The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years
The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years
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DOI：
10.1063/1.5128672
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发表时间：
2019-11-01
影响因子：
2.8
通讯作者：
Minor, Wladek
中科院分区：
文献类型：
--
作者：
Grabowski, Marek;Cymborowski, Marcin;Minor, Wladek
人们越来越认识到，保存和公众获取原始实验数据是经验科学再现性的必要基石。在分子晶体学领域，许多期刊现在建议，提出新晶体结构的手稿作者应该将其主要实验数据（X射线衍射图像）存款近年来创建的专用资源之一。在这里，我们描述了我们的经验，开发的综合资源，用于分子晶体学（IRRMC）的再现，并描述了衍射数据可以在改善以前确定的蛋白质结构中发挥关键作用的几个例子。在最初的四年里，数百名晶体学家已经从世界各地60多个不同的同步加速器光束线或家庭来源进行的5200多个衍射实验中获得了数据。除了改善资源和管理提交的数据外，我们还建立了一个管道，用于提取或在某些情况下重建无缝自动化处理所需的元数据。初步分析表明，大约95%的存档数据可以自动重新处理。高的再处理成功率显示了使用自动元数据提取和自动处理作为原始衍射图像沉积的验证步骤的可行性。IRRMC遵循可查找、可扩展、可互操作和可重用的数据管理原则。
It has been increasingly recognized that preservation and public accessibility of primary experimental data are cornerstones necessary for the reproducibility of empirical sciences. In the field of molecular crystallography, many journals now recommend that authors of manuscripts presenting a new crystal structure should deposit their primary experimental data (X-ray diffraction images) to one of the dedicated resources created in recent years. Here, we describe our experiences developing the Integrated Resource for Reproducibility in Molecular Crystallography (IRRMC) and describe several examples of a crucial role that diffraction data can play in improving previously determined protein structures. In its first four years, several hundred crystallographers have deposited data from over 5200 diffraction experiments performed at over 60 different synchrotron beamlines or home sources all over the world. In addition to improving the resource and curating submitted data, we have been building a pipeline for extraction or, in some cases, reconstruction of the metadata necessary for seamless automated processing. Preliminary analysis indicates that about 95% of the archived data can be automatically reprocessed. A high rate of reprocessing success shows the feasibility of using the automated metadata extraction and automated processing as a validation step for the deposition of raw diffraction images. The IRRMC is guided by the Findable, Accessible, Interoperable, and Reusable data management principles.