Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates (+2 others)
2017 Database: The Journal of Biological Databases and Curation  
Citation details: Ruffier,M., K€ ah€ ari,A., Komorowska,M., et al. Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. Abstract The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome
more » ... urces. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome V C The Author(s) annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at
doi:10.1093/database/bax020 pmid:28365736 pmcid:PMC5467575 fatcat:cyjhn5h6eve3jopkwrbt23gwne