What is the difference between the cdb.dat files provided by the UMLS Small/Full models versus creating own cdb.dat from UMLS DB

[stefanhgm]

Hi everyone,

first of all thanks for your great work! I want to setup MedCatTrainer for UMLS tagging. When using one of the prepared UMLS models (small/large) I get the tagging including the CUI, but no other information. I think the problem is the missing "concepts imported" (red cross for the project). Hence, I tried to upload the necessary concepts (cdb.dat).

I wondered if the cdb.dat files of the prepared UMLS models come with the necessary information already (i.e. UMLS name, types, ...) or if it is still necessary to load the UMLS into Postgres, execute the script from the MedCat paper to get a CSV, and building the cdb. I tried the latter process, but it is very cumbersome and the documentation seems outdated (e.g. prep_cdb.prepare_csvs(paths) as used here https://towardsdatascience.com/medcat-extracting-diseases-from-electronic-health-records-f53c45b3d1c1 does not exist anymore).

In case a newly generated cdb.dat file is needed, I wondered if you could also provide it via the NIH links as the UMLS models. I think this would save a lot of hassle for anyone trying to use the UMLS as a backbone of MedCat.

Cheers!