Page History
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.
Ontology scripts
ontology_create_user.sql - Creates the shrine_ont user, for loading the SHRINE ontology
ontology_create_tables.sql - Creates shrine_ont, creates SHRINE, TABLE_ACCESS, and SCHEMES tables, and sets up schemas within tables.
DB_Lookups script to add ontology to i2b2hive
...
Please refer to this file for the script:
...
ontology table access
You can run this script by running:
Code Block | ||||
---|---|---|---|---|
|
...
INSERT into {{ shrine_i2b2_ont.schema }}.TABLE_ACCESS
( C_TABLE_CD, C_TABLE_NAME, C_PROTECTED_ACCESS, C_HLEVEL, C_NAME, C_FULLNAME, C_SYNONYM_CD, C_VISUALATTRIBUTES, C_TOOLTIP, C_FACTTABLECOLUMN, C_DIMTABLENAME, C_COLUMNNAME, C_COLUMNDATATYPE, C_DIMCODE, C_OPERATOR) values ( 'SHRINE', 'SHRINE', 'N', 0, 'SHRINE Ontology', '\SHRINE\', 'N', 'CA', 'SHRINE Ontology', 'concept_cd', 'concept_dimension', 'concept_path', 'T', '\SHRINE\', 'LIKE');
$ 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:
Code Block | ||||
---|---|---|---|---|
| ||||
$ 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:
Code Block | ||||
---|---|---|---|---|
| ||||
$ 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:
Code Block | ||||
---|---|---|---|---|
| ||||
$ psql -U postgres -d i2b2 -f ont_post_setup |
...
.sql |