A Semantic Mapping transformation applies a semantic mapping to the input field value to set the output field value. This means that each value in the input field is looked up in the semantic mapping, and the matching output value is set in the output field.
Prerequisites
- You must have Manage Data Mappings permission.
- A syntactic mapping should have already been created.
Creating a Semantic Mapping Transformation
To create a Semantic Mapping transformation, complete the following steps.
Step 1: Open the Transformations Panel
- In the Syntactic Mappings page, choose the mapping you want to edit.
- Click the Edit Pencil in the Transformation field for the entry you would like to edit transformations for.
- The Transformations Panel will appear. Click the Add Transformation button.
- Click the dropdown menu to select the desired transformation type.
Select the Semantic Mapping transformation.
Step 2: Fill in the Transformation Configuration
- Note the Source Input and Target Output. It should reflect what you already chose in the syntactic mapping entry.
- Select the target vocabulary of the semantic mapping that you'd like to use in this transformation: OMOP V5.4 or Custom Vocabulary.
- For OMOP - Select the Target Domain.
- For Custom Vocabularies, select the specific Custom Vocabulary to use
- Indicate the transformation output type, which means the type of output to use from the matched term. The output type can be:
- Concept ID or Code - use the matched term's concept ID or code (e.g. "35816080") as the output. For custom vocabularies with no distinction between the term display name and code, the code will be identical to the display name.
- Concept Name or Display Name - use the matched term's concept name or display name (e.g. "Aspirin") as the output.
- Indicate what should happen if the source value matches an entry in the semantic mapping that has not yet been approved in FCP (more information on how to approve semantic mapping entries is here). You can choose to:
- Use the top recommendation from the semantic mapping recommendations generated by FCP
- Treat such values as missing from the mapping.
- Indicate what should happen if the source value is missing from the semantic mapping. You can choose to:
- Skip the row - this entire row will be omitted from the output table
- Fail - the entire code run is failed
- Use the source value - the output value will be set to the source value without any changes
- Set to default - set the output to a default value (e.g. "" or "0" or "MISSING"). If you select "Set to default", another input appears for you to fill in the desired default value.
- When complete, click the Save button.
Editing a Transformation
To edit a transformation, complete the following steps.
- In the Syntactic Mappings page, select the mapping that you want to edit transformations for.
- Find the mapping entry you want to edit, then click the pencil icon in the Transformation column. The Transformations Panel will appear.
- Edit the transformation as desired.
- When complete, click the Save button.