GeneDB--an annotation database for pathogens

Abstract

GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.

Figure 1.

The Rationaliser tool is used to remove inconsistencies from curated data. (A) Search boxes to locate terms. (B) List of colour-coded CV terms used within the annotations of selected organisms. (C) List of all available terms in the CV (also colour-coded). (D) Text box to insert new terms if the correct term does not exist.

Figure 2.

Screen shot of GeneDB homepage with an example of an entry point into an individual organism homepage. (A) Links to available tools. (B) Available data sets. (C) Clicking on ‘Select an organism’ opens a drop-down box with available bacterial genomes. (D) Quick search option. (E) Blast search options. (F) Links to available tools. (G) Links to ongoing projects and data release policy.

Figure 3.

Genes can be accessed by browsing clickable whole chromosome or contig maps. (A) Screen shot of an organism home page showing annotation statistics, blast tools and search tools. (B) List of all chromosomes. (C) Shown is part of a chromosome map. A mouse over shows the systematic IDs of the genes, a click on the gene of interest opens the gene page.

Figure 4.

Screen shot of GeneDB gene page. (A) Graphical display of the gene in web-artemis. The chromosomal location of the gene is shown on the top. (B) Basic gene information. (C) Additional information, including relevant literature. (D) Phenotype information. (E) Gene Ontology terms.