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Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England..
European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England.;Eli Lilly & Co Ltd, Lilly House,Priestley Rd, Basingstoke RG24 9NL, Hants, England..
European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England..
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2017 (English)In: Database: The Journal of Biological Databases and Curation, ISSN 1758-0463, E-ISSN 1758-0463, article id bax020Article in journal (Refereed) Published
Abstract [en]

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. 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 http://github.com/Ensembl and we have an active developer mailing list (http://www.ensembl.org/info/about/contact/index.html).

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2017. article id bax020
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:uu:diva-320207DOI: 10.1093/database/bax020ISI: 000397532900001PubMedID: 28365736OAI: oai:DiVA.org:uu-320207DiVA, id: diva2:1088931
Funder
Wellcome trust, WT108749/Z/15/Z WT200990/Z/16/Z WT201535/Z/16/ZEU, European Research Council, LSHG-CT-2003-503265 284209Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2018-01-13Bibliographically approved

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