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. AquaMine v1.2, which was released in July 2023, contains RefSeq genes and additional annotation data sources that may be available for each species, including Ensembl, KEGG, UniProt, OrthoDB, European Variation Archive and PubMed. The new AquaMine-GO-Annotation dataset contains Gene Ontology (GO) annotations for all species. AquaMine-Ortho is a precomputed orthology dataset that encompasses all species, including those not found in OrthoDB or Ensembl. AquaMine also now contains pre-computed RNA-seq based gene expression levels for some species. Genes of human, fruit fly, owl limpet and zebrafish are included to allow users to leverage information from model organisms based on orthology. 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. See the Release-Update page for a list of new data that is available in AquaMine v1.2.
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.