Protein Data Bank in Europe: XML Information

Extensible Markup Language (XML) is a simple, very flexible text format. Originally designed to meet the challenges of large-scale electronic publishing, XML is also playing an increasingly important role in the exchange of a wide variety of data on the Web and elsewhere.

Much of the power of XML derives from the fact that the classes of data in a given XML, and the relationship between them, can be described in a well defined and machine-readable form as either a DTD or an XML schema.

XML at the PDBe

The PDBe is involved in XML at two levels. We are heavily involved with the development of standard DTDs/XML schemae for representing macromolecular structure and other biological data. For example see:

• structural genomics data exchange packets (with eHTPX)
• nuclear magnetic resonance experimental information (with CCPN)
• macromolecular structure data (with RCSB)

In addition, we are using XML technologies to solve a range of problems:

• data transfer between structural genomics centers (eHTPX)
• data deposition interfaces (EMDep)
• presentation of macromolecular structure results from database queries (PDBeLite)

XML Technical details

The technical side of XML is handled well by w3c. Of special note:

• XML resources
• XML 1.0 specification (also covers DTD)
• XML schema resources

There are many XML tutorials, both printed and on-line. For both basic background on XML and XSLT we have found W3 schools particularly useful.