The STAR format

The Self-Defining Text Archival and Retrieval (STAR) format has become a standard in structural biology. Several scientific databases (e.g. PDB, CCDC, ICDD, BioMagResBank) use the STAR format to store structural, crystallographic diffraction and NMR data. A growing number of programs (e.g. CNS, NMRView, MODELFREE) can utilize the STAR format for their respective data output.

References

STAR specification publications:

• The STAR File: A new Format for Electronic Data Transfer and Archiving
  S. R. Hall
  J. Chem. Inf. Comput. Sci. 31, 326-333 (1990)
• The STAR File: Detailed Specifications
  S. R. Hall and N. Spadaccini
  J. Chem. Inf. Comput. Sci. 34, 505-508 (1994)
• STAR Dictionary Definition Language: Initial Specification
  S. R. Hall and A. P. F. Cook
  J. Chem. Inf. Comput. Sci. 35, 819-825 (1995)

• The Crystallographic Information File (CIF): a New Standard Archive File for Crystallography
  S. R. Hall, F. H. Allen and I. D. Brown
  Acta Cryst. A47, 655-685 (1991)
• Macromolecular Crystallographic Information File
  P. E. Bournce, H. M. Berman, B. McMahon, K. D. Watenpaugh, J. D. Westbrook and P. M. D. Fitzgerald
  Methods in Enzymology 277, 571-590 (1997)

XML

The eXtensible Markup Language (XML) is a standard for semantic markup of data independent of a particular application domain. This independence implies that many parties develop different parsers; software is thoroughly tested across specific problem domains. Besides, parser implementations exist in a wealth of programming languages (including scripting languages), which means more freedom for the scientist wishing to analyze certain data.

Here's a list of the advantages of XML compared to STAR:

• Standard XML parsers: As XML is used in a broad spectrum of application domains, many different parser implementations are available. This enables the programmer to choose a well-tested parser for a given problem.
• Standard XML viewers/editors: With the advent of the next generation of Web browsers, XML will be supported as a standard format for data exchange over the web. Hierarchical information contained in a web file can be displayed and edited in general-purpose XML viewers (such as Microsoft's Internet Explorer 5) or editors (such as IBM's Xeena)
• XML query languages: Currently, various query languages to extract information from XML sources have been proposed. These query languages enable the users to formulate ad-hoc queries in a structured way.
  Two proposed standards are XQL and XML-QL. For both proposals, working prototype implementations are available.
• Validity of documents: XML documents can be validated against a Document Type Definition (DTD). In this way, the integrity of the data can be checked as the document is generated.

Further information

Here's a collection of links relevant to XML:

• W3C XML site is where you'll find all the standards and official activities.
• XML.com is a commercial portal containing good articles and news about XML.
• Cafe con Leche is a weblog/portal sort of thing for your inofficial (read: where the work is done) XML activities update.
• The Python XML topic guide is the starting point for XML processing in Python.