The Bovine Genome Database
The Bovine Genome Database (BGD, http://bovinegenome.org) facilitates the integration of bovine genomic data. BGD is based on an implementation of the Chado schema, a component of GMOD. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), NCBI and Ensembl gene predictions, non-coding RNA, repeats, pseudogenes, SNPs, markers, QTL and alignments to cDNAs, ESTs, and protein homologs. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their gene model annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages were created using Ruby on Rails and integrated with Chado. They display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, gene ontology, annotator comments and references to external databases. Users may search by gene symbol, annotator, GO term or BGD identifier. Each gene page is linked to a wiki page to allow input from the research community.
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