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EBIvariation / opentargets-pharmgkb

Pipeline to provide evidence strings for Open Targets from PharmGKB
Apache License 2.0
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Updates for drugFromSource and drugFromSourceId to support drug combinations #40

Closed apriltuesday closed 2 months ago

apriltuesday commented 3 months ago

As discussed in 22 April meeting, we should make the attribute drugFromSource a list when split on / only (other delimiters have a different semantic in PGKB and should continue to be exploded into separate evidence) and rename the attribute to be plural drugsFromSource.

This is to support drug combinations like ivacaftor / lumacaftor.

To remove complexity and because CHEBI IDs aren't being used by OT, we will remove the drugFromSourceId attribute entirely.

Related OT issue here.

ireneisdoomed commented 2 months ago

After a discussion with @DSuveges we have agreed that the most accurate solution is to create a drugs object. This will be a list of structs with 2 keys:

drugFromSource: name of the drug at source drugId: CHEMBL ID that will be populated by us later on in the drug mapping step, so it will be null in your case

This solution solves the problem of keeping the parity between name and ID. Now that CHEBIs have been removed, you are not affected by this, but it is important for us so that we can map each drug name to the CHEMBL ID after it is mapped.

Thank you very much! Please let us know of any issues

apriltuesday commented 2 months ago

Thanks @ireneisdoomed, this makes sense. I'll make the changes on our end and let you know any questions I have.