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Add Rolfs 2021 halflife data to tractability #3393

Open louwenjjr opened 1 month ago

louwenjjr commented 1 month ago

Hi team, we got the request to add more protein halflife data to the Platform. As a start, we added the data from the Rolfs 2021 study to the tractability pipeline, see the PR here https://github.com/chembl/tractability_pipeline_v2/pull/6. We would of course like to know 1. if you are interested in this, 2. if this is the way to go about it and 3. if additional steps are needed from our end.

Additionally, we noticed an interest for presenting the halflife data in a table on the Profile page, instead of just with a checkmark in the Tractability section. What is your opinion on this?

Background

The Rolfs 2021 study contains halflife data for ~3000 Targets across 8 different tissues, measured in mouse. Taking the existing Mathieson data (8804 Targets) into account, the Rolfs study contains halflife information for 836 new Targets.

Tasks

buniello commented 1 month ago

Thanks @louwenjjr, we have been discussing expansion of our tractability pipeline and possible changes to the widget. We will discuss this internally and feed back to you, but this fits with our plans.

d0choa commented 1 month ago

It's all very reasonable. I will be happy to coordinate the scoping when I return from annual leave. The only concern I have is the reliability of mouse tissues compared to human primary cells. They are probably complementary sources, which adds some extra complexity.

@louwenjjr, we will need to liaise with ChEMBL for this feature, which will increase the turnaround. Apologies in advance if we are a bit slow.

louwenjjr commented 1 month ago

Thanks for your quick responses and indicating your timelines!

Part of the Mathieson data also originates from Mouse neuron cells so I think adding Rolfs data would not create (much) extra reliability issues. I also think that species/celltype/tissue information would be nice to include on the Profile page but this would require representing the halflife data into more of a table format. If this fits in your idea of the updated tractability section, we would be happy to assist with creating this functionality and of course as well with any updated tractability pipelines.