This video will introduce you to mapping. As an example, clinical terms from an Excel spreadsheet will be mapped to SNOMED CT. Afterwards, we’ll generate a standards-compliant reference set for you to share your mapping.Once you’ve seen the video, you can find additional documentation at:
- Getting started with map type reference sets
- User Guide documentation about mapping
- Mapping sets
You might also be interested in our videos about mapping sets:
- Introduction to mapping sets
- Creating and modifying mapping set
- Importing and exporting mapping sets
- Using local codes in value sets and mapping sets
In this video I will show how to create a map between an external code system and SNOMED CT using the automapping function. I’m going to take you through the entire process. We will start with importing an Excel sheet, then we will do automapping, approve the mapped terms, generate a reference, and eventually we will export this reference set.
You can find maps in the the reference set view which is here. This is where our map will eventually be saved as well. There are two different kinds of maps: Simple maps and complex maps
Let’s just take a quick look at a simple map. A simple map is used for one-to-one mappings between SNOMED and alternative coding schemes. So you can map SNOMED CT to custom codes or the other way around and also to the ATC Classification. It’s basically just three columns: This is a map between SNOMED CT which is the referenced component. You can recognize this by the top-level icons and the map target is CTV3 which is here. Of course you can maximize it as well.
You already know this user interface because it’s a reference editor So there is a filter search here Let my type something in and it will filter my members. You can add members, you can remove members, inactivate them, display inactive members and so on.
The complex map looks pretty much the same. It just has a few extra columns. I will show you this one which is SNOMED CT to ICD-10 map. You see, this is again SNOMED CT. By the way if you click this here it will adjust the width of the column. So it’s a little bit easier to see or I can maximize it. So these extra columns are related to specifying the rules for map execution, for instance here. You can also specify the level of generalization and specialization, but I don’t want to go into too much detail now and save this for a later session. I just wanted to show you what a complex map looks like.
Okay, let’s close these and start mapping ourselves. What I want to do is, I will use and existing file with local terms and create a map to SNOMED CT. The file I have is basically just a simple Excel worksheet: It has local codes and here are the clinical terms. There are just very few, just to show you. Obviously in practice what you would use would be a lot bigger.
Let’s close this and I just saved this on my desktop. Before we can import, we have to create a project which is in the project explorer view. A project is a top-level folder in which you can put folders and files, for instance there is the B2i examples project and there are different folders and then different files in each of them and we’re going to create one for us. To do this, all you do is you go into this view and you right-click it to bring up the context menu then you choose > New > Project and you go to > General > Project and > Next and then it asks for a project name.
I will call it Mapping example and just hit Finish and here it is. Now I can import my Excel file which is very easy, just right-click it you go to > New reference set automapping file and then all you have to do is browse for it. It’s already on my desktop so I just open it. If it has headers like my sheet has, you want to leave this box checked and if you don’t just uncheck it. It also is set for skipping empty lines and now I have to give my file a name let’s call it Diagnosis mapping example local to SNOMED CT. Hit Finish. Now you see it’s here and it already opened this mapping view.
Let’s take a closer look at this one. This is the automapping editor and it’s similar to the spreadsheet. It took actually the headers here, so we have the ID codes that I showed you on the Excel sheet. We have that the clinical terms which were in the header and then the two columns for SNOMED CT equivalents and mapping mode are empty because we haven’t performed the mapping yet. If you click this it will adjust the width of the column.
Okay, to do the mapping all you have to do is click this button and then it prompts you in this dialog box the column of source value is not the ID code but the clinical terms. I’m going to choose this. You can restrict it to a top-level concept. Since we have all clinical findings I will choose clinical findings but you don’t have to do this and then all I do is hit OK.
Now you see it filled up the empty columns and you can see the mapping mode is Auto and here are our SNOMED CT equivalents and the mapping hasn’t been accepted yet. The other columns are not so important right now
You see, one here, for the “impacted ear wax” it couldn’t find a match so I’ll have to do this manually. I just click this field and if I a click this ellipsis then the Quick search will come up that you already know and it has impacted ear wax already in it and it shows you the approximate matches and the first one is actually the one that I want to use. So I just click it, hit return and now it fills it in and you can see that the mapping mode is not Auto but Revised.
You can also change the other terms just by simply clicking it and then it will always give you different options. Just hit escape if you want to get out of it.
Okay, to accept them, you can either do it manually just like this, if you click this field. If you just going through them one by one or if you just glance through them and you see that it’s all correct you can also mark all of them and then right-click it. Then you have the option to Approve mapping states. Now you see they’re all accepted and that is important because only the terms that you accepted will be used to generate a reference set. Since we’re finished with this, we can save it here with the save button. You see the little asterisk disappeared Let me minimize it again.
And now we can actually generate a reference set. By the way whenever you bring up this file from now on let me just close this to show you it will already have the mapping saved in it and accepted, but you can of course you can make changes whenever you want to.
Now let’s create a reference set which is this icon here this one is fine a mapping and then this one is for creating reference sets. I have to give my reference set a description. I’m just going to call it Diagnosis mapping example and now my map target is the ID code the ID column is the ID code the source terminology is SNOMED CT, so I don’t have to make any changes. Created reference set Now my changes have been committed.
You see there was a change here as well, because this one showed up. This is the reference set that I just created, a complex map type reference set. It will always generate a complex map, this is required to have the additional data related to whether or not the matches are exact or inexact. So you always end up with this kind of reference set.
If I click this you see it’s again the reference set editor with the filter search and I have nineteen matches because I approved all of them. Now of course I cannot make changes anymore because it’s mapped.
So that’s the difference between this one here you can make changes, this is the automapping editor and this is the reference set editor. Let’s close this again.
So the last thing we want to do is, we want to export this file to our local system. You go to it in the reference set view you can also use this button but let’s try this one here right-click it, there’s the function > Export reference set and now you can chose where the file will be exported to I’m going to call it Diagnosis mapping example I want to save it on my desktop, go to save. You also need to choose the effective time. There’s a little calendar where you can pick it from, so let’s just pick October 15th which is today.
When you hit next, you will see the different components that will be exported for review. Then you get scary warning which you can pretty much ignore because it’s not going to take very long it will actually finish in a few seconds. That’s already it and it tells you that the selected SNOMED CT components have been successfully exported into RF2 format and then you can’t follow this link.
Let’s just go to Finish and I’m just going to show you, it should be on my desktop up now and there it is and I can unzip it and here is your exported reference set of your local Excel sheet mapped to SNOMED CT.