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Module Installation
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This page covers how to install the Oncology CDM Extension. The
+Oncology CDM Extension has not yet been incorporated
+into an official OMOP CDM release. Consequently, the installation of the
+Oncology CDM Extension requires additional steps beyond installing the
+OMOP CDM. The Oncology CDM Extension currently supports OMOP CDM v5.31
+and the following database platforms: PostgreSQL, SQL Redshift.Server,
+Oracle and
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Step 1: Compile the OMOP CDM v5.31 Tables
+
Compile the OMOP CDM v5.31 data model tables from the OHDSI/CommonDataModel
+Github repository. Find the DDL relevant to your database platform
+(PostgreSQL, SQL Server, Oracle and Redshift). See
+the OMOP CDM v5.31 release here. Do not yet compile indexes and
+constraints. Do not yet load the vocabulary tables. We will do these in
+subsequent steps.
+
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Step 2: Compile the Oncology CDM Extension Tables
+
+- Compile the Oncology CDM Extension data model tables from the OncologyWG Github
+repository. This is a temporary additional step that will be removed
+once the Oncology CDM Extension has been incorporated into an official
+OMOP CDM release. Find the DDL relevant to your database platform
+(PostgreSQL, Sql Server, Oracle and Redshift). See DDL
+folder here.
+- For example, for the PostgreSQL database platform, execute the DDL
+script. See
+PostgreSQL DDL script here.
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Step 3: Load the OMOP Standardized Vocabulary Tables.
+
+- Populate the OMOP CDM vocabulary tables with, at minimum, the most
+recent version of the following vocabularies: SNOMED, ICDO3, HemOnc,
+RxNorm, NAACCR, and Episode Type.
+- ATHENA is the recommended approach for navigating and downloading
+OHDSI vocabularies. See ATHENA
+here.
+- Vocabulary ingestion scripts are organized by database platform in
+the OHDSI/CommonDataModel
+Github repository. Refer back to the OMOP CDM v5.31 release you
+downloaded in step 1.
+- Execute the vocabulary patch file from the OncologyWG Github
+repository to support metadata description/reference of the Oncology CDM
+Extension’s new tables and added columns. This is a temporary additional
+step that will be removed once the Oncology CDM Extension has been
+incorporated into an official OMOP CDM release. The patch file currently
+only supports the PostgreSQL database platform. You will need to
+manually translate the vocabulary patch file to other database
+platforms. See
+patch file here.
+- Run the vocabulary ingestion script to populate the Oncology CDM
+Extension’s newly added CONCEPT_NUMERIC vocabulary table from the OncologyWG Github
+repository. This is a temporary additional step that will be removed
+once the Oncology CDM Extension has been incorporated into an official
+OMOP CDM release. The ingestion script depends on a CONCEPT_NUMERIC.CSV
+file. Find the ingestion script (and CSV file) relevant to your database
+platform (PostgreSQL, Sql Server, Oracle and Redshift). See DDL
+folder here.
+
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Step 4: ETL the OMOP Standardized Clinical Data Tables
+
+- This step will be institution-specific and involves transforming
+your local EHR, claims database and other data sources into the common
+data structures and semantics of the OMOP CDM. The OMOP CDM includes
+(among others) representations for patients (PERSON), providers
+(PROVIDER), healthcare facilities (CARE_SITE and LOCATION), healthcare
+encounters (VISIT_OCCURRENCE), diagnoses (CONDITION_OCCURRENCE),
+medication prescriptions and administrations (DRUG_EXPOSURE), labs
+(MEASUREMENT), medical procedures (PROCEDURE_OCCURRENCE) and clinical
+notes (NOTE). See
+ETL creation best practices here.
+- Some implementations will layer the ETL of data into the Oncology
+CDM Extension tables on top of an OMOP CDM instance populated from other
+sources. Other implementations will ETL data into the Oncology CDM
+Extension tables in a satellite OMOP CDM instance and merge the data
+into a main OMOP CDM instance. This will based on local institutional
+practices and strategies.
+
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+
+
Step 5: Compile the indexes and constraints.
+
+- Compile the OMOP CDM v5.31 indexes and constraints from the OHDSI/CommonDataModel
+Github repository. Find the indexes and constraints DDL relevant to your
+database platform (PostgreSQL, SQL Server, Oracle and Redshift). Refer
+back to the OMOP CDM v5.31 release you downloaded in step 1.
+- Compile the Oncology CDM Extension indexes from the OncologyWG Github
+repository. This is a temporary additional step that will be removed
+once the Oncology CDM Extension has been incorporated into an official
+OMOP CDM release. Find the indexes DDL relevant to your database
+platform (PostgreSQL, Sql Server, Oracle and Redshift). See DDL
+folder here.
+
+- Compile the Oncology CDM Extension constraints from the OncologyWG Github
+repository. This is a temporary additional step that will be removed
+once the Oncology CDM Extension has been incorporated into an official
+OMOP CDM release. Find the constraints DDL relevant to your database
+platform (PostgreSQL, Sql Server, Oracle and Redshift). See DDL
+folder here.
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