Snow Owl lets you map existing clinical terms to the SNOMED CT terminology. In the following example, we’ll show you how to map some local terms to SNOMED CT. You’ll end up with a mapping file that can be further edited in Snow Owl and exported in a standard file format (a SNOMED CT Release Format 2 Complex Map Type Reference Set).

Example: Mapping clinical terms from a spreadsheet to SNOMED CT

In our example, we will use an existing file to demonstrate how mapping works. Our test file (Diagnosis examples from local system.automap) is a simple Excel work sheet with 17 clinical terms and their ID codes (here: 1 to 17). In practice, you will have to create a project and import your file (e.g. a comma separated value or Excel file) into Snow Owl before you can start mapping. For further information about this refer to the Snow Owl User Guide .

Ready? Let’s start:

1. Go to the Project Explorer view and expand the B2i examples project.

2. Double-click the Diagnosis examples from local system.automap file in the Mappings folder 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

3. Click the automap button . This will bring up the Automapping configurator dialog

Automapping configurator dialog

4. Pick the following settings: Column of the source values: Label, and Top level concept: Clinical finding

5. Press OK to start the automapping.

6. As you can see in the screenshot below, the SNOMED CT equivalent column and the Mapping mode column are now filled in. Note that impacted ear wax didn’t find a match in SNOMED CT.

Automapping editor after automapping

7. To solve the earwax problem click the ellipsis (…) to display approximate matches (see screenshot below). The first SNOMED CT suggestion isImpacted cerumen. That’s what we’re looking for, so hit return to select it. “Revised” will be displayed in the Mapping mode column to indicate that the mapping was done manually.

Approximate matches for unmapped term

8. Use the drop down function in the Mapping state column to accept your mapping. You can also accept multiple mappings at once. Either by selecting a sequence of adjacent rows or by picking multiple rows that are not adjacent. To accept your selection 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”.

9. When you are done, use the save button in the main tool bar to save your mapping.

10. The last step is to generate a reference set from your mapping. To do this, just click the compass icon in the Automapping editor. Create a title for your new reference set description in the dialog, add a commit comment and hit OK.

Your new reference set file will be displayed in the reference set view as a complex map type reference set.

Tip: You can maximize the mapping editor by double-clicking its title.