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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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.