FAANGMine Genomic Data Warehouse for Farm Animal Species.

The predictive potential of functional annotation requires that regulatory data be interpreted in the contexts of genes, expression, variants and traits. FAANGMine (https://faangmine.elsiklab.missouri.edu/) is a data warehouse that brings them into a single framework, facilitating the exploration of regulatory elements, variants, QTL, genes and gene annotations in farm animal species. It was designed to highlight reference functional annotation datasets generated by members of the Functional Annotation of Animal Genomes (FAANG) Consortium. FAANGMine was developed using the InterMine biological data warehousing system, enhanced to support the integration of tissue-specific functional annotation data, including chromatin states, chromatin accessibility, chromatin architecture, histone modifications and CTCF binding sites. A rich set of associated metadata supports flexible and focused queries. The functional annotation data are integrated with gene annotation data from a variety of sources as well as pre-computed RNA-seq-based gene expression levels. External data sources include RefSeq, Ensembl, KEGG, Reactome, OrthoDB, Online Mendelian Inheritance in Man, UniProt, Gene Ontology, AnimalQTLdb, InterPro and PubMed. Data retrieval with FAANGMine is achieved with web-based search tools or an application programming interface. In addition to the FAANGMine data-mining application, the FAANGMine website includes JBrowse genome browsers for visualization of regulatory elements in the context of genes, expression, QTL and single nucleotide variants.