The ChEMBL-og

    This image was generated using AI.   Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday , and Friday in early June.   A typical Friday in Emma’s week     Fridays are usually meeting-free by design. This allows unbroken time to work deeply on tasks. Such tasks include focused curation, enhancements, or investigation into data quirks or errors. Occasionally, we’re also involved in training, data analysis, or drafting publications. On several recent Fridays, biological curators worked alongside other team members on our recent bioassay annotation paper , particularly in the generation of the gold-standard training set. Our biological curation role also extends to the annotation of the comprehensive drug data that can be found in ChEMBL. This means that we gain an insight into emerging modalities making their way through the clinical pipeline. To capture these entit...

    This image was generated using AI.   Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday , and Friday in early June.   A not-so-typical Wednesday & Thursday in Emma’s week The EMBL-EBI offers flexible working and part-time roles, this is part of what makes the working environment so inclusive. My part-time role (4 days/week) means that Wednesdays are usually a non-working day. However, a very special event brought me to the office on Wednesday 10th and Thursday 11th June. ChEMBL held our 2nd User Group Meeting where we welcomed over 60 delegates to our beautiful campus for two days of presentations, case studies, workshops, and networking. It’s rare that we get an opportunity for such close engagement with our community of database depositors and users in a single session, and the event provided an insight into the value of ChEMBL to the Medicinal Chemistry and wider co...

This image was generated by AI. Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday and Friday during the course of a week in early June.   A typical Wednesday in Sally’s week Since we had a special event this Wednesday on 10th June (see Emma’s next blog article ), I’ll talk about the routine work I completed on 17th June instead. UniProt recently published a new release in which roughly 57 million protein entries were retired. Because ChEMBL maps protein targets to UniProt accessions, my task today is to replace obsolete accessions with active ones wherever possible. This isn’t as straightforward as it may sound, though. I frequently have to go back to the source publication to find more information on a given target. For example, I might need to confirm the exact strain that was studied, compare protein lengths or molecular mass, or check if the authors themselves provided a protein accession...

This image was generated using AI. Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to on a Monday , Tuesday , Wednesday , Thursday and Friday during the course of a week in early June. A typical Tuesday in Sally’s week First thing in the morning of Tuesday 9th June, I dedicate some time replying to Helpdesk enquiries and catching up on any new GitHub data issues . One user reports an assay that has been assigned to the wrong target in ChEMBL. I briefly double check the source document to verify the information and thank the user for reporting the error. Luckily, it’s an error that’s easy to fix, so I write an SQL update statement to correct the target in our internal production database. Then I run a brief check to see if the same issue affected any other assays in ChEMBL. Updating this information ensures that the next ChEMBL release will incorporate the fix. It’s also a good reminder that user feedback plays an important role in helping u...

  This image was generated using AI. Ever wonder what a biological curator for ChEMBL does? Read on to find out what we were up to during the course of a week in early June. There are two biological curators in the ChEMBL team. Together, we'll revisit that week one day at a time, in a new blog post each day. Sally will highlight some of the routine tasks that we might undertake on a Monday , Tuesday or Wednesday , whilst Emma will describe some of the less typical activities that we might be involved in during the second half of the week on a Thursday and Friday . Our days usually begin around 8.30-9am and finish at 5-5.30pm. Two or three of these days are in-person, with some flexibility. The EMBL-EBI offices are part of the Wellcome Genome Campus, a hub of scientific, and particularly genomics, institutes. Wetlands surround the carefully crafted and biodiverse grounds - meaning a lunchtime walk is always tempting! A typical Monday in Sally’s week It’s Monday 8th June and I star...

Slides and recordings from the recent ChEMBL UGM are starting to appear on the meeting website. Here I want to draw attention to the presentation by Nicolas Bosc and myself on " SureChEMBL: Your next source of research data ". Ever since my NextMove Software days, I've been aware of the large amount of scientific data available in patents. This includes everything from large sets of chemical analogs, to bioactivity values, reactions, and NMR spectra. US patents in particular are a rich source of data as they are (a) born digital, and (b) freely available, and thus automated tools to extract relevant data can generate substantial high quality datasets. For example, here's a graph I did back in 2017 to illustrate a NextMove Software blog post entitled "Are more bioactivities available from patents than from the academic literature?". This compared the data deposited from papers into ChEMBL and that extractable by LeadMine from patents (see the talk linked fr...

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...

We are looking for a highly motivated Computational Biologist / Bioinformatician (*) to join the Chemical Biology Resources team at the European Bioinformatics Institute (EMBL-EBI), located on the Wellcome Genome Campus near Cambridge, as part of the Wellcome Trust funded LIGMAP project, a multi-disciplinary collaboration between University College London and EMBL-EBI. LIGMAP is an ambitious multiyear project, led by University College London, to identify the endogenous ligands of the many proteins of unknown function in the proteome using AI-based methods as well as classical machine learning. You will work closely with the PDBe team at EMBL-EBI, as well as leading researchers in structural biology and machine learning at University College London, to deliver the goals of the project. You will develop descriptors to characterise the binding site of proteins in terms of their ability to recognise ligands, and use these to assess druggability of protein binding sites.   This positi...

ChEMBL 37 arrives with nearly three million compounds, a new modality field for capturing targeted protein degraders, and a wave of data quality improvements.    A new field for targeted protein degradation Around 29,000 bioactivity data points have been annotated with     ACTIVITIES.MODALITY  = “Targeted Protein Degradation” , including around 3,000 legacy bioactivities from approximately 1,200 remapped assays. This marks ChEMBL’s first systematic effort to flag TPD data across the database.        Extensive update of literature data Scientific literature remains the backbone of ChEMBL, and ChEMBL 37 brings one of the more substantial literature updates in recent releases. Compared to ChEMBL 36, the literature source gained approximately 79,000 new assays, 270,000 new bioactivity data points, and 52,000 new compound records — pushing the total literature-derived activity count past 9.55 million. Twelve new c...

  ChEMBL extracts data from the core medicinal chemistry literature and therefore reflects ongoing developments in drug discovery. One area currently attracting high interest is targeted protein degradation: compounds that direct disease-causing proteins to the cell’s degradation machinery.  These modalities are both present and rapidly increasing within ChEMBL, providing an important data source for the community.   Targeted Protein Degradation Data in ChEMBL However, new and emerging modalities bring new challenges. Data should be well structured and FAIR, but for newer modalities, controlled vocabularies may not exist or adequately cover the breadth of data being reported. Cu ration effort in this area supports our broader goals towards generating bespoke datasets and improving AI-readiness.  W e recently had the opportunity to attend the first ISCB UK conference where we presented our work towards the capture and annotatio...

The full programme for the  ChEMBL UGM (June 10-11) is now available on our website. If you are interested in registering, you need to be quick as registration closes on 18th May. See you there.

  Dear ChEMBL and SureChEMBL Community, As you know we are dedicated to keeping ChEMBL and SureChEMBL world-class resources for the scientific community, but to do that effectively, we need to hear from you.  To ensure we are consistently meeting your research needs, we are excited to launch our latest ChEMBL User Survey . Why Your Feedback Matters As we plan the next phases and future developments for our platforms, this survey is your opportunity to have a direct impact. By sharing how you interact with our data, you help us understand what works, what doesn't, and what you need next. Your insights will allow us to: Refine the interface: Make navigating and extracting data smoother and more intuitive. Prioritize new features: Focus our development efforts on the tools that will best support your drug discovery and research processes. Evolve with you: Ensure that ChEMBL and SureChEMBL stay in sync with the...

I'm very excited. We now have a list of confirmed speakers for the upcoming ChEMBL UGM (June 10-11). Uday Abu-Shehab, University of Vienna Katie Beckwith, Ignota Labs Evan Bolton, PubChem Giovanni Cincilla, Healx Wei Dai, Queen Mary University of London Wim Dehaen, University of Chemistry and Technology Prague Luca Falciola, SCIBILIS Thierry Hanser, Ixelis Tobias Harren, Universität Hamburg Greg Landrum, ETH Zurich John Mayfield, NextMove Software John Overington, DrugHunter Carl Schiebroek, ETH Zurich Chris Southan, University of Edinburgh Brandon Walts, SciBite I think it's going to be a really exciting line-up covering a diverse range of topics.  If you still haven't signed up , note that the closing date for in-person registration is 18th May. Note also that we have a limit in numbers for Day Two, and it's first come, first served.

Just a quick note to say that Daniel Lowe has released OPSIN v.2.9.0 , the first release since Oct 2023. This is now available via the EMBL-EBI OPSIN server . The release notes describe a mixture of minor bug fixes and improvements: Support for IUPAC recommended primed number-letter locants e.g. 2''a Command-line output now includes warnings e.g. ambiguity SMILES writer now starts from a * atom if one is present Added numbering to nicotine Correctly interpretation of locanted perhalo terms and perhaloalkylalkanes Improved additive bond formation for phosphoryl Corrected locants on tolyl and assume p-tolyl if unspecified triazine is now interpreted as 1,3,5-triazine if unspecified Corrected interpretation of dithiazolium Fixed rare SMILES writing bug where slashes could be inconsistent Fixed ylidenethenylidene being parsed as [ylidene][thenylidene] instead of [yliden][ethenylidene] Fixed bug in spiro superscript inferring when a bridge is length 0 

I recently prepared a few slides on OPSIN for an internal presentation, and was looking for a simple use case. The first thing I tried turned out to be more interesting that I expected. If you visit the OPSIN website , there are three examples provided to illustrate its functionality. Daniel's original website, at the Uni of Cambridge, had 2,4,6-trinitrotoluene (TNT) as the example. With the move to EMBL-EBI and associated rewrite of the frontend, I thought about keeping this but decided that something more biologically-relevant would be appropriate. In the end, I comprised by keeping the 2,4,6- as a nod to the original, but used a saccharide instead: 2,4,6-tri-O-methyl-D-glucopyranose. Now click on "Search Google", to do a search using the InChIKey. My attention was drawn to the AI summary results, which I captured at the time (maybe you can tell when?) in the screenshot below: "The string  UTLUVTKMAWSZKV-NEIVSKJXSA-N is an InChIKey (International Chemical Identifie...

This is a reminder that the 2nd ChEMBL User Group Meeting will take place on June 10-11 on the Wellcome Genome Campus, Hinxton, near Cambridge, UK. This event is dedicated to building and supporting the ChEMBL and SureChEMBL user communities. This is a two day event; while hybrid attendance on Day 1 is possible, we really encourage in-person participation to allow you to meet the team, present your work, network, and to take part in Day 2 setting the scene for the future direction of the group. The deadline for speaker registration is two weeks from now, on 18th March so register now . We hope to see you there.

  A week ago, I had the pleasure of presenting SureChEMBL2.0 at the  Cambridge Cheminformatics Network Meeting , organised by Andreas Bender and kindly hosted by the  Cambridge Crystallographic Data Centre . It was a great opportunity to introduce one of the latest freely available databases of scientifically annotated patents to a broad scientific audience. The recording of the talk is now available  online , along with the  slides . What did I cover during this 30-minute talk? Why scientists should pay attention to patent data Why patents are challenging to work with What SureChEMBL is and what it does How we identify chemical compounds in patent documents What SureChEMBL 2.0 has recently introduced How we annotate patents for genes/proteins and diseases How we are improving the quality of structures extracted from images What you can download from the SureChEMBL core datasets — and what they contain Examples of queries that SureChEMBL h...

  AI-driven bioassay annotation strategy The continued expansion of ChEMBL bioactivity data makes high-quality, structured assay metadata essential for reproducible analysis and machine-learning applications aligned with FAIR principles. Recent work by our team  published in J. Cheminf. describes coordinated manual and AI-driven strategies to enhance the annotation, classification, and interoperability of ChEMBL bioassays.  In this work, we have developed a spaCy-based named entity recognition (NER) model trained on manually curated assay descriptions to identify the Experimental Method within ChEMBL assay descriptions. The model achieved cross-validated precision, recall, and F1-scores of approximately 0.93, 0.95, and 0.94, respectively, and detected experimental methods in ~57 % of binding and functional assays in ChEMBL 35. Extracted method terms were subsequently mapped to the Bioassay Ontology (BAO) , demonstrating good precision at higher confidence thresholds bu...