

S

Shankar Subramamiam

J

Juan Antonio Vizcaíno

O

Ozgur Yurekten

V

Victoria Deleray

S

Simone Zuffa

S

Shipei Xing

H

Helena Mannochio-Russo

I

Ipsita Mohanty

H

Haoqi Nina Zhao

A

Andres M. Caraballo-Rodriguez

P

Paulo Wender P. Gomes

N

Nicole E. Avalon

Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography

T

Trent R. Northen

Joint BioEnergy Institute

B

Benjamin P. Bowen

K

Katherine B. Louie

P

Pieter C. Dorrestein

Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego

M

Mingxun Wang

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