Abstract
The Functional Annotation of ANimal Genomes (FAANG) project is a worldwide coordinated action creating high-quality functional annotation of farmed and companion animal genomes. The generation of a rich genome-to-phenome resource and supporting informatic infrastructure advances the scope of comparative genomics and furthers the understanding of functional elements. The project also provides terrestrial and aquatic animal agriculture community powerful resources for supporting improvements to farmed animal production, disease resistance, and genetic diversity. The FAANG Data Portal (https://data.faang.org) ensures Findable, Accessible, Interoperable and Reusable (FAIR) open access to the wealth of sample, sequencing, and analysis data produced by an ever-growing number of FAANG consortia. It is developed and maintained by the FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). FAANG projects produce a standardised set of multi-omic assays with resulting data placed into a range of specialised open data archives. To ensure this data is easily findable and accessible by the community, the portal automatically identifies and collates all submitted FAANG data into a single easily searchable resource. The Data Portal supports direct download from the multiple underlying archives to enable seamless access to all FAANG data from within the portal itself. The portal provides a range of predefined filters, powerful predictive search, and a catalogue of sampling and analysis protocols and automatically identifies publications associated with any dataset. To ensure all FAANG data submissions are high-quality, the portal includes powerful contextual metadata validation and data submissions brokering to the underlying EMBL-EBI archives. The portal will incorporate extensive new technical infrastructure to effectively deliver and standardise FAANG's shift to single-cellomics, cell atlases, pangenomes, and novel phenotypic prediction models. The Data Portal plays a key role for FAANG by supporting high-quality functional annotation of animal genomes, through open FAIR sharing of data, complete with standardised rich metadata. Future Data Portal features developed by the DCC will support new technological developments for continued improvement for FAANG projects.
Highlights
The Functional Annotation of Animal Genomes Project (FAANG) is a coordinated action to improve availability of high-quality functional annotation of farmed and companion animal genomes (Andersson et al, 2015; Tuggle et al, 2016; Giuffra et al, 2019; Clark et al, 2020)
It is deployed on the EMBL-EBI Embassy Cloud infrastructure2, enabling a flexible and efficient use of computational resources
Functional Annotation of ANimal Genomes (FAANG) utilises the Track Hub Registry3 to seamlessly enable FAANG community generated trackhub annotations to be made discoverable for use with the UCSC (Lee et al, 2020) and Ensembl Genome Browsers (Yates et al, 2020)
Summary
The Functional Annotation of Animal Genomes Project (FAANG) is a coordinated action to improve availability of high-quality functional annotation of farmed and companion animal genomes (Andersson et al, 2015; Tuggle et al, 2016; Giuffra et al, 2019; Clark et al, 2020). The FAANG project comprises multiple globally distributed consortia working across a growing range of species and committed to high-quality data production and interpretation. The FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) ensures that all data generated by the project is richly described, consistently reported, openly available, reusable, and clearly presented (Harrison et al, 2018). The FAANG Data Portal plays a pivotal role by coordinating and presenting the wealth of data generated by the project to the scientific community. We describe the key features of this rich genome to phenome resource and look to future developments that will expand it as research advances
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