Conference: Functional Genomes of Microorganisms Conference, April 8-11, 2008 in Paris, France. Presenter: Lauren Brinkac

1. PATHEMA: A BIOINFORMATICS RESOURCE CENTER
Lauren Brinkac, Tanja Davidsen, Erin Beck, Anuradha Ganapathy*,
Jay Sundaram, Scott Durkin, Owen White*, Granger Sutton
J. Craig Venter Institute, 9704 Medical Center Dr. Rockville, MD, 20850 USA
* Institute for Genome Sciences, 685 West Baltimore St., Baltimore, MD, 21201 USA
Abstract Pathema Organisms
Available Genomes Genome Graphical
Pathema (http://pathema.jcvi.org) is a NIAID Bioinformatics Resource Center
Displays
designed to support bio-defense and infectious disease research. Pathema
Current # Current # Future Total
provides detailed curation of six target pathogens: Bacillus anthracis, Clostridium Genus
Species Strains Genomes Genomes
botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens
Bacillus 4 16 25 41
and Entamoeba histolytica. Each pathogen is represented in one of four distinct
clade-specific Pathema web resources developed to target the data and analysis Burkholderia 5 21 8 29
needs of each scientific community. Included in these resources is a customized Clostridium 7 15 35 50
suite of sophisticated bioinformatics software, an extensive library of literature and Detailed
manually curated data, and comparative analysis tools customized to retrieve, Entamoeba 3 0 0 3
Strain
display, and compute results relevant to ongoing bio-defense research. Curated Total 19 52 68 123
Information
datasets of clade-specific virulence factors, epitopes, and toxins, as well as
bioinformatics tools for cross genome comparisons, identification of metabolic
pathways, and SNP analysis were integrated into Pathema to facilitate the
Pathogenicity
identification of potential targets for vaccine development, therapeutics, and
diagnostics. The overarching goal of Pathema is to provide core resources that will
accelerate scientific progress on understanding, detecting, diagnosing and treating
Category A-C pathogens and other pathogens involved in new and re-emerging
JCVI Curated:
infectious diseases. There are no license restrictions for user access to this data
 Virulence Factors
and all source code for Pathema is managed under an open-source collaborative
development paradigm. In addition, clade-specific training courses are offered to
provide instruction on the use of this system and the underlying databases.
Pathema serves as a focal point for the bio-defense research community by
disseminating data resulting from bacterial genome sequencing projects and
providing access to the results of inter-genomic comparisons.
 Clostridum Toxin Database
Functional Genomics
Genome Properties
KEGG Pathways
 PFGRC Microarray Requests
Functional Curation Comparative Analysis
 Community Annotation Tool Positional Best Protein Hits Multi-Genome Homology
 Experimentally Characterized Protein List Comparison
Genome Region
Comparison
Community Outreach
Individual Gene Pages
 Data exchange & integration Genome sequence analysis
 Custom data analysis Custom tool development
 Pathema & annotation training Contact: pathema@jcvi.org