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ChEBI Web Services Retiring on 1st September

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 ChEBI Web Services Retiring on 1st September


Over the last few years we’ve been rebuilding ChEBI from the ground up so it’s faster, easier to maintain, and ready for the next decade. If you missed the background story and what’s changed under the hood, our earlier post has the details. https://chembl.blogspot.com/2025/07/redevelopment-of-chebi.html

TL;DR

  • The new ChEBI web interface is live at https://www.ebi.ac.uk/chebi/beta/

  • Old SOAP web services will be retired on 01 September 2025; please move to our REST APIs (https://www.ebi.ac.uk/chebi/backend/api/docs/) now. This is the new stable endpoint and will remain so for ChEBI 2.0.

  • Old data product formats are being deprecated end of September 2025; new ChEBI 2.0 data products are already available at https://ftp.ebi.ac.uk/pub/databases/chebi-2 (moving to https://ftp.ebi.ac.uk/pub/databases/chebi after switch-over)

  • Final switch-over: by end of September 2025, the new ChEBI 2.0 interface will replace the current one at https://www.ebi.ac.uk/chebi/

What’s changing and why

We began a full redevelopment of ChEBI because the legacy codebase had become difficult to maintain and upgrade. The new platform uses modern technologies, brings a streamlined PostgreSQL schema, adds a faster search (Elasticsearch + RDKit) and ships a refreshed public UI.

For data consumers, we’ve modernised data products (ontology, TSV, SDF, and database dump), standardised prefixes (including CHEMROF and RO), and improved metadata (license, versioning, datatypes). 

Key dates

  • Now — Beta web interface: https://www.ebi.ac.uk/chebi/beta/.
    Most features of the old site are present; remaining gaps will be filled over time. Please test and report issues

  • 1st September 2025: 

    • Old web services to be deprecated; new Rest APIs available at https://www.ebi.ac.uk/chebi/backend/api/docs/

  • End of September 2025 — Switch-over:

    • New interface moves from https://www.ebi.ac.uk/chebi/beta/ to https://www.ebi.ac.uk/chebi/

    • Old data products deprecated; new products live at https://ftp.ebi.ac.uk/pub/databases/chebi-2 (moving to the standard .../chebi path once the legacy site is turned off).

    • Legacy site is turned off

Web interface

  • Where to try it today: https://www.ebi.ac.uk/chebi/beta/

  • Where it will live after cut-over: https://www.ebi.ac.uk/chebi/
    The beta delivers faster search, structure handling via RDKit, and an improved ontology widget for exploring relationships.

Programmatic access (APIs)

  • Old (to be retired): SOAP web services at https://www.ebi.ac.uk/chebi/webServices.do

  • New (use this now): REST API docs at https://www.ebi.ac.uk/chebi/backend/api/docs/ (Swagger UI)

What to do:
If your workflows call the SOAP endpoints, please switch to the new REST APIs now. You can find a Google Notebook comparing old and new web services here

Data products and downloads

New ChEBI 2.0 data products (ontology, TSVs without secondary IDs, SDF, and a PostgreSQL dump) are available today. During the beta period, they’re hosted under …/chebi-2 and will move to the standard …/chebi FTP location once the legacy site is decommissioned. Detailed changes (including homogenised prefixes and datatype fixes) are described in our data-products post here.

Submission Portal

ChEBI 2.0 introduces a redesigned submission portal, now available in beta at https://www.ebi.ac.uk/chebi/backend/submit/. We encourage you to explore and test the new system, but please continue to submit data through the current portal until the end of September 2025. 

At the final switch-over, the legacy submission portal will be retired and all submissions will move to the new platform. 

You can sign in to the new portal using the same email address you registered with previously. A password reset may be required the first time you log in.

What’s not changing

  • Stable identifiers: ChEBI IDs remain your stable, citable identifiers.

  • Open licence: ChEBI data continue to be available under CC BY 4.0.

  • Data continuity: All ChEBI data from the legacy platform has been migrated to ChEBI 2.0

How you can help us make it great

  • Try it out: use the beta site for your day-to-day lookups.

  • Migrate scripts: move from SOAP to REST, and try the new data products.

  • Share feedback: Please reach out to us if you have any questions or to share feedback about the new platform at chebi-help@ebi.ac.uk

Thank you

ChEBI exists for (and because of) its community of researchers, developers, and curators. Your early testing and feedback on the beta will help ensure a smooth transition for everyone. If you rely on ChEBI in production pipelines, please begin your migration now and reach out if you need help.
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