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

PDBHarvest - 从 CCP4 项目中收获更多更好的元数据，以丰富 PDB 的结构沉积

• 批准号: BB/M020428/1
• 负责人: Sameer Velankar
• 金额: $ 8.94万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FM020428%2F1
• 关键词: PDBHarvest; Harvesting; more; better; metadata

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.

在数据驱动的生物学时代，研究界越来越依赖于在生物数据资源中存档的不同实验的准确而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个全局存储库。 PDB由PDBE是创始成员的全球蛋白质数据库（WWPDB）管理。 PDB中存档的高分辨率数据可以帮助设计和发现与药物，动物健康，食品安全和生物技术行业有关的新疗法。使用X射线晶体学确定PDB中可用的80％的结构。近年来，结构确定方法，仪器和软件取得了迅速的进步。这导致每年确定的结构数量的迅速增长。这些改进还使晶体学家能够解决越来越具有挑战性的生物系统，包括整体膜蛋白和大型大分子机器，例如核糖体和伴侣。混合方法的出现，其中来自广泛实验的数据可以用于结构确定，使研究人员可以研究更大，更复杂的系统。这些科学进步使得有必要准确捕获更​​多且更复杂的元数据。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（“数据收获”）功能来实现。 CCP4是最受欢迎的计划套件之一，它支持结构确定过程中的所有步骤。它被学术界和工业研究人员广泛使用。我们计划在CCP4中实施数据收获的基础架构，以促进自动数据捕获，并易于沉积到PDB。新的收获功能将以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，并可以更好地利用生物医学研究界的档案信息。可以通过晶体学方法开发人员“挖掘”其他信息，以检测迄今未知相关性，并可能获得可能导致更好方法的新见解。为了支持数据收获工作，该项目还将修改WWPDB沉积和注释系统，以便它接受新的收获文件的上传。修改后的WWPDB沉积软件将允许自动提取附加元数据，并简化CCP4用户的沉积过程，同时为整个用户社区提供越来越准确的结构数据。

项目成果

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data.

• DOI: 10.1093/database/bay002
• 发表时间: 2018-01-01
• 期刊: Database : the journal of biological databases and curation
• 作者: Young JY;Westbrook JD;Feng Z;Peisach E;Persikova I;Sala R;Sen S;Berrisford JM;Swaminathan GJ;Oldfield TJ;Gutmanas A;Igarashi R;Armstrong DR;Baskaran K;Chen L;Chen M;Clark AR;Di Costanzo L;Dimitropoulos D;Gao G;Ghosh S;Gore S;Guranovic V;Hendrickx PMS;Hudson BP;Ikegawa Y;Kengaku Y;Lawson CL;Liang Y;Mak L;Mukhopadhyay A;Narayanan B;Nishiyama K;Patwardhan A;Sahni G;Sanz-García E;Sato J;Sekharan MR;Shao C;Smart OS;Tan L;van Ginkel G;Yang H;Zhuravleva MA;Markley JL;Nakamura H;Kurisu G;Kleywegt GJ;Velankar S;Berman HM;Burley SK
• 通讯作者: Burley SK

The archiving and dissemination of biological structure data.

• DOI: 10.1016/j.sbi.2016.06.018
• 发表时间: 2016-10
• 期刊: CURRENT OPINION IN STRUCTURAL BIOLOGY
• 影响因子: 6.8
• 作者: Berman, Helen M.;Burley, Stephen K.;Kleywegt, Gerard J.;Markley, John L.;Nakamura, Haruki;Velankar, Sameer
• 通讯作者: Velankar, Sameer

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive.

• DOI: 10.1016/j.str.2017.01.004
• 发表时间: 2017-03-07
• 期刊: Structure (London, England : 1993)
• 作者: Young JY;Westbrook JD;Feng Z;Sala R;Peisach E;Oldfield TJ;Sen S;Gutmanas A;Armstrong DR;Berrisford JM;Chen L;Chen M;Di Costanzo L;Dimitropoulos D;Gao G;Ghosh S;Gore S;Guranovic V;Hendrickx PMS;Hudson BP;Igarashi R;Ikegawa Y;Kobayashi N;Lawson CL;Liang Y;Mading S;Mak L;Mir MS;Mukhopadhyay A;Patwardhan A;Persikova I;Rinaldi L;Sanz-Garcia E;Sekharan MR;Shao C;Swaminathan GJ;Tan L;Ulrich EL;van Ginkel G;Yamashita R;Yang H;Zhuravleva MA;Quesada M;Kleywegt GJ;Berman HM;Markley JL;Nakamura H;Velankar S;Burley SK
• 通讯作者: Burley SK