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Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects

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Eukaryotic Genomic Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1757))

Abstract

The Hymenoptera Genome Database (HGD; http://hymenopteragenome.org) is a genome informatics resource for insects of the order Hymenoptera, which includes bees, ants and wasps. HGD provides genome browsers with manual annotation tools (JBrowse/Apollo), BLAST, bulk data download, and a data mining warehouse (HymenopteraMine). This chapter focuses on the use of HymenopteraMine to create annotation data sets that can be exported for use in downstream analyses. HymenopteraMine leverages the InterMine platform to combine genome assemblies and official gene sets with data from OrthoDB, RefSeq, FlyBase, Gene Ontology, UniProt, InterPro, KEGG, Reactome, dbSNP, PubMed, and BioGrid, as well as precomputed gene expression information based on publicly available RNAseq. Built-in template queries provide starting points for data exploration, while the QueryBuilder tool supports construction of complex custom queries. The List Analysis and Genomic Regions search tools execute queries based on uploaded lists of identifiers and genome coordinates, respectively. HymenopteraMine facilitates cross-species data mining based on orthology and supports meta-analyses by tracking identifiers across gene sets and genome assemblies.

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Acknowledgments

The authors would like to thank Colin M. Diesh for his contributions to the development of HymenopteraMine, HGD BLAST, and HGD JBrowse/Apollo. This work was supported by USDA National Institute of Food and Agriculture Hatch Project 1009273 and Agriculture and Food Research Initiative Competitive grant no. 2010-65205-20407.

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Authors and Affiliations

  1. Division of Animal Sciences, University of Missouri, Columbia, MO, USA

    Christine G. Elsik, Aditi Tayal, Deepak R. Unni, Gregory W. Burns & Darren E. Hagen

  2. Division of Plant Sciences, University of Missouri, Columbia, MO, USA

    Christine G. Elsik

  3. MU Informatics Institute, University of Missouri, Columbia, MO, USA

    Christine G. Elsik

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  1. Christine G. Elsik
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Correspondence to Christine G. Elsik .

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  1. Group Systems Biology of Motor Proteins, Department of NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany

    Martin Kollmar

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Elsik, C.G., Tayal, A., Unni, D.R., Burns, G.W., Hagen, D.E. (2018). Hymenoptera Genome Database: Using HymenopteraMine to Enhance Genomic Studies of Hymenopteran Insects. In: Kollmar, M. (eds) Eukaryotic Genomic Databases. Methods in Molecular Biology, vol 1757. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7737-6_17

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  • DOI: https://doi.org/10.1007/978-1-4939-7737-6_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7736-9

  • Online ISBN: 978-1-4939-7737-6

  • eBook Packages: Springer Protocols

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