Skip to main content

Posts

A week in the Life of a ChEMBL Biological Curator - Tuesday

By
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...
Post a Comment
Read more
Recent posts

A week in the Life of a ChEMBL Biological Curator - Monday

By
  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...
Post a Comment
Read more

SureChEMBL: Your next source of research data

By
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...
Post a Comment
Read more

Invite to apply for ARISE2 Postdoctoral Fellowship

By
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...
Post a Comment
Read more

Open Position: Computational Biologist / Bioinformatician

By
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...
Post a Comment
Read more

ChEMBL 37 is here: bigger, cleaner, and smarter about protein degradation

By
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...
Post a Comment
Read more

The first PROTAC has been approved: can we find it in ChEMBL?

By
  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...
Post a Comment
Read more