0

I have a set of protein targets. The absolute ideal return for these targets for me, would be a .tsv file that looks like this:

target_name    fda_approved_drug
target1        drug1
target2        -
target3        drug2
target3        drug1

I was trying to link drug to target proteins with openFDA. I found the instructions to use OpenFDA here, but I can't work out if this is possible using this API?

I want to add in code to show an example what I was thinking, but I can't find it so my idea would be something like this: I have a list of UniProt IDs (I can convert if necessary), and then if I could write something like:

for i in list_of_targets; do: fda_api --target_protein i --drugs ;done >> list_of_drugs_and_targets

Is this possible? As a side note, I primarily code in python, I'm wondering if there's a pythonic way of doing this?

1

I'm Jack with the openFDA team. From my understanding, you have a list of target proteins and want to link it with drugs in one of the openFDA endpoints. As I see it, the problem you'll run into is that to my knowledge there's no field in openFDA that details target proteins. If you already know which drugs you're looking for and are searching for more information about those drugs, openFDA would be a great solution, but as I understand your issue, it is outside of the scope of any current openFDA drug endpoints.

0

You can use ChEMBL to link drugs and drug targets. OpenPhacts might provide a direct API for this.

Problem will be, that these databases store (bio)assay information and might not have the semantics that you want.

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.