The ChEMBL-og

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 ...

We are delighted to announce that ChEBI’s beta version is now out and can be accessed at: https://www.ebi.ac.uk/chebi/beta/ As many of you know, ChEBI is a widely used database and ontology of chemical entities of biological interest. It has a growing user base numbered in the hundreds of thousands and with millions of accesses each year. ChEBI has for the past >20 years provided the biological community with access to definitive small molecule information and data, including accurate representations of often complex chemical structures. Additionally, ChEBI is used widely as a reference database and ontology by many important bioinformatics resources such as Rhea, MetaboLights, UniProt, GO, IEDB, Reactome, amongst others. ChEBI is, thus, a fundamental and core component of the global bioscience infrastructure. Outdated infrastructure  Back in 2021, ChEBI's software infrastructure was increasingly fragile. ChEBI's current software code base dates back to its creation in the e...

If our data resources have ever been of use to you, here’s your chance to give back! EMBL-EBI’s impact survey aims to understand the usage, impact and improvement areas of the open data resources managed by EMBL-EBI and collaborators.   As well as ChEMBL and our other Chemical Biology Services , EMBL-EBI hosts some of the world’s most important collections of biological data including UniProt, Ensembl, AlphaFoldDB, and Europe PubMed Central.    Your input is extremely important and will help EMBL-EBI make the case for why open data resources are critical to the life sciences.    EMBL-EBI would be very grateful if you and other users in your organisation could contribute to this study by completing the following survey:    https://www.surveymonkey.com/r/QGFMBH8?channel=[email]     The survey takes around 15 minutes and closes on the 16th of July 2025 . The results of the survey will be aggregated and anonymised, and all personal data treate...