UMLS to PostgreSQL with PgAdmin

This docker container will load UMLS data into a PostgreSQL database and also provide PgAdmin for postgres.

Requirements

• docker 18.06.1-ce or higer
• docker-compose 1.22.0 or higher
• The UMLS data prepared using MetamorphoSys

How to run

1. Place all your .RRF files from META into a folder, e.g. /data/META/<all .RRF files>
2. Run the preparation script that will escape some characters in the .RRF data

cd <umls github repo>
./escape.sh "/data/META"    # Path to the META folder with .RRF files
# If the path to your data is /data/META  all is ready. If non open the docker-compose.yml and edit the bind for the /data directory
docker-compose build
docker-compose up     # Optional add -d 

3. Once the data import is done (it can take hours depending on your machine), you can access the PgAdmin on IP:1234 and PostgreSQL on IP:1234

Note: Username and password for PgAdmin are the ones in docker-compose.yml

Escaping the \ in RRF files

To fix some bugs when importing, escape all the \ in input data.

chmod a+x escape.sh
./escape.sh "<path to the folder containing RRF files>"

#e.g.
./escape.sh "/data/META"

Take care not to run this script multiple times, as it will escape the escaped chars.

Problems

Importing the data can be sometimes problematic:

• There are some problems with the \ - escape chars, easiest solution is to run the small bash script that will escape the \ chars.
• RRF format has bugs and missing rows/columns, sometimes, depending on the UMLS version. You will have to manually check the log of the container to be sure everything was imported nicely
• All tables are not always present, be sure to remove the tables you don't need from the ./postgres/scripts/1_pgsql_all_tables.sql. If you don't do that the improt tends to fail. Or you will have to manually run the scripts using psql.

Ancknowledgements

Some parts of the import sql scripts were taken from: PostgreSQL load & index scripts - by Steve Bedrick, Yeb Havinga available at umls