 About the PathInfo Project:
A vast amount of information about animal and plant pathogens has been
acquired, stored, and displayed in varied formats through different resources,
both electronic and otherwise, some accessible through the Internet. However,
there is no community standard format for organizing this information, nor
agreement on a machine-readable format for data exchange, thereby hampering
interoperation efforts across information systems. To address this, we developed the
Pathogen Information Markup Language (PIML), a free, open, XML-based format
for representing pathogen information. XSLT-based visual presentations of
valid PIML documents were also developed and can be accessed through a
public PathInfo website or as part of the interoperating web services
federation known as
ToolBus/PathPort (TB/PP). Detailed PIML documents are available for 46
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 create larger sets of PIML documents.
Pathogens
available in our PathInfo Database:
All of the available 46 pathogens belong to
CDC category A or B pathogen lists
and/or NIAID
priority category A, B, or C pathogen lists. Eight of these pathogens are
targets of the collaborative MARCE
(Middle Atlantic Regional Center of Excellence in Biodefense and Emerging
Infectious Diseases) project. Virginia Bioinformatics Institute
serves as the Bioinformatics and Genomics Research Core for the entire MARCE consortium of 14 universities,
diverse federal agencies and corporations.
The PathInfo Query System:
The PathInfo Query System is based on PHP programming and XSL transformations. The user can search specific topics
across up to three pathogens. The query results can be shown in a user friendly HTML form.
A cron job runs daily in the background to automatically extract the PIML
documents, from the same XML Xindice database used by TB/PP, via the TB/PP
PathInfo web service. This mechanism ensures that the web-based viewer uses
PIML documents no more than 1 day out of sync with TB/PP while not
overburdening the website with unnecessary updates. To access the PathInfo query system, please click Here.
The TB/PP PathInfo Web Service:
PathInfo is part of the
Pathogen Portal (PathPort) project. PathPort aims to combine information about pathogens (and their near relatives) from around the world with powerful analysis and visualization tools for bioinformatical assistance in biological research on high-priority pathogens. The publicly available
TB/PP software package is built around ToolBus, a platform and domain independent client-side interconnect that provides easy access to web-services from all over the world. The PathInfo web service in TB/PP stores all the PIML documents in an Apache
Xindice XML database, and displays information for a specific pathogen upon request by using an XSLT script for dynamic transformation of the XML document into HTML.
To download TB/PP ToolBus and the PathInfo web service plugin, please click
Here.
The PIML Data
Format:
The PIML DTD
or XML Schema specifies one or more of these various components:
general organism information, epidemiology, infected host information,
laboratory work, references, and curation information. The details of the PIML
data structure are described in Here.
Download:
All the PathInfo related standards and software are freely available to the public for non-commercial use. The download site can be accessed by clicking Here.
Feedback:
Your involvement and collaboration are welcome. Please send your suggestions, comments, or questions to the
PathInfo project team at VBI with email:
pathinfo@vbi.vt.edu.
Maintained by PathInfo Project at VBI.
Last modified on: 09Nov2007
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