This video will introduce you to the layout and basic functions of Snow Owl’s reference set view and reference set editor. Browsing and viewing existing reference sets will be demonstrated as well as creating a simple type reference set.
Once you’ve seen the video, you can find additional documentation at:
- Getting started with reference sets
- Creating reference sets
- Editing reference sets
- Importing and exporting reference sets
- Full user guide documentation about reference sets
- Information about value sets
You might also be interested in our other videos about reference sets and value sets:
- Exporting reference sets as delimiter separated files
- Exporting reference sets to SNOMED CT release format (RF1 and Rf2)
- Working with value sets
- Collaboratively authoring reference sets 1 (one author – one reviewer)
- Collaboratively authoring reference sets 2 (two authors – single reviewer – dual authoring)
- Collaboratively authoring reference sets 3 (two authors – one reviewer – dual blind authoring)
- Collaboratively authoring reference sets 4 (two authors – two reviewers – one adjudicator)
This video will introduce you to the basics of working with reference sets. After a short introduction to the different kinds of reference sets that Snow Owl supports we will look at existing reference sets add members and also create a simple type reference set on our own.
Before we start just a few words about reference sets in general. As you already know, SNOMED CT is a huge terminology; actually the most comprehensive clinical terminology in the world. There’s over 300,000 concepts and since not all of them are needed in practice it makes sense to extract a smaller a collection of concepts from SNOMED CT which we refer to as reference sets.
A reference set is a purpose-built subset of the terminology that contains only the terms that are needed in a specific context, for example, all terms needed for a medical specialty or in an emergency department or for pick lists in clinicians-facing applications like a problem list. Snow Owl is a tool to create and maintain different kinds of reference sets which are named from the SNOMED CT Release Format 2 specifications and you can also use it to compare and export reference sets.
When you’re working with reference sets you can either use the authoring perspective which you see here or you can use the reference set perspective which has only the reference set view and an empty field here where the reference set editor will be launched. The reference set view which you see here on the left side is an overview of the reference sets in the database.
We’ve already included a few reference sets in the “B2i examples” folder you can see the little B2i icon here. So there is a reference set for instance for cardiology for the specialty and if I hover over them you can see how many members each of them have so some are bigger and others are just small reference sets and if you double-click one of them, it opens the reference set editor.
If I open several, they are just stacked in tabs here and you can activate them, you can switch back and forth, you can move them it’s basically the same as what you already know when you open a concept here and it shows up in the concept editor. If I work in the authoring perspective and if I open a reference set here, it will be displayed in the middle. You can see in the reference set perspective we have a little bit more space so it makes it easier to work with it.
The reference sets are organized by their type, this makes the navigation easier if you create a new reference set, it’ll also be grouped by its type so for instance if I create a simple type reference set, it will be in this group here.
You can also delete reference sets simply by right-clicking them and opening up the context menu and there is a delete function.
You can also link the editor to the reference set view with this button so it’s linked and this is unlinked now and now I press it again it’s linked and it will show me which reference set is the active one, which is this one here and it’s displayed here and if I click this for instance then it’s displayed here so it’s exactly the same as in the concepts view there was this link button as well.
This button here is for comparing reference sets it launches the reference set wizard and you can here pick two reference sets that you want to compare with each other but I don’t want to go into further detail here because it’s a little bit more complicated. So we will save this for a later session. I just wanted to show you that the function is here and very easily accessible.
There are three different kinds of reference sets and you see they have different kinds of icons. There’s the simple type reference set. You see this icon is displayed up here as well, so all the ones that I opened are simple type reference sets. A simple type reference set is a plain grouping of concepts by user preferences and we will create one later in the session.
There is also the attribute value type which is this one and it will have this icon if I open one, the attribute value type reference sets allow associating a value concept with the referenced component so you can extend the terminology with custom properties on the concept.
And the last one is the query specification type reference set. Its members are determined based on a semantic query. They can be automatically updated when a new version of SNOMED CT is released which is quite useful and they’re sometimes referred to as intensional reference sets; you might have heard that term before.
There are also simple maps and complex maps in this reference set view but we will talk about them in the next session.
The navigation in the reference set view is pretty simple it’s again like the SNOMED CT view so you can open and close the different groups by clicking the triangles you open one by double-clicking it you can link it, I already talked about this. You can delete them. It’s basically just like in the SNOMED CT navigator or in all of the other navigators.
Okay, so much about the reference set view which is your database and now when you’re actually working with one reference set, when you’re managing the members you will use the reference set editor which is this part. You can drag this and make this bigger and it consists of two components that you are already familiar with. On the left side are the referenced components so the members of your reference set. They’re displayed in a hierarchy just like the SNOMED CT concepts and you can open and close it again, go down in the hierarchy. You can also display it as a flat list this is the toggle button here so it switches between the hierarchy and the flat list.
There’s a filter search here so if I’m looking, if I type in something, this is let’s go to this one for instance, this is a non-human reference set so if I type a new term it will filter and give me only the concepts that match my search terms. If I look for collie it will give me all the clinical findings that match collie and I can have this displayed as well as a flat list or as a hierarchy. If I delete this again it will display all 1,908 members of the reference set.
You can inactivate reference set members by simply clicking it then there’s a dropdown menu here and then you can go to inactivate. You cannot delete members of a reference set that has already been published you can only inactivate them. You can see the inactivated members by hitting this button. If I do this, there two inactive members in this reference set or you can choose just to show the active members which is this but if you create your own reference set you can also delete a member which is simply by clicking on one and then hitting this button but since this is a published one I’m not allowed it to perform this.
Something else that’s quite useful is that you can sort the members of the reference set by simply hitting the title of your column it is sorted alphabetically or the other way around if you hit it again this also works with status but since we’re just displaying the active ones this doesn’t make sense right now. By the way, clicking on the top of a column is a function that you will find in other parts of Snow Owl as well. If you try it out, it works in most parts of the application.
If you want to add a member to a reference set, that’s quite easy. I’ll show this, I’ll show you how this works in the authoring perspective. There are different ways of adding a member.
You can simply go to the SNOMED CT concepts and pick the concept you want to add, for instance, this one explosive force and you just drag it over and that will add this member and if I go to explosive force, you see now it was added to the reference set.
If you want to add a concept and its children like fire for instance you right-click it and there’s the option to add the concept and descendants to the active reference set. You can also only add this particular concept that you picked, the active one or all the descendants which is this one and now if I click on fire, it should be all here so there’s fire that was added.
Let’s go back to the reference set editor. I haven’t talked about the second part which is the actual editor. It’s a lot like your concept editor. It’s basically identical to the overview page so you have three sections one is descriptions, one is properties and then you have the SNOMED CT properties here and you can open them and close them you can acess the different functions just like the way we did it in the previous video.
If you want to see the other pages, you have to double-click a concept, so if I do this and this will open the concept editor and there you have the different pages then you can look at the mappings for instance but the overview page is identical so if you only need the overview page, then it’s enough if you simply click a concept once and it will open this page. But you have all the functions so you can do editing here as well.
Okay, see there’s already a little asterisk that appeared because I added some members but they are unsaved changes so if you want to change it, you just simply click the save button and you can enter a comment if you want to and then it will add these new members to the reference set and actually save this change.
You can also add members to a reference set by using the search view so for instance if you do a semantic query, let me just open one quickly, there’s the “Getting started with semantic queries” examples and I’m just going to do findings by sight. I’ll run this query.
Now I have all my results, over 6,000 results so I’m going to go back to my reference set and if i just wanted to add this single result, I would just right-click it and then add the concept to the active reference set or I can add all results to the active reference set and this is what I do so they were all added to the reference set now. It’s quite easy, so you can either use this button for the quick search you can use the results in your search view or you can drag and drop just one concept or you can right-click it and then use this one to add a concept and its descendants so its children.
So much about adding members to a reference set, now I just want to briefly show you how you create a new reference set. You can do it by using these buttons that’s the easiest so we have different buttons for different kinds of reference sets, so if I want to create a new simple type reference set, I would use this one. This is for a query type reference set and this is for attribute value type reference sets.
So if I click this one, it will open the wizard and it automatically creates a reference set identifier which is here and I can type in a name I’m just going to call it Test2 now. Now I have to pick a referenced component which is a SNOMED CT concept and I go to finish, you can enter a comment if you want to and then it creates a reference set for me, a simple type reference set and the title that I picked is here “Test2” in the editor and you see there are no reference set members because I just created it but I did not add any members to it.
So let’s add some some members. Let’s go to organisms. See there’s no number here. And add for instance all the microorganism so these are over 16,000 SNOMED CT concepts I right-click it, I go to add concept and descendants to the active reference set let’s do this and here we go, and here are the microorganisms and let’s save it.
Now it’s saved and if I go to the history view it will show me that I made over 16,000 changes. Let me make it a little bit bigger. In the first version, I just created a new reference set called “Test2” and then I added all the members and you can actually see all the concepts that were added to “Test2” so you can always see who made the change, when it was made and you can see the whole history of the reference set.
And of course in the comment information view you can see who did it and when changes were made.
Let’s do another one, just to show you. Maybe add some events. Just a simple one “disease outbreak” SNOMED CT concept just by dragging it over and it’s here in the hierarchy. Now I can save it again.
If you change your mind, and say no I don’t want to have it then you just go to this shop icon, the shop icon is always for a reference set and this one has a plus, so this is for adding members and this is for removing them and if I click remove, it disappears.
That’s all I wanted to show you about SNOMED CT reference sets and in the next video we will talk about mapping.