HoPaCI-DB: host-Pseudomonas and Coxiella interaction database

Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database (http://mips.helmholtz-muenchen.de/HoPaCI/) of host–pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3585 experimentally validated interactions between molecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches.

[1]  Christopher J. Rawlings,et al.  PHI-base update: additions to the pathogen–host interaction database , 2007, Nucleic Acids Res..

[2]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[3]  Alfonso Valencia,et al.  Overview of BioCreAtIvE: critical assessment of information extraction for biology , 2005, BMC Bioinformatics.

[4]  F Nistal de Paz,et al.  [Q fever]. , 1994, Medicina clinica.

[5]  Yoshihiro Yamanishi,et al.  KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters , 2012, Nucleic Acids Res..

[6]  Alain Filloux,et al.  The Pseudomonas aeruginosa Reference Strain PA14 Displays Increased Virulence Due to a Mutation in ladS , 2011, PloS one.

[7]  Ni Li,et al.  Gene Ontology Annotations and Resources , 2012, Nucleic Acids Res..

[8]  R. Rappuoli,et al.  Cellular Microbiology Emerging , 1996, Science.

[9]  Hans-Werner Mewes,et al.  CORUM: the comprehensive resource of mammalian protein complexes , 2007, Nucleic Acids Res..

[10]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[11]  Troy Stevens,et al.  Filamin A is a phosphorylation target of membrane but not cytosolic adenylyl cyclase activity. , 2011, American journal of physiology. Lung cellular and molecular physiology.

[12]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[13]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[14]  Christopher N. Larsen,et al.  BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence , 2007, Nucleic Acids Res..

[15]  A. Ruepp,et al.  CIDeR: multifactorial interaction networks in human diseases , 2012, Genome Biology.

[16]  R. Nogales-Cadenas,et al.  Proteopathogen, a protein database for studying Candida albicans – host interaction , 2009, Proteomics.

[17]  Y. He,et al.  PHIDIAS: a pathogen-host interaction data integration and analysis system , 2007, Genome Biology.

[18]  Joseph L. Gabbard,et al.  PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species , 2011, Infection and Immunity.

[19]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..