The ChEMBL-og

  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...

Over a decade ago, when installing cheminformatics toolkits like RDKit was not for the faint-hearted, Michał Nowotka from our team created Beaker — a lightweight web service that exposed RDKit functionality via a simple REST API. The goal was simple: make it easy for anyone to perform cheminformatics operations without having to wrestle with complex build chains, platform quirks, or dependency headaches. For many researchers, Beaker became a convenient gateway into the world of cheminformatics, enabling structure standardisation, property calculation, and more — all without a local installation of RDKit. Why We’re Shutting It Down The landscape today is very different from when Beaker was first released. Installing RDKit has become dramatically simpler, thanks to well-maintained conda packages and PyPI distributions, as well as clear documentation across platforms. With these improvements, the original need for Beaker has largely disappeared. Maintaining Beaker still requires developer...

In support of Egon Willighagen's ' One Million IUPAC Names ' project, we have just released more than 4 million IUPAC names text-mined from patents. Here are the details as listed on Zenodo:    What: This file contains IUPAC names text-mined from patents (US, WIPO, EPO, Chinese, Japanese).  Who: This file is provided by the SureChEMBL project under a CC0 license. We are part of the Chemical Biology Services team at EMBL-EBI. Please cite us appropriately if you use this dataset (thanks!). Format:  This is a gzipped TSV file with two columns, IUPAC Names and SMILES. The IUPAC Names column may itself contain multiple IUPAC names separated by an exclamation mark (!). Each of these names resolves to the same SMILES and they differ only in casing. They are sorted such that the name with fewer uppercase characters comes first. Details: As part of the SureChEMBL text-mining pipeline, we recognise and extract IUPAC names in patents. These are stored in...