Integrated Release available now on Ensembl Beta

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We have released a coordination of genomic resources and analyses to the new Ensembl site: Ensembl Beta – https://beta.ensembl.org/. This Integrated Release, “Beta Release 2025-02”, contains 2,919 genomes, which are available for current and long-term use.

Ensembl Beta Partial and Integrated Releases explained 

There are two types of releases available via Ensembl Beta: Partial releases and Integrated releases. 

Partial releases provide access to new or changed data and are typically scheduled every two to three weeks. Data included in a partial release may be updated or overwritten to apply fixes or patches as needed. Hence, these releases are stable in the short term, but caution should be taken in using this data for long-term processes (read more below). 

Integrated releases provide interoperable datasets for previously released genomes across multiple species. Data in an integrated release are fixed to the time point at which they occur, with an expected frequency of three to four months. Integrated releases offer long-term stability and are better suited for processes that require consistent data over time.

  • Partial releases are data releases that include:
    • Assemblies
    • Annotations
      • Genes, Exons, Transcripts and other Features
      • External References (Xrefs)
      • Statistics
      • Variant data
      • Regulation data
    • Different datasets for the same genome, which are released in different partial releases
    • Data that are delivered as soon as possible 
  • Integrated releases are linkage releases that include:
    • An updated collection of all data across all species 
    • The most comprehensive Ensembl analysis available at the time of release
    • Data that will not change over time (analogous to a traditional Ensembl release)
    • Data that was made available in partial releases, but further developments are coming for whole release processes.
A diagram showing the new Ensembl release cycle. Partial releases can be available every two weeks. Integrated releases include a set of partial releases every three to four months.

Ensembl Release Cycle for the new Ensembl Website

How to tell if a species is on an integrated release

When using the Species selector app to select the assembly you wish to browse, you can find the date of the release in the “Release” column, and the type of the release in the “Release type” column. 

Screenshot of the new Ensembl species selector app with the details of the release type highlighted

View of the Species selector app and the information columns containing release information

You may select any combination of data to browse, including genomes from integrated and partial releases for the same assembly. Doing so will display date bubbles on the lozenges for those assemblies, helping you identify them across other applications on the site.

Screenshot of the species lozenges with the date bubbles enabled and highlighted

View of assembly lozenges with date bubbles enabled.

After an integrated release occurs, you may need to recheck or reset your selection of species to continue using the species you were previously working with. Selected species can be amended by using the “Manage” option above the assembly lozenges.

Using partial release datasets:

Partial releases provide access to data as soon as possible. Partial release data is available on both Ensembl Beta and the Ensembl FTP site. While data released in a Partial release is subjected to automated quality control procedures, manual curation is not likely to have taken place. When required, partial release data may be supplanted when updated, so access to the previous iteration of a partial release will be lost. We expect supplanting to be an infrequent event. 

A selection of partial releases will be selected to be included in an integrated release. Not all partial data releases are guaranteed to be in an integrated release. 

Data found erroneous will not be removed from previous integrated releases, but will not be added to future integrated releases. In these cases, new partial data may go forward into the next integrated release.

The new Ensembl site is still in active development 

The new Ensembl site is currently under development, so you may notice frequent updates and changes. To stay up-to-date about the latest news and data releases, please subscribe to our mailing lists. 

If you have any questions or feedback about the new Ensembl browser or databases, please get in touch with us via the Ensembl Helpdesk.

Authored by: Beth Flint, Daniel Poppleton, Jon Keatley, Jorge Batista da Rocha

Reviewed by: Natalie Willhoft, Aleena Mushtaq, Louisse Paola Mirabueno