Need help for MEDDRA extract directory path

[sdueducn110]

Hi Cristian,

First of all, thanks a lot for your fantastic job.

I strictly followed the process as you mentioned, all is going well except how to deal with cleaning procedure of MEDDRA.
I downloaded the vacabularied WITHOUT MEDDRA separately from ATHENA and downloaded MEDDRA V24.1 zip file from https://www.meddra.org/software-packages with my own license. But I don't know how to deal with the unzipped meddra files.

As mentioned in your whole process, “SETP4 This is needed for a supplementary cleaning procedure. Extract the zip file in the same working directory.” I was a little confuse about that.
Could you please explain in detail what the “working directory” is , and which process in folder "all_script" is for MEDDRA cleaning(I think drug_target_se_computation.py is most likely).

Thank you very much!

[cristian931]

Hi,
Don't know if you still need this but, first of all, sorry to came back to you so late, didn't realize there was another issue.
Second, the whole T-ARDIS procedure is quite tricky and need to be followed strictly unfortunately.
This project uses two format of MEDDRA for different scopes:

• there's the ATHENA formatted one, that cannot be accessed unless you upload it to a relational database (postgres in this case) and is used during the FAERS and MEDEFFECT cleaning procedure together with the SNOWMED codes for mapping. This step comes directly from the original repository (https://github.com/ltscomputingllc/faersdbstats) without modification, so I suggest to include MEDDRA also in the ATHENA vocabularies package.
• Then there's the "text" version of MEDDRA, that I used later on the pipeline to check if effectively all the ADR terms are converted from LLT to PT. It's not very efficient, I have to admit, but it's the best solution I found at the time. This one is downloaded from the MEDDRA website as you've done correctly. Simply unzip it in the same folder where you download all this repository data (i.e where the all_script folder, the "col_name_gaf" file and the run_file.sh are).
• At this point, if everything is setted up correctly, just launch the run_file.sh and the script will take care of every step.

Hope it helps, and if you have any other issue do not hesitate to contact me, I'll try to respond in a more suitable time