Database Commons

a catalog of worldwide biological databases

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.

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.