Enabling pan-repository reanalysis for big data science of public metabolomics data
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.
Authors
- Haoqi Nina Zhao (ORCID: https://orcid.org/0000-0003-3908-630X)
- Yasin El Abiead (ORCID: https://orcid.org/0000-0003-4392-7706)
- Andrés Mauricio Caraballo‐Rodríguez
- Eoin Fahy (ORCID: https://orcid.org/0000-0003-3196-522X)
- Juan Antonio Vizcaíno (ORCID: https://orcid.org/0000-0002-3905-4335)
- Benjamin P. Bowen (ORCID: https://orcid.org/0000-0003-1368-3958)
- Ipsita Mohanty (ORCID: https://orcid.org/0000-0003-0894-4770)
- Mingxun Wang (ORCID: https://orcid.org/0000-0001-7647-6097)
- Paulo Wender Portal Gomes (ORCID: https://orcid.org/0000-0001-5478-2448)
- Helena Mannochio-Russo (ORCID: https://orcid.org/0000-0002-4961-2353)
- Claire O’Donovan (ORCID: https://orcid.org/0000-0001-8051-7429)
- Shipei Xing (ORCID: https://orcid.org/0000-0001-6227-6959)
- Katherine Louie (ORCID: https://orcid.org/0000-0002-6787-7558)
- Özgür Yürekten (ORCID: https://orcid.org/0000-0001-8473-1713)
- Nicole E. Avalon (ORCID: https://orcid.org/0000-0003-3588-892X)
- Pieter C. Dorrestein (ORCID: https://orcid.org/0000-0002-3003-1030)
- Simone Zuffa (ORCID: https://orcid.org/0000-0001-7237-3402)
- Shankar Subramamiam
- Thomas Payne (ORCID: https://orcid.org/0000-0001-7522-981X)
- Michael Strobel (ORCID: https://orcid.org/0009-0000-3829-0048)
- Victoria Deleray (ORCID: https://orcid.org/0009-0002-3201-2578)
Institutions
- University of California, Riverside (US)
- European Bioinformatics Institute (GB)
- Lawrence Berkeley National Laboratory (US)
- Scripps Institution of Oceanography (US)
- San Diego Supercomputer Center (US)
- Joint Genome Institute (US)
- University of California, Irvine (US)
- University of California San Diego (US)
- Irvine University (US)
- Universidade Federal do Pará (BR)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-05-24
- DOI
- https://doi.org/10.1038/s41467-025-60067-y
- Citations
- 24
- Primary Topic
- Metabolomics and Mass Spectrometry Studies
- Type
- article
- Field-Weighted Citation Impact
- 18.54
Funders
- National Science Foundation
- Gordon and Betty Moore Foundation
- European Molecular Biology Laboratory
- National Institutes of Health
- Biotechnology and Biological Sciences Research Council
- Common Fund