BovineMine: A Data Mining Warehouse for the Bos taurus Genome

BovineMine (http://BovineGenome.org/bovinemine) is a data mining and warehousing system based on InterMine. Datasets include bovine gene annotations (NCBI, Ensembl, bovine OGS), protein annotations (UniProt), protein families and domains (InterPro), homologs and orthologs (OrthoDB, TreeFam, EnsemblCompara, HomoloGene) pathways (Reactome), gene-gene interactions (BioGRID), Gene Ontology (GO), QTL (AnimalQTLdb), SNP (dbSNP), and tissue-specific gene expression (SRA). BovineMine provides reports for various entities, such as genes, transcripts, proteins and ontology terms, along with tools that allow users to analyze and download genome-wide datasets. A central feature of BovineMine is the QueryBuilder tool, which allows users to explore the data and construct custom queries that integrate the BovineMine datasets. Researchers can load their own lists of identifiers using the List tool  (which accepts various types of identifiers or symbols) or the Genomic Regions tool (which accepts chromosome identifiers and coordinates), allowing them to connect their data to information in the BovineMine database. Results are provided as tables that can be filtered, reorganized and downloaded in various formats. We have created pre-defined query templates that provide starting points for data exploration. A strong point of BovineMine is the ability to mine tissue specific gene expression levels together with genomic variation data, a function not previously available to bovine researchers. BovineMine enables researchers to leverage the curated gene pathways of model organisms (e.g. human, mouse and rat) based on orthology, and is especially useful for GO and pathway analyses in conjunction with GWAS and QTL studies.