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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti082
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 14, 2004
Revised October 5, 2004
Accepted October 8, 2004

Article

PDBML: the representation of archival macromolecular structure data in XML

John Westbrook 1*, Nobutoshi Ito 2, Haruki Nakamura 3, Kim Henrick 4, and Helen M. Berman 1

1 Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854
2 Protein Data Bank Japan (PDBj), School of Medical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
3 Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
4 EMBL Outstation, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

* To whom correspondence should be addressed.
John Westbrook, E-mail: jwest{at}rcsb.rutgers.edu


  Abstract

Summary: The Protein Data Bank (PDB) has recently released versions of the PDB Exchange dictionary and the PDB archival data files in XML format collectively named PDBML. The automated generation of these XML files is driven by the data dictionary infrastructure in use at the PDB. The correspondences between the PDB dictionary and the XML schema metadata are described as well as the XML representations of PDB dictionaries and data files.

Availability: The current software translated XML schema file is located at http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd, and on the PDB mmCIF resource page at http://deposit.pdb.org/mmcif/. PDBML files are stored on the PDB beta ftp site at ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML.


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