Annual Scientific Report 2015

PDBe Content and Integration
PDBe aims to serve the biomedical community by providing easy access to
macromolecular and cellular structure data. Our team is responsible for the
curation of these data and for ensuring that the PDBe web resources serve the
user community well. We also design tools to facilitate access to integrated,
high-quality structural data.
Major achievements
Our major achievements in 2015 were completing the
redesign of the PDBe website and annotating a record
number of structures. In 2014, the wwPDB partners
made the common deposition and annotation system
available for X-ray crystal structures; as a consequence,
the PDBe team has been handling all the European and
African depositions to the archive, in addition to those
made through the legacy deposition system. In addition,
our curators annotate depositions to the EMDB archive,
processing 4007 depositions to the PDB in 2015 (37%
of 10 886 depositions worldwide) and annotating 452
EMDB depositions (58% of 780 worldwide depositions).
This is more than double the PDB depositions handled
by the PDBe team in 2013. We managed this increase
efficiently, returning more than 90% of the depositions
to the depositors within two working days.
As part of wwPDB development, we were involved
in implementing the new common deposition and
annotation system. This system provides, for the first
time, a single interface for the deposition of data to the
PDB and EMDB archives, and allows users to submit
structures determined using X-ray, NMR and Electron
Microscopy techniques. It was put into production in
January 2016.
The completion of the PDBe redesign project was
a major milestone. It addressed the need to provide
long-term sustainability through a robust weekly
production process and improved management of
PDBe infrastructure. It also put into effect an efficient
data-discovery mechanism, providing intuitive,
consistent data presentation based on user-centric
approaches as a major step towards fulfilling our
mission of ‘bringing structure to biology’.
In 2014 and 2015, we redesigned the
PDBe infrastructure to support a
robust weekly production process. We
reworked the database infrastructure
with help from the Systems
Infrastructure team, and redesigned
the web infrastructure with help from
the Systems Applications and Web
Production teams. The new weekly
production pipeline has proven to be
more robust and easier to maintain
than the old system.
The redesign of the PDBe infrastructure addressed data-quality
issues and augmented the data with value-added annotations. It also
incorporated a more robust system for the weekly release process.
The PDBe database is now the central store for all information made
accessible via the PDBe REST API. This API is used internally to
generate the completely redesigned PDB and EMDB entry pages on
our website. A powerful new search system, based on Apache Lucene
Solr, provides basic data-analysis tools to identify the “best” quality
structure for a given macromolecule or ligand-macromolecule
complex or a particular protein-sequence family.
A user survey conducted in 2012
highlighted issues related to the quality
of data entries in the PDB archive,
and since then we have carried out
extensive remediation work to improve
data quality. This gave rise to new
quality-control measures that are
now part of the weekly production
process that we consider essential, as they improve data
accessibility and discoverability. It has also resulted
in a better user experience when querying the PDB
archive. To enrich the PDB data with value-added
information, we also worked on integrating annotations
from the SIFTS resource as well as data analysis tools
such as PISA for assembly information. Thanks to the
availability of data-quality information based on the
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2015 EMBL-EBI Annual Scientific Report