An Integrated Annotation Data Warehouse at the Hymenoptera Genome Database

The Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org) is a genome informatics resource for hymenopteran insect species. HGD includes genomic data of three honey bee species (Apis mellifera, A. florea, A. dorsata), two bumble bee species (Bombus terrestris and B. impatiens), nine ant species (Acromyrmex echinatior, Atta cephalotes, Camponotus floridanus, Cardicondyla obscurior, Harpegnathos saltator, Linepithema humile, Pogonomyrmex barbatus, Solenopsis invicta, Wasmannia auropunctata), a parasitoid wasp (Nasonia vitripennis) and a sweat bee (Lasioglossum albipes).  We have used InterMine to deploy a new data warehouse called HymenopteraMine to allow fast and flexible queries of annotation and ortholog data across species. HymenopteraMine integrates information from many data sources including RefSeq, UniProt, InterPro, OrthoDB, Pubmed and Gene Ontology. Users may perform a “Quick Search” or use the “Query Builder” for specialized searches. The “Genome Region Search” and “Overlapping Feature Search” allow users to download annotations with a specified genomic context. Links between genes and publications facilitate access to relevant scientific literature. Users may download query results in various formats, such as tab-delimited files, GFF, Fasta, BED, JSON and XML. In addition to HymenopteraMine, users may leverage the HGD genome browsers (GBrowse and JBrowse), BLAST searching and data download pages to access genome assemblies, computed and manually-annotated genes, protein homologs, cDNA sequences, non-coding RNA sequences, RNAseq-based expression data and genetic markers.