[ensembl-dev] Notice for developers using Ensembl APIs and FTP services

[Jorge Batista da Rocha]

Dear Developers,
As highlighted in our publication in Nucleic Acids Research <https://academic.oup.com/nar/article/53/D1/D948/7916352>, work on the new Ensembl platform is well underway and can already be explored at beta.ensembl.org <http://beta.ensembl.org/>. As we continue to transition to the new platform, we would like to share important updates on upcoming changes that will affect how Ensembl data can be accessed programmatically.
With the release of Ensembl 116 (vertebrates) and Ensembl Genomes 63 (non-vertebrates), which we expect in spring 2026, the current Ensembl APIs and public MySQL servers will be frozen. The FTP access points https://ftp.ensembl.org/ <https://ftp.ensembl.org/pub/> and https://ftp.ensemblgenomes.ebi.ac.uk/ <https://ftp.ensemblgenomes.ebi.ac.uk/pub/> will also be frozen. Access to the existing endpoints and databases will remain until new Ensembl platforms offer equivalent functionality. However, they will no longer receive new data or be updated.
Going forward, all new and updated data will be made available exclusively through the new Ensembl site, beta.ensembl.org <http://beta.ensembl.org/>. We are actively developing programmatic access to new data, such as the Ensembl GraphQL service <https://beta.ensembl.org/help/articles/using-graph-ql>, the Ensembl refget service <https://beta.ensembl.org/help/articles/accessing-ensembl-s-refget-services>, and the Ensembl Beta FTP <https://ftp.ebi.ac.uk/pub/ensemblorganisms/>. Please note that the structure of the Ensembl Beta FTP <https://ftp.ebi.ac.uk/pub/ensemblorganisms/> is under active development and is expected to change. We will inform you via this Ensembl Dev mailing list <https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org> as soon as new resources or updates become available.
Please also note that in summer 2026, the URL for ensembl.org <http://ensembl.org/> will redirect to the site currently hosted at beta.ensembl.org <http://beta.ensembl.org/>. We will implement URL resolution to ensure the navigation of hard-coded URL links remains intact as far as possible. The Ensembl 116 and corresponding Ensembl Genomes 63 sites will be moved to our archive <https://www.ensembl.org/info/website/archives/index.html> collection, and these will maintain enhanced tool functionality beyond what standard archives offer, including the Ensembl VEP interface. We will begin to sunset the tool functionality of these sites when sufficient parity is offered through beta.ensembl.org <http://beta.ensembl.org/>.
We encourage you to review your use of Ensembl APIs and MySQL servers, and plan to migrate your workflows to the new Ensembl platform over time.
We greatly appreciate your collaboration and patience during this transition. If you have any questions, concerns or require assistance, please do not hesitate to contact us via the Ensembl Helpdesk at helpdesk at ensembl.org <mailto:helpdesk at ensembl.org>.
All the best,
Ensembl Outreach
(on behalf of the Ensembl team)


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