AquaMine is a data mining system that integrates genome assemblies and gene annotation data for aquatic eumetazoan species of importance to US aquaculture and fisheries. The first database release (AquaMine v1.1) contains RefSeq genes and additional annotation data sources that may be available for each species, including Ensembl, KEGG, UniProt, Gene Ontology, PubMed, and OrthoDB. Genes of human, fruit fly, owl limpet and zebrafish are also included to allow users to leverage information from model organisms based on orthology. AquaMine also contains a precomputed orthology dataset called AquaMine-Ortho that encompasses all species, including those not found in OrthoDB or Ensembl. The AquaMine Taxonomy page shows all AquaMine species in their taxonomic context. A complete list of data sources is provided on the AquaMine Data Source page.
AquaMine was developed using the InterMine genomic data mining platform, which includes a web application that provides several search tools, including a simple key word search, predefined template queries, the QueryBuilder Tool for creating custom queries, the Regions Search Tool for coordinate-based queries, and the List Tool for uploading and searching with lists of identifiers. Query results are exportable in several formats, including tab-delimited.
We are working to incorporate pre-computed RNA-Seq based gene expression levels and comprehensive Gene Ontology annotation to augment the data from existing resources, into future AquaMine releases. We also seek data from US aquaculture genome researchers, including genomic variation and functional annotation data.