The wwPDB Common Annotation and Deposition Tool Development


John Westbrook1, Martha Quesada1, Jasmine Young1, Zukang Feng1, Tom Oldfield2, Sameer Velankar2, Jawahar Swaminathan2, Takanori Matsuura3, Eldon Ulrich4, Steve Madding4, Gerard Kleywegt2, Haruki Nakamura3, John Markley4, Helen Berman1

1RCSB PDB, Rutgers Chemistry, United States,
2PDBe, European Bioinformatics Institute, United Kingdom,
3PDBj, Osaka University, Japan,
4BMRB, University of Wisconsin-Madison, United States

2010 Annual Meeting of American Crystallographic Association (Chicago, Illinois, USA, 2010.7.24 - 2010.7.29)

The Worldwide Protein Data Bank (wwPDB) is committed to using the highest standards of curation and processing for experimentally-determined 3D biomolecular structure data. The wwPDB Common Deposition and Annotation Tool project was initiated to produce a set of common deposition and annotation processes and tools across the wwPDB that will serve to support the goals of quality and dependability over the next 10 years. The new tools make use of interactive interfaces and best of breed visualization tools to ensure the quality of data curation and communication with the originating scientists. To date, the project has delivered a sequence processing workflow, supported by a graphical user interface and managed by a workflow engine. The annotation processes are described in XML and are accessed by the workflow engine through a Python API. The resulting architectural foundation will be used to complete the full deposition and annotation workflow. The new processes were defined using business process re-engineering methodologies resulting in process-driven requirements and the incremental design and delivery of products. The wwPDB Common Deposition and Annotation suite of tools are built on Python, the Boost.Python Library and C++, supporting work automation, as well as computationally intensive tasks.

wwPDB members are: RCSB PDB (supported by NSF, NIGMS, DOE, NLM, NCI, NINDS and NIDDK), PDBe (Wellcome Trust, EU, BBSRC, NIH and EMBL), PDBj (BIRD-JST) and BMRB (NLM).



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MATSUURA Takanori
t.matsuu%gmail.com (Please change the mark “%” to “@”)

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