Introduction

Brucella species are Gram-negative, facultative intracellular bacteria that cause brucellosis in humans and animals. Sequences of many Brucella genomes have been published, and various Brucella gene and genome data and analysis resources exist. A web gateway to integrate these resources will greatly facilitate Brucella research. Brucella genome 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-based Brucella gene annotation would increase understanding of complicated Brucella pathogenesis mechanisms.

The Brucella Bioinformatics Portal (BBP) is developed to integrate existing Brucella genome data and analysis tools with literature mining and curation. The BBP InterBru database and Brucella Genome Browser allow users to search and analyze genes of currently available Brucella genomes and link to more than 20 existing databases and analysis programs. Brucella literature 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 annotate Brucella genes 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. At the original study, the Limix system was used to quickly find and confirm 107 Brucella gene mutations including 75 genes shown to be essential for Brucella virulence. The 75 genes are further clustered using COG. In addition, 62 Brucella genetic interactions are extracted from literature publications. These results make possible more comprehensive investigation of Brucella pathogenesis. In summary, BBP is a gateway for Brucella researchers to search, analyze, and curate Brucella genome data originated from public databases and literature. Brucella gene mutations and genetic interactions are annotated using Limix leading to better understanding of Brucella pathogenesis. The BBP paper was published in BMC Bioinformatics in 2006.

Since the publication of the original BBP paper, many updates have been made. One major change is that we have moved the BBP system into the PHIDIAS project as a model system. The methods we have learned from our BBP development have been expanded and used to develop PHIDIAS for pathogen-host interaction data intergation and analysis for a large number of pathogens (instead of only Brucella). With this move, the web interface design has been changed. However, the majority of the features in the original BBP system remain. Some more features have been developed. For example, we have updated our list of sequenced Brucella genomes in our database. Some new features available in PHIDIAS have also been available in BBP. One major addition is that we have added our development of the Brucellosis Ontology (IDOBRU) in the BBP.

In summary, BBP is a gateway and portal for Brucella research. It targets for the analysis of Brucella pathogenesis and host-Brucella interactions by curating, storing, searching, analyzing, and interlinking Brucella or Brucella-associated data originated from public databases and literature.