OHDSI Home | Forums | Wiki | Github

Newbie Vocabulary import

Last year (2021) I was able to load the vocab data in the tables using some scripts I found in the OHDSI CDM repository, but this time around I didnt find the scripts.

error1
I have changed the delimiter to Tab and I got this error

I think the problem is that even though the file name suffix is csv, the files are actually tab separated. Try again after changing the delimiter to a tab. Respond to the forum if that was the solution.

I have managed to load all the tables except for the concept and concept_synonym tables where I am still getting errors even if i use Tab and UTF-8. For the other tables I used delimiter ‘TAB’ and UTF-8 encoding.

Again, to provide help, you need to be more specific about the errors you are getting. I know in the past people have had problems because of “foreign” characters, causing an error either because the loader rejects the string or because the “foreign” character is translated into multiple characters and then the length is exceeded. Different databases have different options for handling foreign characters which may help. Another option, I have used, is to use the Unix stream editor sed to remove foreign characters from the concept and concept_synonym files prior to loading into the database.

t