PIML: the Pathogen Information Markup Language

Bioinformatics. 2005 Jan 1;21(1):116-21. doi: 10.1093/bioinformatics/bth462. Epub 2004 Aug 5.


Motivation: A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data.

Results: The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents.

Availability: All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacteria / classification*
  • Bacteria / pathogenicity*
  • Database Management Systems*
  • Documentation / methods*
  • Information Storage and Retrieval / methods*
  • Internet
  • Natural Language Processing
  • Programming Languages*
  • Software
  • User-Computer Interface
  • Viruses / classification*
  • Viruses / pathogenicity*