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

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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.