The ChEMBL-og

Last year, when I wanted to look at the evolution of ChEMBL over time I found it quite tricky . There were 34 releases at that point, but there was only one database format which was available for all 34 versions - MySQL. But downloading and installing all of these versions was painful as the contents of the .tar.gz are mostly but not exactly consistent, and the appropriate install command has changed a bit over the years. At the same time, since ChEMBL 19 we have provided SQLite versions of ChEMBL. This format is one of the few recommended formats for datasets as specified by the US Library of Congress (alongside JSON, CSV and XML). SQLite is an inherently simpler database format to deal with as it doesn't require the user to setup a server and import the database; rather we provide a .sqlite file which the user can use straightaway after unzipping the .tar.gz. A member of our community, Charles Tapley Hoyt, has gone further and built on this with the ChEMBL Downloader project...

  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...

Image generated using DALLE-3 Introduction Dear ChEBI users, If you have visited the ChEBI website recently, you have been able to intuit that something really great is just about to come. Our team has been working for the last three years on the redevelopment of ChEBI , which includes: a new website, modern infrastructure, a new submission and curator tool and improvements in the ChEBI data products (ontology, TSV flat files, SDF files, database dump). Many things to cover in one single post, for that reason, this is one in a series of blog posts describing ChEBI 2.0. Today, we are going to take a look at the ChEBI data products enhancements. What is new? We are going to describe the changes according to the type of product, starting with one of our most widely used data products: the ChEBI Ontology. ChEBI Ontology These are the changes we have implemented: Homogenized prefixes We decided to homogenise the ChEBI prefixes. In the past, we used to have http://purl.obolibrary.org/obo/ch...

The Chemical Biology Services team invites applications for a 3-year ARISE2 Postdoctoral Fellowship – a unique postdoctoral opportunity that combines advanced research training with hands-on experience in developing innovative technologies and methods to enhance scientific services. Why apply? Make an Impact: Collaborate on high-impact projects that will directly shape and improve the scientific services we provide. Tailored to You: Each fellowship project is developed in collaboration with the fellow and the host team – possibly even involving an industry partner – to ensure a project that combines your ideas with the vision of of the host. Prepare for the Future: The ARISE2 Fellowship is designed to prepare fellows for dynamic careers within research infrastructures, providing both technical depth and professional development. If this sounds interesting, please get in touch by the end of August at oboyle@ebi.ac.uk with your CV. Note that we recruit worldwide. Here is a ...