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jump-cellpainting / JUMP-Target

Lists and 384-well plate maps of compounds and genetic perturbations designed to assess connectivity in profiling assays
MIT License
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Identify JUMP IDs for Target-2 compounds #35

Closed goncinious closed 3 months ago

goncinious commented 3 months ago

I'm struggling to find the corresponding JUMP IDs for all the 306 (+1 with DMSO) compounds present in the Target-2 plates.

My approach so far was to join the Target-2 compound metadata table with JUMP's compound metadata by InChIKey to obtain the Metadata_JCP2022 for these. However, 125/307 of the InChIKeys aren't in the JUMP's compound table. Attached is a CSV of the compounds missing.

target2_not_in_jump.csv image

Are these InChIKeys expected to be found in the JUMP's compound or perhaps there's a better approach to obtain the JUMP IDs?

niranjchandrasekaran commented 3 months ago

Hi @goncinious, we just updated the metadata file (in the fix-target2-columns branch). If you use the InChIKey_standardized column in that file, you should be able to map them to the InChIKeys in the JUMP compound dataset. Please let us know if this doesn't work.

goncinious commented 3 months ago

Thanks you - that's sorted 👍🏼

goncinious commented 3 months ago

If you use the InChIKey_standardized column in that file

Just to note that the column is named InChIKey and not InChIKey_standardized in the table in fix-target2-columns branch.