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Bovine Genome Database: Tools for Mining the Bos taurus Genome

  • Darren E. Hagen
  • Deepak R. Unni
  • Aditi Tayal
  • Gregory W. Burns
  • Christine G. Elsik
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1757)

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.

Key words

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

Notes

Acknowledgments

The authors would like to thank Colin M. Diesh for his contributions to the development of BovineMine, BGD BLAST, and BGD JBrowse/Apollo. This work was supported by funding from the European Union’s Seventh Framework Programme for research, technological development, and demonstration under grant agreement no. 613689.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Darren E. Hagen
    • 1
  • Deepak R. Unni
    • 1
  • Aditi Tayal
    • 1
  • Gregory W. Burns
    • 1
  • Christine G. Elsik
    • 1
    • 2
    • 3
  1. 1.Division of Animal SciencesUniversity of MissouriColumbiaUSA
  2. 2.Division of Plant SciencesUniversity of MissouriColumbiaUSA
  3. 3.MU Informatics InstituteUniversity of MissouriColumbiaUSA

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