The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data.
The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data.
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DOI：
10.1186/s12859-023-05423-9
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发表时间：
2023-07-24
影响因子：
3
通讯作者：
中科院分区：
文献类型：
--
作者：
用于编程访问代谢组学工作台（Metabolomics Workbench, Metabolomics swb）数据存储库的mwtab Python包的更新版本于2021年初发布。除了更新包以匹配对MetabolomicsWB的“mwTab”文件格式规范的更改并增强包的功能外，还使用了包含的验证工具来检测和编目录MetabolomicsWB中所有公开可用数据集中的文件不一致和错误。开发MetabolomicsWB文件状态网站是为了提供对MetabolomicsWB数据文件的持续验证，并为所有发现的不一致和错误提供有用的接口。这个可检测的问题/错误列表包括格式解析错误、格式遵从性问题、通过metabolicswb的REST接口访问问题，以及其他可能妨碍可重用性的小的不一致。该网站使用mwtab Python包拉出并验证每个可用的分析文件，然后生成一个html报告。该网站每周更新一次。此外，Python网站设计利用GitHub和GitHub。Io，为实现其他元数据、虚拟和元存储库提供了一个易于复制的模板。MetabolomicsWB文件状态网站提供了验证元数据的元数据存储库，以促进对MetabolomicsWB数据存储库中现有代谢组学数据集的公平使用。
An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB. The MetabolomicsWB File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to all found inconsistencies and errors. This list of detectable issues/errors include format parsing errors, format compliance issues, access problems via MetabolomicsWB’s REST interface, and other small inconsistencies that can hinder reusability. The website uses the mwtab Python package to pull down and validate each available analysis file and then generates an html report. The website is updated on a weekly basis. Moreover, the Python website design utilizes GitHub and GitHub.io, providing an easy to replicate template for implementing other metadata, virtual, and meta- repositories. The MetabolomicsWB File Status website provides a metadata repository of validation metadata to promote the FAIR use of existing metabolomics datasets from the MetabolomicsWB data repository.
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mwtab Python 库，用于 RESTful 访问和增强代谢组学工作台数据存储库的质量控制、沉积和管理。
影响因子：
4.1
作者：
Powell CD;Moseley HNB
通讯作者：
Moseley HNB
影响因子：
14.9
作者：
Sud M;Fahy E;Cotter D;Azam K;Vadivelu I;Burant C;Edison A;Fiehn O;Higashi R;Nair KS;Sumner S;Subramaniam S
通讯作者：
Subramaniam S
影响因子：
6.1
作者：
Joosten RP;Salzemann J;Bloch V;Stockinger H;Berglund AC;Blanchet C;Bongcam-Rudloff E;Combet C;Da Costa AL;Deleage G;Diarena M;Fabbretti R;Fettahi G;Flegel V;Gisel A;Kasam V;Kervinen T;Korpelainen E;Mattila K;Pagni M;Reichstadt M;Breton V;Tickle IJ;Vriend G
通讯作者：
Vriend G
影响因子：
9.8
作者：
Wilkinson MD;Dumontier M;Aalbersberg IJ;Appleton G;Axton M;Baak A;Blomberg N;Boiten JW;da Silva Santos LB;Bourne PE;Bouwman J;Brookes AJ;Clark T;Crosas M;Dillo I;Dumon O;Edmunds S;Evelo CT;Finkers R;Gonzalez-Beltran A;Gray AJ;Groth P;Goble C;Grethe JS;Heringa J;'t Hoen PA;Hooft R;Kuhn T;Kok R;Kok J;Lusher SJ;Martone ME;Mons A;Packer AL;Persson B;Rocca-Serra P;Roos M;van Schaik R;Sansone SA;Schultes E;Sengstag T;Slater T;Strawn G;Swertz MA;Thompson M;van der Lei J;van Mulligen E;Velterop J;Waagmeester A;Wittenburg P;Wolstencroft K;Zhao J;Mons B
通讯作者：
Mons B
影响因子：
7.8
作者：
Haug K;Salek RM;Steinbeck C
通讯作者：
Steinbeck C