i2b2 ontologies have a column c_totalnum that can store the total count of patients associated with every item in the ontology tree. This can be visualized in the i2b2 webclient to assist with query building (e.g., to find concepts that have many patients) or be used for data quality (to find areas where patient counts do not make sense). It is also used by the query builder to optimize queries. The ENACT network uses these counts for additional analytics across their network. We recommend you run these counts after each ETL.

Installation

This should have already occurred in previous sections of this guide, but verify you have run these steps:

1. If upgrading, create the totalnum and totalnum_report tables. In Release_1-7/Upgrade/Metadata, run the ant upgrade script. This will create the totalnum and totalnum_report tables.
   ant -f data_build.xml upgrade_tables_release_1-7-12a
2. In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures. 
   ant -f data_build.xml create_metadata_procedures_release_1-7 
3. Set privileges: If using multiple schemas, the stored procedure should be run from the metadata schema. Make sure the stored procedure can read the tables in the crcdata schema (observation_fact, visit_dimension, patient_dimension) and can both read an update ontology tables in the metadata schema (including table_access). 

Fast Totalnum

i2b2 1.8 introduces a version that is 5-10x faster. This faster version is presently only available for MSSQL and has only been extensively tested with the ACT ontology. 1.8.1 and later versions will improve on this faster version. These replace the pat_count_dimensions and run_all_counts stored procedures.

Configuration

1. The first time you run this and when your local ontology changes, you must run the preparatory procedure. This creates a view of distinct concept codes and patient nums (OBSFACT_PAIRS), a unified ontology table (TNUM_ONTOLOGY) and a transitive closure table (CONCEPT_CLOSURE). It could take an hour to run.

   • exec FastTotalnumPrep or exec FastTotalnumPrep 'dbo'
   • Optionally you can specify the schemaname, as above.
   • ACT_VISIT_DETAILS_V4 and ACT_DEM_V4 table names are presently hardcoded, so change if your table names are different.
   • If you use more than one fact table, the obsfact_pairs view will need to be customized. (See example in the code comments).

2. Run the actual counting. This relies on the i2b2 data tables and the closure and ontology tables created in step 1. It takes no parameters. Its output goes into the totalnum table, which was created when upgrading/installing i2b2 1.7.12 or 1.7.13 or 1.8. It typically runs in 1-3 hours.

   • exec FastTotalnumCount

3. Output the results to the totalnum_report table (as obfuscated counts) and into the totalnum column in the ontologies (for viewing in the query tool).

   • exec FastTotalnumOutput or exec FastTotalnumOutput 'dbo','@'

   • Optionally you can specify the schemaname and a single table name to run on a single ontology table (or @ for all).

Execution 

Run the following commands in a SQL client.

1. exec FastTotalnumPrep or exec FastTotalnumPrep 'dbo' (Run once when ontology changes.)
2. exec FastTotalnumCount (Actual counting, takes several hours.)
3. exec FastTotalnumOutput or exec FastTotalnumOutput 'dbo','@' (Output results to report table and UI.)

Some additional notes on running on OMOP

It is possible to run counts on OMOP tables through the ENACT-OMOP feature in i2b2 1.8. The new 1.8 totalnum procedure works on OMOP - simply load the file totalnum_usp/sqlserver/totalnum_fast_prep_OMOP.sql instead of totalnum_fast_prep.sql.

Totalnum Classic (slower but more compatible with ontologies that use dimcode-based queries)

Configuration

1. If using multiple fact tables, the recommended approach is to create a fact table view as the union of all your fact tables. (This is essentially going back to a single fact table, but it is only used for totalnum counting. This is needed to correctly count patients that mention multiple fact tables within a hierarchy.)

       e.g., 
          create view observation_fact_view as
          select * from CONDITION_VIEW 
          union all
          select * from drug_view

   1. If running the counting script in SQL Server, add the wildcard flag, to ignore multifact references in the ontology: e.g. exec RunTotalnum 'observation_fact_view','dbo','@','Y'
      This is automatically accounted for in the other database platforms. Note this approach does not work if you have conflicting concept_cds across fact tables.

Execution

See database-specific instructions below. After running the scripts, results are placed in: c_totalnum column of all ontology tables, the totalnum table (keeps a historical record), and the totalnum_report table (most recent run, obfuscated). These total counts will also be visible in the ontology browser in the web client.

MSSQL Version

By Mike Mendis and Jeff Klann, PhD based on code by Griffin Weber, MD, PhD

Run with:

exec RunTotalnum or exec RunTotalnum 'observation_fact','dbo','@' 

The optional parameters are:

1. Observation table name (for multi-fact-table setups)
2. Schema name
3. A single ontology table name (specify to to run on a single ontology table - otherwise (or if '@' is specified) runs on all tables in table_access)
4. A wildcard flag that will ignore multifact references in the ontology if 'Y'. (See below for the use case.)

Note that visit and patient dimension will only be counted in conjunction with the default (observation_fact) tablename!

To use with multi-fact-table setups:

Option 1) If you have at most one fact table per ontology, run this once with each fact table specified!
e.g., to use on a fact table called derived_fact with just the act_covid ontology: exec RunTotalnum 'derived_fact','dbo','act_covid'

Option 2) Create a fact table view as the union of all your fact tables. (This is essentially going back to a single fact table, but it is only used
for totalnum counting. This is needed to correctly count patients that mention multiple fact tables within a hierarchy.)
e.g.,

      Example 1: Counting using OMOP tables

   create view observation_fact_view as
   select * from CONDITION_VIEW 
   union all
   select * from drug_view

And then run the totalnum counter with the wildcard flag, to ignore multifact references in the ontology, e.g., 

   exec RunTotalnum 'observation_fact_view','dbo','@','Y'

      Example 2: Counting using a derived fact table and the regular fact table, using a single ontology

   create view observation_fact_view as
   select * from observation_fact 
   union all
   select * from derived_fact

Run the totalnum counter with the wildcard flag, to ignore multifact references in the ontology, and specify an ontology table, e.g., 

    exec RunTotalnum 'observation_fact_view','dbo','act_covid_v4','Y'

Note this approach does not work if you have conflicting concept_cds across fact tables.

Oracle Version

By Mike Mendis, based on SQL Server code by Griffin Weber, MD, PhD
Performance improvements by Jeff Green and Jeff Klann, PhD 03-20

Run the procedure like this (but with your schema name instead of i2b2demodata):

begin
runtotalnum('observation_fact','i2b2demodata');
end;

You can optionally include a table named if you only want to count one ontology table (this IS case sensitive):

begin
runtotalnum('observation_fact','i2b2demodata','I2B2');
end;

Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command:
grant create table to (DB USER)  

Postgres Version

Original PostgreSQL code by Dan Vianello, Center for Biomedical Informatics, Washington University in St. Louis
2019 - Modified for i2b2 1.7.12 release by Mike Mendis, Partners Healthcare
2020 - Updated to support reporting and single-table runs by Jeff Klann, Massachusetts General Hospital

Usage example:

select runtotalnum('observation_fact','public')

• Replace 'public' by the schema name for the fact table.
• If using a schema other than public for metadata, you might need to run "set search_path to 'i2b2metadata','public' " first 
• You can optionally specify a single table name, to count using only one ontology table. This is case sensitive.

Running using ANT

Run the ant command to execute the data_build.xml file with below specified target 

• POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
• ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
• SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver

Some additional notes on running Postgres

Some users have reported difficulty executing the totalnum scripts due to user permissions. Lav Patel at UKMC has offered some solutions:

1. Make sure the i2b2 user has access to insert, select, and update all i2b2 schemas... e.g., GRANT ALL PRIVILEGES ON DATABASE i2b2 to i2b2
2. Make the i2b2 user a super user: ALTER USER i2b2 with SUPERUSER;
3. Change the schema ownership to the i2b2 user (requires function in the postgres directory of this repository):

select change_schema_owner('i2b2demodata', 'i2b2');
select change_schema_owner('i2b2metadata', 'i2b2');
select change_schema_owner('i2b2pm', 'i2b2');
select change_schema_owner('i2b2hive', 'i2b2');

Output

The scripts produce three outputs:

1. The c_totalnum columns in your ontology tables contain numbers (not nulls). These total counts will be visible in the ontology browser in the web client.
2. The totalnum table will be appended with a row for each concept that was counted, with its count and the date. This can be used for analytics on totalnum counts.
3. The totalnum_report will be truncated and populated with a row for each concept that was counted, with an obfuscated count using the same approach as SHRINE and the date. This can be used for sharing deidentified counts with collaborators (with IRB approval). (Note that the date is the date the script was run, and so it is not a HIPAA-protected date.)

Parent folders will get counts (of all patients with facts in the leaves) except for ontology folders derived from visit_dimension or patient_dimension. These cannot be rolled up because of the way these terms are defined in the ontology. They will have no count at all (not a zero).