It is with heavy hearts but also excitement for the future to announce that the next release of WormBase will also be its last.

WS298 — scheduled for release in October 2025 — will be the final major WormBase release. This includes the process of data analysis and aggregation that creates the WormBase database (the “build”, in our parlance) as well as major development of the WormBase website.

In lieu of generating new releases of WormBase, we will accelerate our efforts to incorporate existing data and services into the Alliance of Genome Resources.  In particular, we will pay special attention to datasets unique to the C. elegans field — think such things as lineage, anatomy, reagents, for example — to ensure that they are not lost. Data types that lack representation at the Alliance will continue to be available via the archival WormBase website.

This transition to the Alliance of Genome Resources architecture will bring new opportunities, tools, and capabilities. Moreover, it will ensure long-term access to the highly curated data that make WormBase such a critical resource for scientists around the world. Here’s what you can expect over the coming months.

Schedule

Date	Expected events
Now through October	WS297 release available on https://www.wormbase.org/ Streamlining of features, including such things as the retirement of WormBase user accounts, user interface changes to accommodate the upcoming archival release, etc.
Mid October	Test release of WS298
End of November	Production release of WS298

Upcoming Changes

Curation

Our experienced team of biological curators will continue their work of extracting data from the scientific literature. Some curation activities may necessarily slow during this transition as we align our efforts with the Alliance of Genome Resources. And as with the current WormBase release cycle, there may be a delay of up to several months before new data is visible on the Alliance website. 

Website

We will continue to maintain the WormBase website. After October 2025, the website will be anchored to the WS298 database release and entered into an archival maintenance mode where only critical bug fixes are addressed. To make long term maintenance easier, we will scale back or retire some features that won’t be replicated at the Alliance. This includes things like user accounts, site customization, and so on. In the coming months, we’ll be highlighting data that hasn’t yet been incorporated into the Alliance.

ACeDB

We’ll maintain a running instance of ACeDB — the canonical database for WormBase — until at least June 2026. We will provide database backup files in both the native .ace and xml formats and the underlying software on our downloads site for the long term. With these files it’s possible to run ACeDB locally. 

Tools

WormMine

There will be one final build of the data mining tool WormMine synchronized with the WS298 release. We will maintain this version of WormMine for the foreseeable future. Development and loading of the AllianceMine will continue and eventually surpass the contents and capability of WormMine.

Genome Browsers

WormBase has already migrated Genome Browsers to the Alliance. However, some species and datasets are still unrepresented there. These will continue to be available through the WormBase website pinned to the WS298 release.

API

The WormBase API will be unaffected although we encourage users to begin transitioning their use to the Alliance API.

Community Outreach

Our community outreach and help desk efforts will remain unchanged for now.  If you have any questions or need any assistance, please contact [email protected]. We aim to respond to all queries within 24 hours.

Archives

In addition to the various files that we already produce and make available with each release, we are preparing a variety of flat files for archival purposes. This will include backup files of all critical databases at WormBase in a variety of formats, flat files of data classes and commonly used datasets, a compressed package of the software that powers the site, and the entirety of the WormBase website as JSON and rendered HTML.  We will make all of these files available on the WormBase downloads site.

Easing the transition

We realize that these changes probably represent an unwelcome disruption to your research. We’re here to help.

To begin, we will introduce features to the WormBase website that will assist in mapping data and functionality to the Alliance site. On select pages, you’ll be presented with an interstitial dialog that will provide an option to view the archived WormBase page or the corresponding page at the Alliance. Later, we will visually highlight data at WormBase that does not exist at the Alliance, making it clearer which data has been migrated and which will only be available at the archived WormBase site. We hope that these changes will make it easier and faster to start using the Alliance in support of your research.

We’ll be available to help you find data on the Alliance, to download important datasets from WormBase, to assist with migrating workflows, and to ensure that no important data sets are lost during this transition. 

Questions, comments, or concerns?  Please contact us at [email protected].