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...