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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 start my week in the same way I suspect many people do: by checking emails and preparing for the week ahead. The first meeting on Monday morning is our weekly ChEMBL data team meeting. We share what each team member has been working on in the previous week, what we are planning to focus on next and discuss the status of individual datasets. To keep track of our tasks, we use GitLab issue boards. These allow us to follow datasets through each step of the data loading process, from initial data checks and depositor feedback to curation and final release preparation. Team members can add comments along the way so that all discussions and decisions are captured in one place.Next up is a meeting on our drug and clinical candidate data. Our team has a dedicated curator for these data, but Emma and I are involved in the curation of drug indications and mechanisms of actions. We talk about upcoming curation tasks on approved vaccines and decide who takes on which task.
In the afternoon, it’s time for focused work on the database. Today, I’m running checks on a newly deposited dataset. Before it can be incorporated into ChEMBL, I look for anything that seems unusual using Jupyter notebooks: Do the reported activities make sense in the context of the assay? Have experimental details such as targets, cell lines and tissues been captured correctly? Are there any duplicate assays or activity records? Do compound names and structures conflict with existing ChEMBL records? Any issues found are captured in GitLab for discussion with the team. By the end of the day, I hope I’ve caught everything that might cause issues later and I can log off knowing that the dataset is one step closer to becoming part of ChEMBL.
Salesia Werner and Emma Manners
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