Bovinemine: Integrating Genomic Data of Ruminant Livestock Species

BovineMine (http://BovineGenome.org/bovinemine) is an InterMine-based data mining and warehousing system initially developed for the bovine genome. We have recently expanded BovineMine to include information for other ruminant species (sheep and goat). Researchers can use orthology to integrate information across the ruminants and leverage model organisms (human, mouse and rat) for pathways and interactions. Data includes gene annotations (NCBI RefSeq, Ensembl, official gene set), protein annotations (UniProt), protein domain and families (InterPro), orthologs (OrthoDB, TreeFam, EnsemblCompara, HomoloGene), pathway information (Reactome, KEGG), interactions (BioGRID), GO annotations (GO Consortium, UniProt), QTL (AnimalQTLdb), tissue-specific gene expression (SRA), SNP (dbSNP), and computed SNP annotations. BovineMine provides a simple report-like interface for genomic entities such as genes, transcripts, proteins and variants. Users can explore the data using predefined query templates, or can construct complex queries using the QueryBuilder tool. Query results are provided as tables that can be filtered, reorganized, expanded to include more information, and downloaded in various formats. The List and Genomic Regions tools allow users to upload lists of identifiers or chromosome coordinates, respectively, to create custom integrated datasets. Functions such as List Intersection are useful for meta-analyses.