GOBASE is a collaboration between the laboratories of Dr. Gertraud Burger (PI) and Dr. B. Franz Lang, who are members of the OGMP (Organelle Genome Megasequencing Program). GOBASE is supported by the Canadian Institute for Health Research (CIHR). This database was initially devised by Dr. Tim Littlejohn and implemented by Dr. Maria Korab-Laskowska (analysis, database design and development), Pierre Rioux (analysis, development and system administration) and Nicolas Brossard (programming).
Starting in 2002, we developed a second database, the Protist EST Database (PEPdb), as part of the Protist EST Program, an interdisciplinary research collaboration between six Canadian universities funded by Genome Canada.PEPdb, renamed TBestDB (Taxonomically Broad EST DataBase) after the conclusion of the Protist EST Program in 2006, stores and analyses large volumes of data concerning the expressed sequences of a phylogenetically broad range of single-celled eukaryotes.
Bioinformatics development at Université de Montréal has historically been organised in two groups. The Database Group is made up of Dr. Emmet A. O'Brien (database design, systems analysis and development), Yue Zhang (data curation) and Wole Badejoko (interface and database population programming).. The development and integration of tools for working with the data previously carried out by the AnaBench Group has been folded into the Database Group's operations as of June 2006.
A more detailed description of the individual group members' contributions to these projects is listed below.
Individual Contributions
- Conceptual database design (contents and links)
- Expert work resolving and standardizing gene names using pop2links
- Expert work rectifying sequence features in the database
- Query form design
- Conceptual design of the gene name resolution tool pop2links
- Secondary structure designs of ribosomal RNAs (in collaboration with R. Gutell)
- Conceptual database design (contents and links)
- Genetic Maps
- Expert work rectifying sequence features in the database
- Query form design
- Choice of database model and software
- Basic concepts of the database
UdeM Database Group
O'Brien, Emmet A. (Group Leader February 2002-present)
- Generation and maintenance of GOBASE releases 6 and subsequent
- Analysis of existing Sybase implementation of GOBASE
- Ongoing design and development for PostgreSQL implementation of GOBASE
- Design and implementation of TBestDB on PostgreSQL
- Ongoing design of PHP interfaces for both databases
Zhang, Yue (September 2002 - present)
- Generation of GOBASE updates and curation of new data
- Identification and correction of errors in existing data
- Processing new data for PEPdb
Badejoko, Wole (November 2007 - present)
- Maintenance and development of GOBASE population programs
- Implementation of PHP interface
Wang, Eric (June 2002 - October 2007)
- Data transfer from Sybase to PostgreSQL GOBASE versions
- Modification of GOBASE population programs to work with PostgreSQL - autopop, data validation, secondary table population
- Development of population programs for PEPdb
- Implementation of PHP interfaces 2004-2007
Marie, Veronique (intern May-August 2002, June-August 2003; database curation Jan 2004 - Feb 2007)
- Update and reorganisation of GOBASE RNA data including secondary
structures
- Development of gene distribution pages for GOBASE
- Generation of GOBASE updates and curation of new data
- Identification and correction of errors in existing data
- Processing new data for PEPdb
Student Internships
Cesaire, Chris (September 2005 - March 2006)
- Development of representation for RNA substitution editing in GOBASE.
Chapeaublanc, Remi (March-June 2004)
- Development work on mf2asn, gobase2mf programs
Diallo, Ousman (July-September 2006)
- Development of representation for RNA substitution editing in GOBASE.
Fraissard, Sandrine (March-June 2004)
- Initial development of systems for detecting chimerism in PEPdb data
Letort, Sebastien (March-September 2003)
- Development of graphics for PEPdb - clusters, ORFs, tracefiles
Luo, Ning (June-August 2002)
- Modification of GOBASE population programs to work with PostgreSQL - taxonomy, autopop
Ricault, Carole (June-August 2003)
- Verification of automatic gene name assignment in GOBASE
Tremblay-Savard, Olivier (May-July 2007)
- Development of interface and processing of data for RNA insertion/deletion editing.
affiliated:
Koski, Liisa (January 2004 - December 2005)
- Development of automatic annotation procedures for potential genes in PEPdb
UdeM AnaBench Group
Ricault, Carole (internship February-September 2004, project member January 2005 - May 2006)
- Enhancements of the Anabench workbench
- Integration of RNAMOTIF application
- Design and implementation of Application/Data Driven approach
Bretin, Cécile (internship February-September 2004, project member January 2005 - April 2006)
- Enhancements of the Anabench workbench
- Integration of new bioinformatics applications
- Database maintenance
Fares, Sherif (Former Project Leader)
Badidi, Elarbi (Former Project Leader)
- UML design of AnaBench
- Design and implementation of AnaBench database using MySQL
- IDL specification and implementation of AnaBench CORBA server using ORBACUS for Java
- Design and implementation of AnaBench JSP interfaces
- Design of GOBASE-AnaBench integration
De Sousa, Cristina (internships June-September 2001, February-July 2002)
- Design and implementation of CLUSTAL W JSP interface
- Implementation of JSP interfaces for input, saving, and display of analysis results
Duclouet, Bruno (internships June-September 2002, February-August 2003)
- Design and implementation of the FLIP JSP interface
- Implementation of Deferred Execution in AnaBench
- Design and implementation of protocol applet
Wang, Kun (internship September 2002-January 2003)
- Design and implementation of a Remote BLAST JSP interface
Former members of Bioinformatics Group
Barbasiewicz, Ania (2001-2002)
- automated database population (Java)
- initial development of Java expert correction interface
Brossard, Nicolas (1995-1999)
- Programming of SYBASE table population tool pop1
- Programming of Query form maintenance tool mkgoforms
Korab-Laskowska, Maria (1995-1999)
- Gobase database design, development and management
- Query form design and development
- Specification of GOBASE population tools from ASN.1 structures
- Conceptual design of gene name resolution tool pop2links
- Integration of the NCBI Taxon database
- Analysis of the integrated data
- Design and implementation of systematic error correction and reannotation methods
Liu, Lin (1999-2002)
- graphical interface design and implementation
- database population scripts (Perl)
Nip, Alexander (Informatics Group Leader 1999-2001)
- development and enhancement of bioinformatics tools (mapit,mf2asn, etc.)
- basic concepts of the workbench
- system administration
Rioux, Pierre (1993-1999)
- Design and programming of SYBASE table population tool pop2
- Design and programming of gene name resolution tool pop2links
- Design of Query form maintenance tool mkgoforms
- Design and programming of Taxonomy label maker tool mklabels
- CGI interface sybgw for Genera reprogrammed and extended in perl
- Modifications to Genera software tools sybfmt and sch2sql
- Query form design
- SYBASE and UNIX system administration
Rodriguez, Sabrina (January-December 2004)
- Integrating Gene Ontology information into GOBASE
- Development and implelmentation of methods for assessing chimerism
in PEPdb
Shimko, Nelli (1999-2002)
Yang, LiuSong (2001-2004)
- Design and implementation of PHP3 interfaces for PEPdb and GOBASE
- Implementation of Java expert correction interface
Yu, Maria (August 2004 - June 2005)
- Implementation and maintenance of PHP interfaces for GOBASE and
PEPdb
© 2006 Departement de Biochimie, Université de Montréal
Comments and questions to:
gobase@BCH.UMontreal.CA