Configuring OpenCDISC Validator for External Dictionaries
MedDRA, SNOMED, and other external dictionaries can be added to your local installation so the OpenCDISC Validator can access them while running validations. Follow these instructions to enable validation against these dictionaries:
- Medical Dictionary for Regulatory Activities (MedDRA) is commonly used for coding Adverse Events. Since MedDRA is only available through a commercial subscription, it’s not included as part of OpenCDISC Validator distribution. Therefore, we have created this easy process by which you can add your company’s licensed copy of MedDRA to OpenCDISC Validator.
- Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT) is a comprehensive clinical terminology used for coding Trial Indication and Diagnosis Group in Trial Summary domain. Since all users of SNOMED need to have a valid license, it’s not included as part of OpenCDISC Validator distribution.
- SNOMED file (sct2_Description_Full-en.txt) has 9 columns, some of which cause entire rows to be unreadable by OpenCDISC. Fortunately the problematic columns are not needed by OpenCDISC
- To use SNOMED, you must remove all columns except for conceptId and term. It is advised to remove duplicates thereafter. Dave Scocca from RhoWorld has contributed a script to preprocess the file. Thanks Dave.
- We are currently collaborating with SNOMED to understand the issue so that they may fix it before publication.
Use the following instructions to enable your External Dictionaries. MedDRA is the example shown below, but you can replace this with SNOMED or any other dictionary you use:
- After successful installation of OpenCDISC Validator, navigate to the /components/config/data/MedDRA folder. This is where you will store MedDRA files to make them available to the Validator. Each version of MedDRA should be stored in a separate sub-folder (14.0, 14.1, etc.) as is shown below
- The next step is to locate your company’s licensed copies of MedDRA. These are typically maintained by your IT department and are distributed in zip files. Here are the contents of a MedDRA v14.0 zip file
- Copy the contents of the MedAscii folder to [version] folder under MedDRA. In our example, we would copy the files into /components/config/data/MedDRA/17.0 folder as is show below
- Repeat steps 2 and 3 for each version of MedDRA you need to support
- The configuration is now complete, you are ready to validate data against MedDRA
Selecting MedDRA version for Validation
By default OpenCDISC Validator will use the MedDRA version specified in Define.xml for validation. For example
<CodeList OID="ExternalCodeList.AEBODSYS" Name="MedDRA Adverse Events Dictionary" DataType="text"> <ExternalCodeList Dictionary="MedDRA" Version="14.0"/> </CodeList>
However, if you don’t have Define.xml or it doesn’t specify a MedDRA version, you can now use a new MedDRA field available in the bottom right corner of the Validator screen (see below). The field will become visible once you configure at least one MedDRA version as described in the section above. Also, please note that MedDRA field cannot be used to override a version specified in Define.xml.
Using a MedDRA version with CLI (Command line Interface)
Using MedDRA with the OpenCDISC CLI is extremley simple. From the command line, include this parameter with a valid version of MedDRA based on the above examples.
For more information about using the command line, visit CLI usage in the documentation tab