For some years we have made our database admin interface publicly available via the Ensembl “public-plugins” repository, allowing you to edit certain fields in your core databases via a web form. However we are now using an alternative interface developed by our production team (written in Python), and will therefore be retiring the old plugin in release 97 (scheduled for June 2019).

If you are currently using the plugin and would like to know more about migrating your project to the new code, please contact us and we’ll try to help!

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.
Continue reading

As the community’s capacity for genome sequencing expands, so do its ambitions. Recently, many exciting global genomics projects have been launched, including the Vertebrate Genomes Project (VGP), Darwin Tree of Life (DToL), Earth Biogenome Project EBP, i5K (insects) and 10KP (plants). Between them, they aim to sequence the genomes of every eukaryote on Earth, and Ensembl are excited to take on the annotation of some of those genomes.

Continue reading

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.
Continue reading

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.

Continue reading