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MetaFetcheR: An R package for complete mapping of small compound data

View ORCID ProfileSara A. Yones, Rajmund Csombordi, View ORCID ProfileJan Komorowski, View ORCID ProfileKlev Diamanti
doi: https://doi.org/10.1101/2021.02.28.433248
Sara A. Yones
1Department of Cellular and Molecular Biology, Uppsala University, Uppsala, Sweden
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  • For correspondence: sara.younes@icm.uu.se
Rajmund Csombordi
1Department of Cellular and Molecular Biology, Uppsala University, Uppsala, Sweden
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Jan Komorowski
1Department of Cellular and Molecular Biology, Uppsala University, Uppsala, Sweden
2Institute of Computer Science, Polish Academy of Sciences, Warsaw, Poland
3Washington National Primate Research Center, Seattle, WA, USA
4Swedish Collegium for Advanced Study, Uppsala, Sweden
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Klev Diamanti
1Department of Cellular and Molecular Biology, Uppsala University, Uppsala, Sweden
5Department of Immunology, Genetics and Pathology, Division of Medical Genetics and Genomics, Uppsala University, Uppsala, Sweden
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Abstract

Motivation Small-compound databases contain large amount of information for metabolites and metabolic pathways. However, the plethora of such databases and the redundancy of their information lead to major issues with analysis and standardization. Lack of preventive establishment of means of data access at the infant stages of a project might lead to mislabelled compounds, reduced statistical power and large delays in delivery of results.

Results We developed MetaFetcheR, an open-source R package that links metabolite data from several small-compound databases, resolves inconsistencies and covers a variety of use-cases of data fetching. We showed that the performance of MetaFetcheR was superior to existing approaches and databases by benchmarking the performance of the algorithm in two independent case studies based on two published datasets.

Availability MetaFetcheR is available at https://github.com/komorowskilab/MetaFetcheR/.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/komorowskilab/MetaFetcheR/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 13, 2021.
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MetaFetcheR: An R package for complete mapping of small compound data
Sara A. Yones, Rajmund Csombordi, Jan Komorowski, Klev Diamanti
bioRxiv 2021.02.28.433248; doi: https://doi.org/10.1101/2021.02.28.433248
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MetaFetcheR: An R package for complete mapping of small compound data
Sara A. Yones, Rajmund Csombordi, Jan Komorowski, Klev Diamanti
bioRxiv 2021.02.28.433248; doi: https://doi.org/10.1101/2021.02.28.433248

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