Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

URL: http://gobase.bcm.umontreal.ca/
Full name: Organelle Genome Database
Description: GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.
Year founded: 2009
Last update: 2017-04
Version: v25
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Canada
Data type:
DNA
Data object:
NA
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: University of Montreal
Address: 2900 Edouard-Montpetit, Montreal QC, Canada H3T 1J4
City: Montreal
Province/State: QC
Country/Region: Canada
Contact name (PI/Team): Emmet A. O’Brien
Contact email (PI/Helpdesk): eobrien@bch.umontreal.ca

Publications

18953030
GOBASE: an organelle genome database. [PMID: 18953030]
O'Brien EA, Zhang Y, Wang E, Marie V, Badejoko W, Lang BF, Burger G.

The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing data, with substitutions, insertions and deletions displayed using multiple alignments; (ii) addition of medically relevant information, such as haplotypes, SNPs and associated disease states, to human mitochondrial sequence data; (iii) addition of fully reannotated genome sequences for Escherichia coli and Nostoc sp., for reference and comparison; and (iv) a number of interface enhancements, such as the availability of both genomic and gene-coding sequence downloads, and a more sophisticated literature reference search functionality with links to PubMed where available. Future projects include the transfer of GOBASE features to NCBI/GenBank, allowing long-term preservation of accumulated expert information. The GOBASE database can be found at http://gobase.bcm.umontreal.ca/. Queries about custom and large-scale data retrievals should be addressed to gobase@bch.umontreal.ca.

Nucleic Acids Res. 2009:37(Database issue) | 37 Citations (from Europe PMC, 2021-06-19)
16381962
GOBASE--a database of organelle and bacterial genome information. [PMID: 16381962]
O'Brien EA, Zhang Y, Yang L, Wang E, Marie V, Lang BF, Burger G.

The organelle genome database GOBASE is now in its twelfth release, and includes 350,000 mitochondrial sequences and 118,000 chloroplast sequences, roughly a 3-fold expansion since previously documented. GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated. All these sequences are now accessible through a single unified interface. Enhancements to the functionality of GOBASE include addition of pages for RNA structures and a page compiling data about the taxonomic distribution of organelle-encoded genes; incorporation of Gene Ontology terms; addition of features deduced from incomplete annotations to sequences in GenBank; marking of type examples in cases where single genes in single species are oversampled within GenBank; and addition of graphics illustrating gene structure and the position of neighbouring genes on a sequence. The database has been reimplemented in PostgreSQL to facilitate development and maintenance, and structural modifications have been made to speed up queries, particularly those related to taxonomy. The GOBASE database can be queried at http://gobase.bcm.umontreal.ca/ and inquiries should be directed to gobase@bch.umontreal.ca.

Nucleic Acids Res. 2006:34(Database issue) | 17 Citations (from Europe PMC, 2021-06-19)
11125069
GOBASE: the organelle genome database. [PMID: 11125069]
Shimko N, Liu L, Lang BF, Burger G.

GOBASE (http://megasun.bch.umontreal.ca/gobase/) is a network-accessible biological database, which is unique in bringing together diverse biological data on organelles with taxonomically broad coverage, and in furnishing data that have been exhaustively verified and completed by experts. So far, we have focused on mitochondrial data: GOBASE contains all published nucleotide and protein sequences encoded by mitochondrial genomes, selected RNA secondary structures of mitochondria-encoded molecules, genetic maps of completely sequenced genomes, taxonomic information for all species whose sequences are present in the database and organismal descriptions of key protistan eukaryotes. All of these data have been integrated and organized in a formal database structure to allow sophisticated biological queries using terms that are inherent in biological concepts. Most importantly, data have been validated, completed, corrected and standardized, a prerequisite of meaningful analysis. In addition, where critical data are lacking, such as genetic maps and RNA secondary structures, they are generated by the GOBASE team and collaborators, and added to the database. The database is implemented in a relational database management system, but features an object-oriented view of the biological data through a Web/Genera-generated World Wide Web interface. Finally, we have developed software for database curation (i.e. data updates, validation and correction), which will be described in some detail in this paper.

Nucleic Acids Res. 2001:29(1) | 15 Citations (from Europe PMC, 2021-06-19)
9399818
The Organelle Genome Database Project (GOBASE). [PMID: 9399818]
Korab-Laskowska M, Rioux P, Brossard N, Littlejohn TG, Gray MW, Lang BF, Burger G.

The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data.

Nucleic Acids Res. 1998:26(1) | 27 Citations (from Europe PMC, 2021-06-19)

Ranking

All databases:
1705/5061 (66.331%)
Gene genome and annotation:
517/1350 (61.778%)
1705
Total Rank
96
Citations
4.174
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Record metadata

Created on: 2015-07-27
Curated by:
Lina Ma [2018-07-24]
Dong Zou [2018-07-24]
Lina Ma [2018-06-12]
Dong Zou [2018-02-07]
lin liu [2016-04-17]
lin liu [2016-03-26]
Jian Sang [2015-12-05]