Infect-DB—A Data Warehouse Approach for Integrating Genomic Data of Infectious Diseases

With the expansion of biological data sources available online, integration is a major challenge facing researchers wishing to explore this information. Users often need to integrate data derived from multiple, diverse and heterogeneous sources for investigation. This paper presents the features of Infect-DB, a data warehouse that can localize and integrate genomes of pathogenic species, retrieved from NCBI, based on information from the American Biological Safety Association (ABSA). The list of bacteria and their corresponding host specificity were programmatically accessed from ABSA and integrated into Infect-DB. The list of organisms obtained from ABSA was used to target the automated download of corresponding genomes from the NCBI FTP site. Infect-DB provides a set of analysis tools, including a comparison of genomes using local-BLAST, dN/dS analysis, multiple sequence alignment, phylogenetic analysis and visualization tools. To date, Infect-DB has integrated 854 bacterial genomes from 207 genera considered as important pathogens causing infectious diseases.