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...

  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...

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...

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...