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- 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. +
- 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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- For example, for the PostgreSQL database platform, execute the +ingestion script. See +PostgreSQL ingestion script here. +
+ - 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. +
- 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.
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- For example, for the PostgreSQL database platform, execute the +indexes DDL script. See +PostgreSQL indexes DDL script 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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- For example, for the PostgreSQL database platform, execute the +constraints DDL script. See +PostgreSQL constraints DDL script here. +
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OHDSI Medical Image WG
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+ OHDSI Medical Image WG
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+OMOP Oncology Installation
+
+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 Server, Oracle and +Redshift.
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+Installation
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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
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+Step 3: Load the OMOP Standardized Vocabulary Tables.
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+Step 4: ETL the OMOP Standardized Clinical Data Tables
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+Step 5: Compile the indexes and constraints.
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