Creating a project for automapping

Before you can start automapping, you have to create a project and import your file (e.g. a comma separated value or Excel file) into Snow Owl. Go to the Project Explorer view, right-click and select New > Project from the context menu.

Starting the new project wizard
On the first page of the wizard, select General > Project, click Next to proceed.
Creating a new project
Enter your project name, click "Finish" to complete the process.
Specifying the new project
Your new project folder can now be found in the Project Explorer View. If you right-click this folder, you have to option to chose different types of files from the context menu. For automapping, you will need a New reference set automapping file..

Importing files for automapping

Importing a spreadsheet

Spreadsheets from comma separated value (csv) and Microsoft Excel formats (xls and xlsx) can be imported into the workspace to support automapping with external codesystems and terminologies.

Creating new automap file from main menu

Use the browse button to select the source file (e.g. your Excel spreadsheet). If your spreadsheet does not have headers or empty lines, uncheck the boxes. Automapping supports the creation of both simple type and complex type mapping reference set. The target reference set has to be specified at the spreadsheet import. By default, a complex map type reference set is created, but you can also select a simple map as a reference set type. Hit Next to proceed.

Selecting a source file for automapping

Specify which column of the spreadsheet contains the IDs (codes), and which one the labels (terms). The header of your spreadsheet will be displayed in the drop-down menu (e.g. "Medical term"). By default, the first column is used for IDs, and the second one for labels. If your spreadsheet has a different header configuration, you have to use the drop-down menu to adjust the settings. Hit Next to proceed.

Specifying header configuration for automapping

Enter the name for your automapping file. If you started the wizard from the main menu, you fill also have to select a project folder. Click Finish to close the wizard.

Specifying name and location of the automap file

Your new automap file is now displayed in the project explorer.

Automap file in project explorer

Comparing a new version of a spreadsheet during import

When importing a new version of a spreadsheet, it can be compared to a previous version. Changes or new items will be listed in the wizard. The new feature can be invoked by clicking Open import and compare with file dialog in the toolbar of the automap editor.

To start the comparison

Selecting a file for comparison

Now you can review a list of differences between the two versions. Select the ones you want to import by checking the boxes, and click Finish.

Compare wizard showing differences between two versions of an automap spreadsheet

The automap file has been updated with the new version. You can see that the newly imported items have not been mapped yet. Save the file, and click automap to map the new items.

Automap file after update

Automapping editor

Double-click an automapping file to open the Automapping editor. The layout of the Automapping editor is similar to a spreadsheet: ID codes are displayed in the ID column, clinical terms in the Label column. The column titles in your spreadsheet will be automatically used. The SNOMED CT equivalent column and the Mapping mode column are empty, because the clinical terms haven't been mapped yet.

Automapping editor before mapping

Running the automapping

Click on the button to invoke the automapping configurator dialog.

Restricting mapping targets to clinical findings

Now Snow Owl performs a lexical search for each of the labels from the external terminology. The automap feature is based on frequency of usage and your search profile. It works similar to the quick search, the first term that would appear in the quick search list is the one that is used for automapping.

Automapping editor after automapping

Note: Since the automap feature uses the active search profile, you can change your profile to identify more relevant suggested mappings. For example, if you're mapping an in-house list of cardiology codes, you can activate the built-in Cardiology search profile (Preferences > Snow Owl > Search Profiles > Cardiology) to increase the relevancy of the matched terms. For more information please refer to the section about the Search Profile.

Cardiology search profile

Assisted manual mapping

When automatic mapping fails to locate a match, the manual mapping will display approximate matches for you to choose from. You can also use this function to change the mapping of an item. Simply click on the cell to bring up the quick search.

Approximate matches for unmapped term

Reviewing and validating the mapping

For each mapping the automap editor indicates whether automatic ("Auto") or manual ("Revised") mappings have been executed. If you want to review a concept, simply double-click it in the SNOMED CT equivalent column to open the concept editor. Once you are done reviewing, you need to validate the mapping by changing the mapping state from "Not accepted" to "Accepted": You can either validate the mapping individually by clicking on the cell and selecting "Accepted",

Accepting a mapping suggestion

Or you can accept multiple mapping at once. Mark the mappings you want to accept, you can select multiple rows that are not adjacent, or a sequence of adjacent rows (see screenshot below). Once you are done right-click and choose Approve mapping state(s). The change will be indicated in the column "Mapping state" which will switch from "not accepted" to "accepted".

Approving multiple mappings in the automapping editor

Note: When generating the Simple map type reference set only the "Accepted" maps are included.

Editing the automap file

The automap file can be further edited. For example, the type of individual mapping (generalization, specialization, equivalence, etc.) using the IHTSDO standard method can be specified. Also correlation identifier concept can be added to the maps. Besides correlation, terminology specific map rules and advices can also be specified for the mappings.

Setting correlation for automapped components

Generating reference sets

Generating a complex map type reference set from an automap file

Snow Owl now transforms automap files into SNOMED CT complex maps, which allows specifying the type of each individual mapping (generalization, specialization, equivalence, etc.) using the IHTSDO standard method. It also allows adding a correlation identifier concept to the maps. Besides correlation, terminology specific map rules and advices can also be specified for the mappings.

To generate a complex map type reference set from your automap file, click the compass icon in the editor.

Enter a file path description in the dialog, add a commit comment and hit OK.

Generating a reference set from a mapping
The new reference set file will be displayed in the reference set view as a complex map type reference set.

Complex map type reference set created from automap

Generating a simple map type reference set from an automap file

Creating a simple map type reference set from an automap file is similar to the process described for complex map type reference sets. If you have simple map, a map icon will be displayed in the toolbar allowing you to generate a simple map type reference set.

Creating a simple map type reference set from an automap file

The new map type reference set can be opened from the reference set view.

Simple map type reference set created from an automap file

Updating reference set from automap file

When you made changes to an automap file, for example by importing a newer version of a spreadsheet, you can easily update the corresponding reference set. During the update new members will be added to the reference set. Members that are not present in the new version of the automap file are not removed from the reference set - this enables collaborative update of the same reference set from different sources. If the label changes (ID remains the same), the old mapping is inactivated (deleted) and a new one is created.

Click OK to start the update.

Updating existing reference set

A dialog informs you about redundant members that were ignored at the update. These are the members that did not change. Click OK to complete the update.

List of redundant members