Bovine Genome Database: Tools for Mining the Bos taurus Genome

Methods Mol Biol. 2018:1757:211-249. doi: 10.1007/978-1-4939-7737-6_9.

Abstract

The Bovine Genome Database (BGD; http://bovinegenome.org ) is a web-accessible resource that supports bovine genomics research by providing genome annotation and data mining tools. BovineMine is a tool within BGD that integrates BGD data, including the genome, genes, precomputed gene expression levels and variant consequences, with external data sources that include quantitative trait loci (QTL), orthologues, Gene Ontology, gene interactions, and pathways. BovineMine enables researchers without programming skills to create custom integrated datasets for use in downstream analyses. This chapter describes how to enhance a bovine genomics project using the Bovine Genome Database, with data mining examples demonstrating BovineMine.

Keywords: Bos taurus; Bovine; BovineMine; Cattle; Data mining; Gene expression; Genome annotation; Genome database; InterMine; Orthology; Pathway; Single nucleotide polymorphism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cattle
  • Computational Biology / methods
  • Data Mining / methods
  • Databases, Genetic*
  • Gene Expression
  • Genetic Variation
  • Genome*
  • Genome-Wide Association Study
  • Genomics* / methods
  • Meta-Analysis as Topic
  • Molecular Sequence Annotation
  • Quantitative Trait Loci
  • Software
  • User-Computer Interface
  • Web Browser*