PDBHarvest - Harvesting more and better metadata from CCP4 projects to enrich structure depositions to the PDB

在数据驱动的生物学时代，研究界越来越依赖于生物数据资源中不同实验的准确和完整的元数据信息的可用性。蛋白质数据库（PDB）是高分辨率三维（3D）大分子结构数据的单一全球存储库。PDB由世界蛋白质数据库（wwPDB）联盟管理，PDBe是该联盟的创始成员之一。PDB中存档的高分辨率数据可以帮助设计和发现与制药、动物健康、食品安全和生物技术行业相关的新疗法。PDB中超过80%的可用结构是用x射线晶体学确定的。近年来，在结构测定方法、仪器和软件方面取得了快速进展。这导致每年确定的结构数量迅速增长。这些改进也使晶体学家能够研究更具挑战性的生物系统，包括整体膜蛋白和大型大分子机器，如核糖体和伴侣。混合方法的出现使研究人员能够研究更大、更复杂的系统，从广泛的实验中获得的数据可以用于结构确定。这些科学进步使得准确捕获额外和更复杂的元数据成为必要。这可以通过在晶体学家使用的流行软件包中实现自动数据捕获（“数据收集”）功能来实现。CCP4是最流行的程序套件之一，它支持结构确定过程中的所有步骤。它被学术界和工业界的研究人员广泛使用。我们计划在CCP4中实现数据收集基础设施，以促进自动数据捕获和轻松沉积到PDB。新的收集功能将以mmCIF文件格式导出元数据；这是一种灵活的格式，允许将来的扩展来捕获更多的元数据。额外的元数据将丰富PDB档案中可用的信息，并允许生物医学研究界更好地利用档案信息。晶体学方法的开发人员可以“挖掘”额外的信息，以检测迄今为止未知的相关性，并可能获得新的见解，从而产生更好的方法。为了支持数据收集工作，该项目还将修改wwPDB存储和注释系统，以便它能够接受新收集文件的上传。修改后的wwPDB沉积软件将允许自动提取额外的元数据，并简化CCP4用户的沉积过程，同时为整个用户群体提供越来越准确的结构数据。

In the era of data-driven biology, the research community is increasingly dependent on the availability of accurate and complete metadata information for different experiments archived in the biological data resources. The Protein Data Bank (PDB) is the single global repository of high-resolution three-dimensional (3D) macromolecular structure data. The PDB is managed by the Worldwide Protein Data Bank (wwPDB) consortium of which PDBe is a founding member. The high-resolution data archived in the PDB can help in the design and discovery of new therapeutics relevant to the pharmaceutical, animal health, food safety and biotechnology industries. Over 80% of the structures available in the PDB are determined using X-ray crystallography. In recent years there have been rapid advances in structure-determination methodology, instrumentation and software. This has resulted in a rapid growth of the number of structures determined each year. The improvements have also enabled crystallographers to address ever more challenging biological systems including integral membrane proteins and large macromolecular machines such as ribosomes and chaperones. The emergence of hybrid methods, where data from a wide range of experiments can be used in structure determination allows researchers to study even larger and more complex systems. These scientific advances make it necessary to accurately capture additional and more complex metadata. This can be achieved by implementing automated data-capturing ("data-harvesting") functionality in popular software packages used by crystallographers. CCP4 is one the most popular program suites that supports all steps in the structure-determination process. It is widely used by researchers in academia and industry. We plan to implement data-harvesting infrastructure in CCP4 to facilitate automatic data capture and easy deposition to the PDB. The new harvesting functionality will export the metadata in mmCIF file format; this is a flexible format that allows for future extensions to capture even more metadata. The additional metadata will enrich the information available in the PDB archive and will allow for better use of the archive information by the biomedical research community. The additional information can be "mined" by crystallographic methods developers to detect hitherto unknown correlations and possibly gain new insights that could lead to better methods. To support the data-harvesting efforts, the project will also modify the wwPDB deposition and annotation system so that it will accept the upload of the new harvest file. The modified wwPDB deposition software will allow for automatic extraction of the additional metadata and simplify the deposition process for CCP4 users, while providing the entire user community with more and more accurate structural data.