Patterns of Pathogenesis
March 2007
Lynette Hirschman, The MITRE Corporation
Alexander Morgan, The MITRE Corporation
Marc Colosimo, The MITRE Corporation
ABSTRACT
This MSR has focused on the development of tools to analyze infectious pathogens. The
rationale is that many pathogens share a set of functions that allow them to invade a host cell,
evade the host cell defenses, multiply inside the host cell, and eventually escape both the cell and
the host organism to spread infection. Our goal has been to bring to bear the rich set of
bioinformatics resources that are becoming available, from gene sequences to knowledge
embedded in the biological literature, in order to understand these "virulence factors." We have
focused on: 1) identifying relevant datasets and resources; 2) developing a pipeline for analysis of
experimental data; and 3) developing flexible tools to integrate information from the biomedical
literature. A deeper understanding of virulence mechanisms will make it possible to create
improved disease models, to identify countermeasures, and to speed up the "bug-to-drug"
pipeline. Our accomplishments include the creation of an international challenge evaluation for
text mining in biology (BioCreAtIvE); the creation of an international community focused on text
mining tools to support for curation of biological databases; support to DARPA to pitch a
BioOntologies program; the award of a grant from NSF; and the publication of 20 peer reviewed
papers and book chapters.
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