XXX - Bill Simons - what have we got to map the ACT ontology to the demo data set? That'll need to go in here, too.


This chapter briefly describes the settings necessary to set up the ACT ontology in the i2b2 ONT cell, and the Lucene indexes and adapter mappings file for SHRINE. If you are setting up or joining a different network, you will need to use the correct ontology, Lucene indexes, and mappings file for that network.

The University of Pittsburgh maintains the ACT ontology. The most recent version is 2.0.1. You will also need the COVID-19 ontology enhancement.  Please refer to the ontology section in the official ACT Network Wiki at https://dbmi-pitt.github.io/ACT-Network/ontology.html for how to install the ACT ontology and the COVID-19 enhancement. The entirety of the ACT ontology must be installed properly in the i2b2 host. The SHRINE host must have the correct adapter mappings file and Lucene index files.

When you have finished the ACT ontology installation, you should check the following places in the database to make sure that they are pointing SHRINE to the ACT ontology.

  • For i2b2.public.ont_db_lookup table, there should be exactly one (1) row that has the following values (only the relevant values are highlighted here):

    c_domain_id = local site's i2b2 domain name
    c_project_path = "ACT/"
    c_db_fullschema = "i2b2metadata"
    c_db_datasource = local site's datasource
    c_db_servertype = local site's database engine type

  • For i2b2.public.crc_db_lookup table, There should be exactly one (1) row that has the following values (only the relevant values are highlighted here):

    c_domain_id = local site's i2b2 domain name
    c_project_path = "/ACT/"

  • For i2b2.i2b2metadata.table_access table, if you run "select c_table_cd,c_table_name,c_name from table_access;", you should see the following entries:

    i2b2.i2b2metadata.table_access
         c_table_cd     |      c_table_name       |               c_name               
--------------------+-------------------------+------------------------------------
 ACT_LAB_LOINC_2018 | ACT_LOINC_LAB_2018AA    | ACT Laboratory Tests (Provisional)
 ACT_MED_VA_2018    | ACT_MED_VA_V2_092818    | ACT Medications VA Classes
 ACT_PX_CPT_2018    | ACT_CPT_PX_2018AA       | ACT Procedures CPT-4
 ACT_PX_HCPCS_2018  | ACT_HCPCS_PX_2018AA     | ACT Procedures HCPCS
 ACT_DEMO           | NCATS_DEMOGRAPHICS      | ACT Demographics
 ACT_DX_10_9        | NCATS_ICD10_ICD9_DX_V1  | ACT Diagnoses ICD10-ICD9
 ACT_LAB            | NCATS_LABS              | ACT Laboratory Tests
 ACT_VISIT          | NCATS_VISIT_DETAILS     | ACT Visit Details
 ACT_MED_ALPHA_2018 | ACT_MED_ALPHA_V2_121318 | ACT Medications Alphabetical
 ACT_PX_ICD9_2018   | ACT_ICD9CM_PX_2018AA    | ACT Procedures   ICD-9-Proc
 ACT_PX_ICD10_2018  | ACT_ICD10PCS_PX_2018AA  | ACT Procedures ICD-10-PCS
 ACT_DX_ICD9_2018   | ACT_ICD9CM_DX_2018AA    | ACT Diagnoses  ICD-9-CM
 ACT_DX_ICD10_2018  | ACT_ICD10CM_DX_2018AA   | ACT Diagnoses ICD-10
 ACT_COVID_V1       | ACT_COVID               | ACT COVID-19