MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

Small-compound databases contain a 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. A lack of preventive establishment of means of data access at...

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Autores principales:	Sara A. Yones, Rajmund Csombordi, Jan Komorowski, Klev Diamanti
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	small-compound databases metabolomics metabolites queue-based algorithm Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/73fdb4b1d34945649c5cff5865efa025
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id	oai:doaj.org-article:73fdb4b1d34945649c5cff5865efa025
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spelling	oai:doaj.org-article:73fdb4b1d34945649c5cff5865efa0252021-11-25T18:20:36ZMetaFetcheR: An R Package for Complete Mapping of Small-Compound Data10.3390/metabo111107432218-1989https://doaj.org/article/73fdb4b1d34945649c5cff5865efa0252021-10-01T00:00:00Zhttps://www.mdpi.com/2218-1989/11/11/743https://doaj.org/toc/2218-1989Small-compound databases contain a 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. A 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. 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 three independent case studies based on two published datasets.Sara A. YonesRajmund CsombordiJan KomorowskiKlev DiamantiMDPI AGarticlesmall-compound databasesmetabolomicsmetabolitesqueue-based algorithmMicrobiologyQR1-502ENMetabolites, Vol 11, Iss 743, p 743 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	small-compound databases metabolomics metabolites queue-based algorithm Microbiology QR1-502
spellingShingle	small-compound databases metabolomics metabolites queue-based algorithm Microbiology QR1-502 Sara A. Yones Rajmund Csombordi Jan Komorowski Klev Diamanti MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
description	Small-compound databases contain a 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. A 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. 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 three independent case studies based on two published datasets.
format	article
author	Sara A. Yones Rajmund Csombordi Jan Komorowski Klev Diamanti
author_facet	Sara A. Yones Rajmund Csombordi Jan Komorowski Klev Diamanti
author_sort	Sara A. Yones
title	MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
title_short	MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
title_full	MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
title_fullStr	MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
title_full_unstemmed	MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data
title_sort	metafetcher: an r package for complete mapping of small-compound data
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/73fdb4b1d34945649c5cff5865efa025
work_keys_str_mv	AT saraayones metafetcheranrpackageforcompletemappingofsmallcompounddata AT rajmundcsombordi metafetcheranrpackageforcompletemappingofsmallcompounddata AT jankomorowski metafetcheranrpackageforcompletemappingofsmallcompounddata AT klevdiamanti metafetcheranrpackageforcompletemappingofsmallcompounddata
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MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data

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