ArticleBioinformatics (Oxford, England)2022
MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Synthetic Biology in Natural Product Biosynthesis.Chemical reviews · 2025Review
- Recent advances in mass spectrometry-based computational metabolomics.Current opinion in chemical biology · 2023Review
- Pickaxe: a Python library for the prediction of novel metabolic reactions.BMC bioinformatics · 2023Article
- Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.Bioinformatics (Oxford, England) · 2023Article
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4 authors.
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Abstract
summaryAlthough advances in untargeted metabolomics have made it possible to gather data on thousands of cellular metabolites in parallel, identification of novel metabolites from these datasets remains challenging. To address this need, Metabolic in silico Network Expansions (MINEs) were developed. A MINE is an expansion of known biochemistry which can be used as a list of potential structures for unannotated metabolomics peaks. Here, we present MINE 2.0, which utilizes a new set of biochemical transformation rules that covers 93% of MetaCyc reactions (compared to 25% in MINE 1.0). This results in a 17-fold increase in database size and a 40% increase in MINE database compounds matching unannotated peaks from an untargeted metabolomics dataset. MINE 2.0 is thus a significant improvement to this community resource. AVAILABILITY AND IMPLEMENTATION: The MINE 2.0 website can be accessed at https://minedatabase.ci.northwestern.edu. The MINE 2.0 web API documentation can be accessed at https://mine-api.readthedocs.io/en/latest/. The data and code underlying this article are available in the MINE-2.0-Paper repository at https://github.com/tyo-nu/MINE-2.0-Paper. MINE 2.0 source code can be accessed at https://github.com/tyo-nu/MINE-Database (MINE construction), https://github.com/tyo-nu/MINE-Server (backend web API) and https://github.com/tyo-nu/MINE-app (web app). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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