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Bioinformatics Advance Access originally published online on August 5, 2004
Bioinformatics 2005 21(1):116-121; doi:10.1093/bioinformatics/bth462
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Bioinformatics vol. 21 issue 1 © Oxford University Press 2005; all rights reserved.

PIML: the Pathogen Information Markup Language

Yongqun He *, Richard R. Vines , Alice R. Wattam , Georgiy V. Abramochkin , Allan W. Dickerman , J. Dana Eckart and Bruno W. S. Sobral

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University 1880 Pratt Drive, Blacksburg, VA 24061–0477, USA

*To whom correspondence should be addressed.

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/

Contact: pathinfo{at}vbi.vt.edu

Received on January 29, 2004; revised on July 30, 2004; accepted on July 30, 2004

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