MINet: the Molecular Interaction Network applied to Microbial Pathogenesis
 About the
MINet Project:
Microbial pathogenesis includes all processes by which pathogens
(e.g., bacteria, viruses, fungi) invade, survive, and induce diseases in hosts
such as humans, animals, plants or other microbes. Although richly documented in
peer-reviewed publications, the network of molecular and cellular interactions
that occur during microbial pathogenesis are underrepresented in current
bioinformatics systems, probably due to the difficulty in integration of such
diverse data. We designed an XML-based Molecular Interaction Network
Markup Language (MINetML) as the pathogenesis data exchange format and based on
MINetML developed an automatic visualization tool integrated in the
ToolBus/PathPort (TB/PP)system. Unlike the System Biology Markup
Language (SBML) and
CellML that are oriented to numerically
explicit models with detailed kinetic parameters, MINetML is focused on a high
level description of molecular and cellular objects and their interactions,
including phenomena not known at biochemical detail. It emphasizes thoroughness
of curatorial attribution and cross-referencing to external databases and
ontology systems. Since many details in the microbial pathogenesis networks are
not known, MINetML represents interactions very flexibly by using inputs,
co-factors and outputs. MINetML emphasizes literature curation and it includes GO
evidence code, curator information and images, which are not implemented in the
BioPAX. Detailed MINetML documents are available for 9
pathogens deemed of high priority with regard to public health and national
biological defense. Continuing efforts are being taken to include
other groups' supporting MINetML and create larger sets of MINetML documents.
Pathogens
available in our MINet Database: Most of the available 9 pathogens belong to
CDC category A or B pathogen lists
and/or NIAID
priority category A, B, or C pathogen lists. Some of these pathogens are
targets of the collaborative MARCE
(Middle Atlantic Regional Center of Excellence in Biodefense and Emerging
Infectious Diseases) project and the PATRIC
(VBI PathoSystems Resource Integration Center) project.
The TB/PP MINet Web Service:
MINet 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
MINet web service in TB/PP stores all the
MINetML documents in an Apache
Xindice XML database, and displays information for a specific pathogen upon
request. To download TB/PP ToolBus and the MINet web service plugin, please click
Here.
The
MINet Data Format:
The
MINetML format supports information on the following topics: BioObject,
Interaction, Pathway, DataSource, ImageUnit, and CurationInfo.
The MINetML
DTD
or XML Schema specifies these specific components
and the details of the MINetML data structure are described in
Here.
Download:
All the MINet 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
MINet project team at VBI with email:
minet@vbi.vt.edu.
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