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RefXAS:一个X射线吸收光谱的开放获取数据库。

RefXAS: an open access database of X-ray absorption spectra.

作者信息

Paripsa Sebastian, Gaur Abhijeet, Förste Frank, Doronkin Dmitry E, Malzer Wolfgang, Schlesiger Christopher, Kanngießer Birgit, Welter Edmund, Grunwaldt Jan Dierk, Lützenkirchen-Hecht Dirk

机构信息

Fk. 4, Physik, Bergische Universität Wuppertal, Gaußstraße 20, D-42097 Wuppertal, Germany.

Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Engesserstraße 20, D-76131 Karlsruhe, Germany.

出版信息

J Synchrotron Radiat. 2024 Sep 1;31(Pt 5):1105-1117. doi: 10.1107/S1600577524006751. Epub 2024 Aug 27.

DOI:10.1107/S1600577524006751
PMID:39190503
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11371060/
Abstract

Under DAPHNE4NFDI, the X-ray absorption spectroscopy (XAS) reference database, RefXAS, has been set up. For this purpose, we developed a method to enable users to submit a raw dataset, with its associated metadata, via a dedicated website for inclusion in the database. Implementation of the database includes an upload of metadata to the scientific catalogue and an upload of files via object storage, with automated query capabilities through a web server and visualization of the data and files. Based on the mode of measurements, quality criteria have been formulated for the automated check of any uploaded data. In the present work, the significant metadata fields for reusability, as well as reproducibility of results (FAIR data principles), are discussed. Quality criteria for the data uploaded to the database have been formulated and assessed. Moreover, the usability and interoperability of available XAS data/file formats have been explored. The first version of the RefXAS database prototype is presented, which features a human verification procedure, currently being tested with a new user interface designed specifically for curators; a user-friendly landing page; a full list of datasets; advanced search capabilities; a streamlined upload process; and, finally, a server-side automatic authentication and (meta-) data storage via MongoDB, PostgreSQL and (data-) files via relevant APIs.

摘要

在DAPHNE4NFDI项目下,已经建立了X射线吸收光谱(XAS)参考数据库RefXAS。为此,我们开发了一种方法,使用户能够通过专门的网站提交原始数据集及其相关元数据,以便纳入数据库。数据库的实施包括将元数据上传到科学目录,并通过对象存储上传文件,通过网络服务器实现自动查询功能以及数据和文件的可视化。根据测量模式,已经制定了质量标准,用于自动检查任何上传的数据。在本工作中,讨论了对于结果的可重用性以及可重复性(FAIR数据原则)而言重要的元数据字段。已经制定并评估了上传到数据库的数据的质量标准。此外,还探索了现有XAS数据/文件格式的可用性和互操作性。展示了RefXAS数据库原型的第一个版本,其具有人工验证程序,目前正在通过专门为策展人设计的新用户界面进行测试;一个用户友好的着陆页;数据集的完整列表;高级搜索功能;简化的上传过程;最后,通过MongoDB、PostgreSQL进行服务器端自动认证和(元)数据存储,通过相关API进行(数据)文件存储。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/9f95e8578675/s-31-01105-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/59289d632f8a/s-31-01105-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/d2cfe08a378b/s-31-01105-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/0bcb87c17496/s-31-01105-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/63849ce076b5/s-31-01105-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/9f95e8578675/s-31-01105-fig5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/59289d632f8a/s-31-01105-fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/d2cfe08a378b/s-31-01105-fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/0bcb87c17496/s-31-01105-fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/63849ce076b5/s-31-01105-fig4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0068/11371060/9f95e8578675/s-31-01105-fig5.jpg

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