This chapter goes through the steps that are involved in loading the 'demo' SHRINE ontology and setting up the corresponding adapter mappings file. In network specific setups, you will be loading a network specific ontology and will be mapping terms specific to that ontology.

The first thing you will need to do is to create the tables that will contain the SHRINE ontology.

Please refer to this file for the script: ontology_create_tables.sql

You can run this script by running:

$ psql -U postgres "dbname=i2b2 options=--search_path=shrine_ont" -a -f ontology_create_tables.sql

Next, you will need to download the demo SHRINE SCHEMES file to load into the shrine_ont schema. The file is hosted on our SVN repository here:

https://open.med.harvard.edu/svn/shrine-ontology/SHRINE_Demo_Downloads/trunk/SCHEMES.sql

Once you have downloaded the script, you can run this script by running:

$ psql -U postgres "dbname=i2b2 options=--search_path=shrine_ont" -a -f SCHEMES.sql

Next, you will need to load the demo SHRINE ontology into the newly created tables. This will populate the ontology tree within the SHRINE webclient. You can download the demo ontology file here:

https://open.med.harvard.edu/svn/shrine-ontology/SHRINE_Demo_Downloads/trunk/ShrineDemo.sql

Once you have downloaded the script, you can run this script by running:

$ psql -U postgres "dbname=i2b2 options=--search_path=shrine_ont" -a -f ShrineDemo.sql

Finally, you will need to point the DB lookup tables within i2b2hive to look at the newly created schemas in its database for the SHRINE ontology. You will also add the SHRINE demo ontology path into the TABLE_ACCESS table within the shrine_ont schema.

Please refer to this file for the script: ont_post_setup.sql

You can run this script by running:

$ psql -U postgres -d i2b2 -f ont_post_setup.sql