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Invite to apply for ARISE2 Postdoctoral Fellowship

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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 during July or at the latest by early August. You can find my contact information on our group’s...
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The Redevelopment of ChEBI

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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 Outdated infrastructure  Back in 2021, ChEBI's software infrastructure was increasingly fragile.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...
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Support ChEMBL - EMBL-EBI user survey!

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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...
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OPSIN's new home is at EMBL-EBI

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  We are delighted to announce that the OPSIN web app has become a member of the Chemical Biology Services here at EMBL-EBI and can be accessed at: https://www.ebi.ac.uk/opsin OPSIN converts systematic IUPAC names to structures, and is an invaluable service for curators of chemical and biochemical structures or automated chemical text-mining systems. It was originally developed at the University of Cambridge by the Peter Murray-Rust group, with Daniel Lowe continuing to develop it since then. Here's a quote from the History page on the original website: During the development of OSCAR the need to have a program to convert identified chemical names to connection tables arose. Due to the absence of any open source efforts with broad coverage of organic nomenclature work was started by Peter Murray-Rust and Joe Townsend on such a program. This work was continued by Peter Corbett culminating in the creation of a system broadly similar to the current incarnation ( Corbett and...
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Even more RDKit in SureChEMBL2.0!

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      Dear SureChEMBL users, Welcome to the third blog post in our SureChEMBL2.0 series! If you missed the previous ones [ 1 , 2 ], be sure to check them out when you have a moment.   Today, we're diving into what has changed under the hood of SureChEMBL!   At the end of last year, we announced the integration of RDKit for compound depiction and various types of chemistry searches. But of course, we didn’t stop there. In line with our goal to simplify the service architecture, but also to improve the data quality, we’ve decided to follow the lead of our sister resource ChEMBL in how we manage compound structures.   What’s Changing? SureChEMBL handles compound structures at several stages in the pipeline. Regardless of how a compound is identified in a patent, the first step is to standardise its structure — and we’re now using the ChEMBL standardiser for this. Next, we register compounds using an RDKit-based hash , which helps us avoid introducing duplica...
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