The SARS-CoV-2 pandemic presents a serious challenge to healthcare, economies and societies across the globe, one that has demanded an unprecedented scientific response. Projects across multiple disciplines are now re-directing their usual analytical efforts to meet this challenge head-on, and GENCODE are no exception. Our project produces human gene annotation, and we’re contributing to this scientific effort by re-examining human genes that may be relevant to viral infection and COVID-19 disease. We hope this work will support further research along these lines. For example, updated gene annotation could benefit studies to find disease-linked variants in patients with severe COVID-19 symptoms, including work by Genomics England and others.
Continue readingTag: Ensembl
Reduced functionality: 10th March – 16th April 2020
Update: The Ensembl and Ensembl Genomes services have now been restored following this period of reduced functionality.
Continue readingEnsembl 99 has been released!
We’re pleased to announce the release of Ensembl 99, and the corresponding release of Ensembl Genomes 46. Along with updates of human gene annotation and variation data, we have a menagerie of new and updated vertebrate species in Ensembl plus a whole set of new plants, mosquitos and flies in Ensembl Genomes.
What’s coming up in Ensembl release 99?
Ensembl 99 (and Ensembl Genomes 46) are due out in December and we plan to include a bumper set of new and updated species. As with all releases, we cannot guarantee that anything listed here will make it into the final release.
Getting to know us: Astrid from Outreach
Ever wondered what an Outreach Officer does? Meet Astrid who talks about her job and how she got here.
Ensembl 97 and Ensembl Genomes 44 have been released!
Ensembl 97 and Ensembl Genomes 44 have been released! In this release you’ll find many new species, including some hybrid livestock, as well as important changes to gene sets for human and mouse and a new update to the human Regulatory Build.
Read on to explore the full details.
Changes to FTP directory layout in Ensembl Genomes 43 / Ensembl 96
We will make changes to the directory layouts of both the Ensembl Genomes FTP server (ftp://ftp.ensemblgenomes.org/pub/) and the Ensembl GRCh37 FTP server (ftp://ftp.ensemblorg.ebi.ac.uk/pub/grch37/) that may affect your pipelines. These changes will come into effect in Ensembl Genomes release 43/Ensembl release 96, which are scheduled for April 2019. Here are the details, so that you can plan any required updates to existing scripts and pipelines ahead of the releases.
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Joint REST server for Ensembl and Ensembl Genomes in Ensembl 96
As of Ensembl release 96/Ensembl Genomes release 43, we will retire rest.ensemblgenomes.org and invite you to use rest.ensembl.org instead.
Removal of ontology database patching SQL scripts from Ensembl repository in Ensembl 96
In the next release of Ensembl (Ensembl 96) we will remove our ontology database patching scripts from the main Ensembl repository.
There is now a dedicated module using the EBI OLS service to load Ensembl required ontologies. Considering this module is now in charge of loading the required data, the previous databases patches have been moved to the ols-ensembl-loader repository.
If you need to update your system with future patches, please now refer to the ols-ensembl-loader repository sql directory where files are already available.
Please contact the Ensembl Helpdesk if you have any questions or want to find out more about how this might affect your work.
Getting to know us: Guy from Ensembl Plants
Today we are meeting Guy, who works in the Plants team of Ensembl Genomes. He talks about how he came to Ensembl, his interests and experiences so far.