The FAANG (Functional Annotation of ANimal Genomes) Consortium is "a coordinated international action to accelerate genome to phenome" and aims to generate comprehensive maps of functional elements in genomes of domesticated animals. Data generated by the FAANG Consortium will enhance the use of animal models in the biological and biomedical sciences. It will hasten discoveries in fundamental biology, as well as those that impact human health, animal well-being and agricultural production. In order for the FAANG effort to have substantial impacts on science and society, the data must be accessible to scientists and students of diverse disciplines. Effective use of the FAANG data will require data mining tools that enable easy search and retrieval.
FAANGMine is a project supported by the National Science Foundation to address the need for a high performance data mining resource that enables fine-grained querying and integrating the heterogeneous FAANG data with existing information, such as functions of known genes and research datasets. The specific aims of the project are to 1) develop FAANGMine - a high-performance data mining system that integrates genome assemblies and currently available annotation data for FAANG species, 2) extend FAANGMine by integrating new data generated by the FAANG Consortium, 3) create a FAANGMine user community that consists of students and scientists working on genetics of domesticated animal species. FAANGMine will empower animal researchers, with or without bioinformatics programming skills, to leverage the FAANG data in their research, thereby accelerating discoveries that elucidate the genetic basis of phenotypic variation.
FAANGMine v1.1 (July 2019) is available. The first FAANGMine release integrates the reference genomes of cat, cattle, chicken, dog, goat, horse, pig, sheep and water buffalo with a variety of external data sources, including genes (NCBI, Ensembl), proteins (UniProt), protein families and domains (InterPro), orthologs and paralogs (Ensembl Compara, OrthoDB, TreeFam), pathways (KEGG, Reactome), interactions (BioGRID, IntAct), Gene Ontology (UniProt), variants and variant effects (Ensembl Variation), QTL (AnimalQTLdb) and publications (PubMed). We regret that due to a data integration issue, pig variants and variant effects are not available in this release; we are working to resolve the issue. Future releases will include gene expression levels computed based on reference RNA-seq datasets, and analyzed FAANG datasets with metadata (e.g. computed regulatory elements and chromatin states).
Please contact us if you have questions or suggestions for FAANGMine.