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.

Due to a major loss of cooling incident at one of the EMBL-EBI data centres, there was reduced Ensembl functionality between Saturday 2nd February and Wednesday 6th February.

However, as of Wednesday 6th February, all Ensembl and Ensembl Genomes services have now been restored and are working as normal.

If you encounter any further issues, please report them to the Ensembl Helpdesk.

Thank you for your understanding and patience while we worked to fully restore our services.

This blog post is a joint contribution by Joannella Morales, Jane Loveland, Adam Frankish, Fiona Cunningham and Astrid Gall.

We are pleased to introduce the Matched Annotation from the NCBI and EMBL-EBI (MANE) project. This new joint initiative between EMBL-EBI’s Ensembl project and NCBI’s RefSeq project aims to release a genome-wide transcript set that contains one well-supported transcript per protein-coding locus. All transcripts in the MANE set will perfectly align to GRCh38 and will represent 100% identity (5’UTR, coding sequence, 3’UTR) between the RefSeq (NM) and corresponding Ensembl (ENST) transcript.
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Functional genomics data from DANIO-CODE has been released to the public. This international effort, similar to ENCODE in human and mouse, seeks to characterise the functional elements in the zebrafish (Danio rerio) genome. Announced on Saturday at the International Zebrafish Conference, the DANIO-CODE dataset exists as a track hub, which can be viewed in Ensembl.

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From Ensembl 93 onwards, we plan to recommend newer versions of Perl (5.14- 5.26) and BioPerl (1.6.924) when using the Ensembl Perl API. This may affect pipelines which employ the Ensembl Perl API, since we will no longer actively support older versions of Perl and BioPerl.

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I am writing in my capacity as leader of the Ensembl project based at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) based near Cambridge, England. Ensembl is one of the world’s leading sources of genome information and a central aggregation point for genomic data.

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Please note that the archive websites for Ensembl releases 71 (April 2013) and 72 (June 2013) will be retired in July when version 85 is released.

This is in accordance with our rolling retirement policy, whereby archives more than three years old are retired unless they include the last instance of the previous assembly from one of our key species (human, mouse and zebrafish).

For more information about how to use archives, please see our previous blog post on the topic; a list of all current archives is available on the main website.