euHCVdb®: about euHCVdb

About

INTRODUCTION

The development of the European Hepatitis C Virus database (euHCVdb) started in 1999 as the French HCV Database (HCVDB, Combet et al.,2004). The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of HCV (Penin et al., 2004). In order to make the existing HCV databases as complementary as possible, the current developments are coordinated with the other databases (Japan and Los Alamos) as part of an international collaborative effort (Kuiken et al., 2006).

It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database management system (PostgreSQL). Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a reference set of HCV complete annotated well-characterized genomes of various genotypes.

This automatic procedure ensures standardisation of nomenclature for all entries and provides genomic regions/proteins present in the entry, bibliographic reference, genotype, interesting sites (e.g. HVR1) or domains (e.g. NS3 helicase), source of the sequence (e.g. isolate) and structural data that are available as protein 3D models.

BOARD

The members of the scientific board of euHCVdb are:

Pr Amos Bairoch (Swiss Institue for Bioinformatics, Switzerland)
Pr Dr Ralf Bartenschlager (University of Heidelberg, Germany)
Dr Helmut Diepolder (University of Munich, Germany)
Pr Darius Moradpour (Centre Hospitalier Universitaire Vaudois, Switzerland)
Pr Jean-Michel Pawlotsky (Henri Mondor University Hospital, France)
Dr Francois Penin (Institut de Biologie et Chimie des Proteines, France)
Dr Charles Rice (Rockfeller Univeristy, USA)
Pr Christian Trepo (Lyon University Hospital, France)

FUNDS

The euHCVdb is funded as part of the HepCVax cluster (EC grant QLK2-CT-2002-01329) and viRgil network of excellence (EC grant LSHM-CT-2004-503359).

CITATION

HCV databases: Hepatitis C databases, principles and utility to researchers.
Kuiken C, Mizokami M, Deléage G, Yusim K, Penin F, Shin-I T, Charavay C, Tao N, Crisan D, Grando D, Dalwani A, Geourjon C, Agrawal A, Combet C.
Hepatology, 2006, 43:1157-1165.
This database: euHCVdb: the European hepatitis C virus database.
Combet C., Garnier N., Charavay C., Grando D., Crisan D., Lopez J., Dehne-Garcia A., Geourjon C., Bettler E., Hulo C., Mercier PL., Bartenschlager R., Diepolder H., Moradpour D., Pawlotsky J.M., Rice C.M., Trepo C., Penin F. and Deléage G.
Nucleic Acids Res, 2007, 35:D363-D366.
Original french database: HCVDB: Hepatitis C Virus Sequences Database.
Combet C., Penin F., Geourjon C. and Deléage G.
Appl. Bioinformatics, 2004, 3:237-240.

TEAM

The euHCVdb is developped by the Laboratoire de Bioinformatique et RMN Structurales (LBRS, headed by Pr G. Deléage and Dr F. Penin) of the Institut de Biologie et Chimie des Proteines (IBCP-UMR5086-CNRS-UCBL).

The development team involved:

Name	Function	Time in project	Role in project
Dr C. Combet	CR2-CNRS	Partial time	euHCVdb development coordinator
Dr C. Geourjon	IR2-CNRS	Partial time	Protein 3D atomic models building programs
Dr E. Bettler	MC-Univ. Lyon 1	Partial time	3D atomic models analysis tools
C. Charavay	HepCVax staff (09/2004-08/2005)	Full time	Database modelling and entry annotation
D. Crisan	HepCVax staff (09/2004-08/2005)	Full time	Database parsing, SQL queries and query interface
D. Grando	VIRGIL staff (03/2005-06/2006)	Full time	Website and applets, Number tool
J. Lopez	VIRGIL staff (01/2006-12/2007)	Full time	Database and website management, tools
N. Garnier	PhD Student	Partial time	Protein 3D atomic models database managment system and WWW viewing interface
A. Dehne-Garcia	Lab's temporary staff	Partial time	Protein 3D atomic models database scheme

DISCLAIMER

This server and its associated data and services are for research purpose only, not for commercial use. It is a non-profit service to the scientific community. The responsibility of HepCVax, VIRGIL and IBCP is limited to applying best efforts in providing and publishing good programs and data. HepCVax, VIRGIL and IBCP have no responsibility for the use of results, data or information which have been provided through this server.