New Data Mining Interfaces at the Bovine Genome Database

The Bovine Genome Database (BGD, http://BovineGenome.org) is an informatics resource for Bos taurus. We have used InterMine to deploy a new data warehouse called BovineMine to provide a fast and flexible query interface. BovineMine integrates information from many data sources including RefSeq, Ensembl, UniProt, InterPro, OrthoDB, Homologene, Pubmed, Gene Ontology and BioGRID. BovineMine also includes data that we provide on our genome browsers, such as the Bovine Official Gene Set, RNAseq data, SNP and QTL. Users may perform a “Quick Search” or use the “Query Builder” for specialized searches. The “Genome Region Search” and “Overlapping Feature Search” allow users to download annotations with a specified genomic context. Users may download query results in various formats, such as tab-delimited files, GFF, Fasta, BED, JSON and XML.

In addition to BovineMine, users may access data through genome browsers (GBrowse and JBrowse) and BLAST. We have also created specialized search interfaces that focus on differences in annotations and assembly versions, and provide easy navigation to novel genes on genome browsers. The Annotation Assembly Comparison Tool allows users to lookup locations of genes on two bovine assemblies (UMD3.1 and Btau_4.6.1). The Ensembl-NCBI Comparison Tool allows users to investigate disagreements in gene models across  gene sets. The Predicted Transcript RNAseq Read Count Tool provides counts of spliced RNAseq read alignments to predicted transcripts to aid selection of RNAseq tracks in JBrowse. The Candidate Novel Protein Coding Gene Search Tool allows users to easily navigate to locations candidate novel genes in JBrowse.