Data Deposition and Annotation

In the first quarter of 2017, 3800 experimentally-determined structure coordinate entries were deposited to the archive.

65.7% were deposited with a release status of hold until publication; 29.6% were released as soon as annotation of the entry was complete; and 4.7% were held until a particular date.

93.4% of these entries were determined by X-ray crystallographic methods; 3.3% by NMR methods; and 3.2% by 3DEM.

During the same period, 3350 structures and 222 EMDB maps were released in the PDB.

The 10th International Biocuration Conference was held at Stanford University, Palo Alto California, USA on March 26-29, 2017.

At the 2016 meeting, it was announced that RCSB PDB's John Westbrook would be recognized by the society's first Career Award in recognition of his contributions to the field of biocuration.

More than twenty years ago, while still a graduate student, John recognized the importance of a well-defined data model for ensuring the delivery of high quality and reliable data to the user community.

He was the principal architect of the PDBx/mmCIF data representation for biological macromolecular data. It is based on a simple, context-free grammar free of column width limitations. Data are presented in either key-value or tabular form. All relationships between common data items (e.g., atom and residue identifiers) are explicitly documented within the PDBx Exchange Dictionary. This permits software applications to evaluate and validate referential integrity with any PDB entry. The current PDBx/mmCIF dictionary contains over 4000 definitions for the experiments involved in macromolecular structure determination and descriptions of the models themselves. This dictionary is the basis for the all deposition and annotation procedures used by the wwPDB and is the Master Format for the PDB archive. John also established the Chemical Component Dictionary to maintain and distribute small molecule chemical reference data in the PDB.

In his award lecture at this year's meeting, John described his Perspectives on the Evolution of the Data Architecture.

In addition, Jasmine Young presented a poster on the Biocuration of Experimentally-Determined 3D Macromolecular Structures and their Complexes at the wwPDB. wwPDB Biocurators were recently highlighted in a Cell Press Cross Talk blog post entitled OneDep is a step in the right direction.