Welcome to PHIDIAS!
PHIDIAS is a web-based database and analysis system that aims to manually curate, computationally analyze, and address different scientific issues in the areas of pathogen-host interactions (PHI, or called host-pathogen interactions or HPI). PHIDIAS has emphasized the study of those pathogens that cause various infectious diseases in humans and animals.
Some key features about PHIDIAS:
One central theme in PHI research is the identification and understanding of virulence factors from various pathogens. We have generated a manually curated database, which is called Victors, to store and analyze various virulence factors from different pathogens that infect humans and animals. The Victors data has now been utilized by different groups and projects, including the PATRIC Specialty Genes resource.
PHIDIAS was initially generated by expanding our internally developed Brucella Bioinformatics Portal (BBP). BBP is a valuable resource and portal for Brucella researchers around the world.
As reported in the original PHIDIAS paper, PHIDIAS collects and analyzes valuable information related to PHI in different aspects, such as general PHI information (Phinfo), PHI network information annotation (Phinet), and biohazard information (HazARD).
Another ongoing PHIDIAS research focus is to explore how ontologies can be used to better represent and integrate PHI data. For example, we have developed a Brucellosis Ontology (IDOBRU) to represent Brucella and brucellosis-related terms and the relations among these terms. Such an ontology can be used as a knowledge base to support data integration and advanced data analysis.
Note: 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.
Please cite the following PHIDIAS-related publication(s):
- For general PHIDIS: Xiang Z, Tian Y, He Y. PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biology. 2007 Jul 30;8(7):R150. PMID: 17663773. PMCID: PMC2323235
- For BBP: Xiang Z, Zheng W, He Y. BBP: Brucella genome annotation with literature mining and curation. BMC Bioinformatics. 2006 Jul 16;7(1):347. PMID: 16842628. PMCID: PMC1539029
- For HazARD: He Y, Rush HG, Liepman RS, Xiang Z, Colby LA. Pathobiology and management of laboratory rodents administered CDC Category A agents. Comparative Medicine. 2007. Feb;57(1):18-32. PMID: 17348288.
- For Brucellosos Ontology: Lin Y, Xiang Z, He Y. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. PMID: 22041276. PMCID: PMC3217896.