The ChEMBL-og

ChEBI 2.0 is here! We’re excited to announce the release of ChEBI 2.0!  The next generation of the Chemical Entities of Biological Interest database. If you missed the background story and the details of the redevelopment, you can catch up in our earlier blog post here . What’s Changed: The new ChEBI web interface is live at https://www.ebi.ac.uk/chebi/   Legacy SOAP web services are deprecated — please migrate to our REST APIs  New ChEBI 2.0 data products (ontology, TSV, SDF, PostgreSQL dump) are available at https://ftp.ebi.ac.uk/pub/databases/chebi Submitter accounts have been migrated — you’ll need to reset your password before logging into the new submission portal Why ChEBI 2.0? The legacy ChEBI codebase had become increasingly difficult to maintain and update. ChEBI 2.0 has been rebuilt from the ground up with:  Simplified PostgreSQL schema  Faster search powered by Elasticsearch + RDKit  Refreshed public user interface modern infrastructure (Kuberne...

     The Basics of ChEMBL Data Deposition Shortly, we are starting work on ChEMBL 37. Thus, we are running a 1 hour data depositor webinar , for anyone who is planning to deposit data to ChEMBL 37. If you are subscribed to the ChEMBL-depositors mailing list you will have heard about this already. If not, and you have an interest in depositing data to ChEMBL in future, we strongly reccommend you sign up to this  depositor mailing list . This will give you updates on the submission process and deadlines.   Webinar Info We are running on Friday 3 Oct , at 10:00 am , on Zoom . We will post the meeting link to the  ChEMBL-depositors  mailing list the day before.  Learning Objectives of the Webinar This webinar is designed to: Familiarise new depositors with the basic requirements for ChEMBL input data. Re-familiarise former depositors with the deposition process, and explain any new requirements.      A Reminder About ChEMBL 37 deadli...

Breaking news  📢   We are excited to announce our new journal article that presents the comprehensive drug data in ChEMBL. The paper describes the state-of-the-art processes to curate and integrate the high-quality drug and clinical candidate drug data. The drug curation processes have been developed over more than 15 years and this is the first time that they have been published.  https://pubs.acs.org/doi/10.1021/acs.jmedchem.5c00920 Published as a 'Perspectives' article in the Journal of Medicinal Chemistry, the paper educates ChEMBL users, helping them to understand the nature of the drug and clinical candidate data and the rationale that underlies curation decisions. G iven the increasing reliance on high-quality data in computational drug discovery, AI and machine learning, the integrated nature of the drug data within the ChEMBL bioactivity resource is a critical asset. This is a bumper week for drug data in ChEMBL! On Monday, our latest ChEMBL 36 release included ...

📊 Database Scale 🆕 New Data Sources Src_ID 72 – Chemical Probe data from Scientific Literature NLP and manual extraction from probe-related publications. Includes phenotype/disease context , mapped to EFO ontology . Stored in assay_parameters . 🔄 Updated Data Sources AI-driven Structure-enabled Antiviral Platform (ASAP) Active Ingredient of a Prodrug BindingDB Patent Bioactivity Data British National Formulary (BNF) Clinical Candidate Compounds EMBL Heidelberg Gut Microbiome–host Interactions EUbOPEN Chemogenomic Library EUbOPEN Chemogenomic Library Literature Data European Medicines Agency (EMA) FDA Novel Drugs and Biotherapeutics FDA Orange Book Drugs International Nonproprietary Names (INN) for Pharmaceutical Substances SGC Frankfurt - Donated Chemical Probes Scientific Literature United States Adopted Names (USAN) WHO Anatomical Therapeutic Chemical (ATC) Classification of Drugs Withdrawn Drugs ___________________________________________________________________________...

Before starting a new drug discovery project, it’s useful to compile existing data on compounds and targets of interest. Open access bioactivity databases such as ChEMBL support these efforts, offering structured and curated data in an easy-to-mine resource. To make the best use of ChEMBL, it’s important to understand the data types, structure and format. With this in mind, the ChEMBL team is providing a free “ Drug Design ” webinar! This webinar provides background on the ChEMBL database alongside worked examples highlighting some common scenarios in drug discovery initiatives. We’ve also included interface demos so that users can follow the examples and build upon these to extract data of interest to their project. We welcome feedback, questions, and suggestions and, as always, you can get in touch with us on our Helpdesk . In addition to this webinar, you can find our other training materials online, such as our deposition guide and introduction to the  API, as well as an FAQ ...

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...