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XML stands for EXtensible Markup Language. It was designed to store, exchange and transform data. Many bioinformatic applications relies on XML, for example KEGG KGML (see also KEGGgraph), PSI-MI 2.5 XML standard (see also RpsiXML).


  • XML Tutorial: XML tutorial by w3schools, covering basic concepts of the XML
  • XML DOM Tutorial: XML Document Object Model (DOM) tutorial by w3schools, with detailed introduction into the concepts and usage of XML DOM parsing.

Two types of parsing

Simple API for XML (SAX)
Document Object Model (DOM)