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’re fortunate to be part of the EMBL European Bioinformatics Institute (EBI), which puts us alongside stellar bioinformaticians and resources in every discipline. From this, great collaborations can grow. We’ve already worked with our colleagues at Gene Expression Atlas and Reactome to embed widgets in Ensembl for viewing baseline gene expression and biochemical pathways respectively, but our latest collaboration is with the Protein Data Bank in Europe (PDBe) to show genetic variation on protein structures.

Continue reading

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

Joannella Morales, Jane Loveland and Adam Frankish contributed to this post.

Back in October, we introduced you to our new joint initiative with the NCBI — the Matched Annotation from the NCBI and EMBL-EBI (MANE) transcript set. We are now pleased to update you on our progress so far.

The goal of this project is to share annotation and converge on a high-confidence, genome-wide transcript set, with a matched transcript in both RefSeq and Ensembl/GENCODE. We are doing this in two phases. During phase 1, we will release the “MANE Select” transcript set to include one well-supported transcript for every protein-coding locus. We envision the adoption of the MANE Select set as a default set across genomics resources. In phase 2, we intend to release an expanded set (“MANE Plus”) to include additional transcripts per locus that are well-supported or of particular user interest.

Continue reading