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Description :
Literature-curated database for validatedly or potentially pathogenic roles of dysregulated miRNAs in human disease


Description :
Infectious Disease Biomarker Database

Biodefense Proteomics Resource Center

Description :
Proteomics and host-pathogen interactions for biodefense-related microorganisms


Description :
The treatment of infections is increasingly compromised by the ability of bacteria to develop resistance to antibiotics through mutations or through the acquisition of resistance genes. Antibiotic resistance genes also have the potential to be used for bio-terror purposes through genetically modified organisms. In order to facilitate the identification and characterization of these genes, we have created a manually curated database - the Antibiotic Resistance Genes Database (ARDB) - unifying most of the publicly available information on antibiotic resistance. Each gene and resistance type is annotated with rich information, including resistance profile, mechanism of action, ontology, COG, and CDD annotations, as well as external links to sequence and protein databases. Our database also supports sequence similarity searches and implements an initial version of a tool for characterizing common mutations that confer antibiotic resistance. The information we provide can be used as compendium of antibiotic resistance factors as well as to identify the resistance genes of newly sequenced genes, genomes, or metagenomes. Currently, ARDB contains resistance information for 13,293 genes, 377 resistance types, 257 antibiotics, 632 genomes, 933 species and 124 genera.

Recent develoments :
Several analyses provided by our database now also produce output in tab-delimited spreadsheet format (with .xls extension for easy access from OpenOffice or MS Office). Such output is now available for comparisons of resistance profiles between two or more organisms in our database, as well as for genome annotation. Several of the algorithms underlying our database have been improved resulting in faster access and eliminating browser time-outs for the more intensive queries.


Description :
Enteropathogen Resource Integration Center


Description :
Stanford Tuberculosis Database

Aspergillus Genomes

Description :
Unified Aspergillus resource with medical and genomic data

Description :
Genome resources for anaerobic pathogens Trichomonas vaginalis and Giardia lamblia


Description :
Metabolic evolution resource and its application to Plasmodium evolution


Description :
Genome analysis of Plasmodium, Entamoeba, Trypanosoma and Leishmania


Description :
Genetic variation in Trypanosoma cruzi

Magnaporthe grisea Database

Description :
Magnaporthe grisea integrated physical/genetic map


Description :
SchistoDB ( is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide (1,2). It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, ORFs, metabolic pathways and drugs. The computational analysis we provide has helped genome annotation. The construction of a relational database containing the parasite genomic data enables us to perform and combine approximately 30 different queries and also provided access to several tools for analyzing, retrieving or viewing the data such as BLAST, PathwayTools (3) and GMOD Genome Browser (4).
One highlight of the database is its integration to the metabolic pathway prediction generated using the SRI PathwayTools software (3). Pathway analysis allowed us to select putative drug target candidates. The database also contains all drugs available on the Kegg drug database (5), thus enabling us to indicate enzymes known to be targeted in other organisms.

Aknowledgement :
The authors would like to acknowledge the genome sequencing consortium, TIGR, and WTSI for the availability of the genome assembly and annotation of S. mansoni. Without their generous pre-publication contribution, this integrated database resource would not be possible. Special thanks to the GUS developers and to the EupathDB group, that provided essential support to accomplish this work. This work was supported by the National Institutes of Health - Fogarty International Center [5D43TW007012-03].

References :
1. WHO (accessed July 15, 2008) Schistosomiasis.
2. Chitsulo, L., Engels, D., Montresor, A. and Savioli, L. (2000) The global status of schistosomiasis and its control. Acta Trop., 77, 41-51.
3. Karp, P.D., Paley, S. and Romero, P. (2002) The Pathway Tools software. Bioinformatics, 18 Suppl 1, S225-32.
4. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res, 12, 1599-1610.
5. Kanehisa, M., Araki, M., Goto, S., Hattori, M., Hirakawa, M., Itoh, M., Katayama, T., Kawashima, S., Okuda, S., Tokimatsu, T. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res, 36, D480-4.

PIG - Pathogen Interaction Gateway

Description :
Host-pathogen protein-protein interactions

MUGEN Mouse Database

Description :
Murine models of immune processes and immunological diseases14