BBP:Brucellagenome annotation with literature mining and curation

Abstract

Abstract Background Brucellaspecies are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of fourBrucellagenomes have been published, and variousBrucellagene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitateBrucellaresearch.Brucellagenome data in current databases is largely derived from computational analysis without experimental validation typically found in peer-reviewed publications. It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation. It is further hypothesized that literature-basedBrucellagene annotation would increase understanding of complicatedBrucellapathogenesis mechanisms. Results TheBrucellaBioinformatics Portal (BBP) is developed to integrate existingBrucellagenome data and analysis tools with literature mining and curation. The BBP InterBru database andBrucellaGenome Browser allow users to search and analyze genes of 4 currently availableBrucellagenomes and link to more than 20 existing databases and analysis programs.Brucellaliterature publications in PubMed are extracted and can be searched by a TextPresso-powered natural language processing method, a MeSH browser, a keywords search, and an automatic literature update service. To efficiently annotateBrucellagenes using the large amount of literature publications, a literature mining and curation system coined Limix is developed to integrate computational literature mining methods with a PubSearch-powered manual curation and management system. The Limix system is used to quickly find and confirm 107Brucellagene mutations including 75 genes shown to be essential forBrucellavirulence. The 75 genes are further clustered using COG. In addition, 62Brucellagenetic interactions are extracted from literature publications. These results make possible more comprehensive investigation ofBrucellapathogenesis. Other BBP features include publication email alert service,Brucellaresearchers' contact database, and discussion forum. Conclusion BBP is a gateway forBrucellaresearchers to search, analyze, and curateBrucellagenome data originated from public databases and literature.Brucellagene mutations and genetic interactions are annotated using Limix leading to better understanding ofBrucellapathogenesis.http://deepblue.lib.umich.edu/bitstream/2027.42/112359/1/12859_2006_Article_1086.pd