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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/11/11/743 |
| _version_ | 1797509375637585920 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T05:16:49Z |
| format | Article |
| id | doaj.art-73fdb4b1d34945649c5cff5865efa025 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T05:16:49Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-73fdb4b1d34945649c5cff5865efa0252023-11-23T00:20:53ZengMDPI AGMetabolites2218-19892021-10-01111174310.3390/metabo11110743MetaFetcheR: An R Package for Complete Mapping of Small-Compound DataSara A. Yones0Rajmund Csombordi1Jan Komorowski2Klev Diamanti3Department of Cellular and Molecular Biology, Uppsala University, 751 24 Uppsala, SwedenDepartment of Cellular and Molecular Biology, Uppsala University, 751 24 Uppsala, SwedenDepartment of Cellular and Molecular Biology, Uppsala University, 751 24 Uppsala, SwedenDepartment of Cellular and Molecular Biology, Uppsala University, 751 24 Uppsala, SwedenSmall-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.https://www.mdpi.com/2218-1989/11/11/743small-compound databasesmetabolomicsmetabolitesqueue-based algorithm |
| spellingShingle | Sara A. Yones Rajmund Csombordi Jan Komorowski Klev Diamanti MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data Metabolites small-compound databases metabolomics metabolites queue-based algorithm |
| title | 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_short | MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data |
| title_sort | metafetcher an r package for complete mapping of small compound data |
| topic | small-compound databases metabolomics metabolites queue-based algorithm |
| url | https://www.mdpi.com/2218-1989/11/11/743 |
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