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

By Magali Ruffier, Andreas Kähäri, M. Komorowska, S. Keenan, Matthew R. Laird, Ian Longden, G. Proctor, S. Searle, D. Staines, K. Taylor and 4 more. 2016

63 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

CADD: predicting the deleteriousness of variants throughout the human genome (2018, positive): “The proxy-neutral variants have an allele frequency of 95–100% in humans but are absent in the inferred genome sequence of the human-ape ancestor (i.e. human-derived and fixed or nearly fixed; identified from Ensembl EPO (14) whole genome alignments; 15 million SNVs and 1.8 million In-Dels).”
Ensembl 2020 (2019, methodology): “Ensembl offers training (http://training.ensembl.org/) to researchers across the world where we deliver one of our three courses: an Ensembl browser course aimed at wetlab researchers and clinicians, an Ensembl REST API course aimed at bioinformaticians and Ensembl Train the Trainer (TtT) courses.”
Ensembl 2021 (2020, methodology): “These data can be accessed via our website, programmatically via a number of application programming interfaces (APIs) (7,8), and downloaded in numerous standard file formats.”