Influenza a virus informatics: genotype-centered database and genotype annotation

Recent outbreaks of highly pathogenic avian influenza A virus infections in poultry and humans have caused considerable concerns about a future influenza pandemic in humans. In order to prepare such an unavoidable pandemic incident, effective methods for detecting and identifying dangerous virus strains that are lethal to human life must be developed. For this purpose, we developed a Web tool called FluGenome for genotyping Influenza A viruses with genome sequences. This tool can effectively detect known virus strains and identify new ones. However, it does not provide any other biological meanings to the genotypes. To annotate influenza genotypes effectively, we developed a genotype-centered database that stores various information, including sequences, genotypes, outbreak information, as well as scientific literature, and applied information retrieval and text mining techniques at the term, sentence, and abstract levels. Here we report a genotype-centered database in its design and implementation, and describe the preliminary text-mining result of influenza genotype annotation. The preliminary result demonstrated that the information retrieval and text mining techniques are valuable for the discovery of the knowledge related to influenza genotypes.