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Welcome to PHIDIAS!The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based module system and centralized resource for biomedical researchers to investigate integrated genome sequences, curated literature information, and gene expression data related to pathogen-host interactions (PHI, also called host-pathogen interactions or HPI) for pathogens with high priority in public health and biological defense. Infectious diseases remain among the most common and fatal of diseases. According to estimations of the World Health Organization, infectious diseases caused 14.7 million deaths in 2001, accounting for 26% of the total global mortality. Infectious disease is the result of an interactive relationship between a pathogen and its host. Integration and analysis of various data related to pathogens and pathogen-host interactions will yield a better understanding of and means for the control of infectious diseases induced by pathogens. PHIDIAS is aimed at organizing and elucidating the fundamental PHI insights. The development of PHIDIAS was initiated with the development of the Brucella Bioinformatics Portal (BBP). Brucella is a facultative intracellular bacterium that causes brucellosis, one of the most common zoonotic diseases in the world in humans and a variety of animal species. BBP integrates different data sets about Brucella, including genomic DNA and protein sequence data, gene-gene interactions, and literature mining data. BBP has been used as one of the most important bioinformatics portals for the brucellosis community. The literature annotation of Brucella related information was based on an internally developed semi-automatic literature mining and curation system (Limix). Such a literature mining and curation system has later been updated and used in many of our database development, including VIOLIN (http://www.violinet.org/), the most comprehensive vaccine database and analysis resource. With the success of the BBP, we have extended many styles used in BBP to other pathogens and eventually developed the PHIDIAS! Many new features are also included in BBP. One central theme in PHI research is the identification and understanding of virulence factors from various pathogens. A new release from PHIDIAS is the recent announcement of the PHIDIAS Victors program, which includes thousands of manually curated virulence factors from ~100 pathogens important for the health of humans and animals. We have focused our research and development on manual annotation and analysis of virulence factors, host immune defenders, and how they interact during the intricate PHI processes. Another focus of our research is to explore how ontologies can be used to better represent, integrate, and analyze important factors in pathogen-host interactions. Note that the PGBrowser genome browsing program, which was reported in the original PHIDIAS paper, has been retired in PHIDIAS. Many genome browsing programs exist online. For example, the NIH/NIAID Bioinformatiics Resource Centers (BRCs) provide such services, including PATRIC for bacterial organisms, EuPathDB for eukaryotic pathogens, ViPR for virus pathogens. We anticipate and wish that PHIDIAS become a system for researchers to address scientific PHI questions with the ultimate goal of successfully fighting against various infectious diseases. Phidias was a great Greek sculptor and architect in the 5th Century B.C. It was said that Phidias alone had seen the exact images of the gods. He established forever image conceptions of Zeus in the Statue of Zeus at Olympia and Athena in the Parthenon. It is our wish that like Phidias who achieved his greatness in his career, PHIDIAS will help us to elucidate the fundamental mechanisms beyond the intimate interactions between pathogens and hosts. |