TY - JOUR T1 - Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation JF - bioRxiv DO - 10.1101/087239 SP - 087239 AU - Magali Ruffier AU - Andreas Kähäri AU - Monika Komorowska AU - Stephen Keenan AU - Matthew R. Laird AU - Ian Longden AU - Glenn Proctor AU - Searle Steve AU - Daniel Staines AU - Kieron Taylor AU - Alessandro Vullo AU - Andrew Yates AU - Daniel Zerbino AU - Paul Flicek Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/11/087239.abstract N2 - 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 resources. 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 annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. Our databases and APIs are publicly available and all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl. ER -