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PDBML: the representation of archival macromolecular structure data in XML
John Westbrook1, Nobutoshi Ito, Haruki Nakamura
1Research 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, USA. jwest@rcsb.rutgers.edu
Bioinformatics (Oxford, England)
|October 29, 2004
Summary
The Protein Data Bank now offers data files and a dictionary in XML format, called PDBML. This new format, PDBML, is automatically generated using the PDB
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- The Protein Data Bank (PDB) is a crucial repository for structural biology data.
- Standardized data formats are essential for data sharing and analysis.
Purpose of the Study:
- To introduce and describe the PDBML format, a new XML-based representation of PDB data.
- To explain the automated generation process of PDBML files.
Main Methods:
- Development of XML schema and DTDs for PDB data.
- Mapping PDB dictionary elements to XML metadata.
- Automated generation of PDBML files from existing PDB data.
Main Results:
- Successful release of PDB Exchange dictionary and archival data files in PDBML format.
- Demonstration of automated PDBML file generation.
- Detailed description of the correspondence between PDB dictionary and XML schema.
Conclusions:
- PDBML provides a standardized XML format for PDB data, enhancing data accessibility and interoperability.
- The automated generation ensures consistency and efficiency in data representation.