Video 3: Browsing SNOMED CT with the concepts view

Published on September 28, 2012 by Dr. Sonja Ulrich using Snow Owl v2.0.

In this video you will learn how to use the SNOMED CT concept view to browse the SNOMED CT terminology. We'll demonstrate different ways to browse and display the terminology.

Transcript

In this video I will show you how to browse SNOMED CT and other terminologies and how to use the different functions of the SNOMED CT view which is this part of the user interface. We will also talk a bit about the parents view which is down here and the editor which will be in this part.

The SNOMED CT view organizes the concepts in a tree-like structure by their IS A relationships. The default setting that you can see here only displays the top-level concepts. There are nineteen overall and in the next video we will talk a little bit more about the concepts if you are curious about their content.

If you want to browse through the hierarchy, just simply click one of those triangles and it will reveal the children of a concept. You can go deeper into the hierarchy until you eventually reach a concept that doesn't have children any more and you can recognize it because it doesn't have a little triangle, like these concepts don't have children anymore so you are at the end of the hierarchy.

If you want to reset the tree to its default state, just click this button, it's "Collapse all nodes" on the toolbar, like this and then you're back where you started from.

If you want to take a closer look at a certain part of the terminology, and omit high-level concepts, or sibling concepts, you can do the following. Let's open the "Clinical Findings" again. Let's say you just want to look at "complication" so you click on this and then there is this button "Set concept as a root" and then it will just display this part of the terminologies so you can see everything that's underneath this concept.

If you want to return, then just click this and then it's back at the root concepts, so this is what we have and that "collapse all nodes" again. I'll show you one more time. Let's take something else. Let's go to "Events" and this one "Set it as a root concept" here you go back to where you started from and here you can collapse.

Maybe you remember double-clicking this one will maximize, so if you need more space you can use this as well and then that's quite helpful when you have a bigger terminology and then the buttons are here. OK, and I'll go back.

A useful feature is this text field here which is the filter search. I'll talk about this in more detail as well in the video about doing searches but I already wanted to show it to you. If you type in a term, let's say "puffer fish" it will display the matching concepts either as a tree, or as a flat list and there's a toggle button for this so if you toggle here you can switch between the tree so you can see the hierarchy or you can just have the results as a flat list back and forth.

As you can see, there are different icons in front of the search results, so in Snow Owl each top-level concept has its own dedicated icon. This icon will also be used for its children. When you open the hierarchy you can see that all the children have the same icon. This lets you identify what type of concept you are working with wherever you see it.

So you see this concept is under the hierarchy of the "Clinical findings." This here belongs to "Events." This one to "Organisms" and this one to "Substances." If I have the flat list, I still have the icon here.

If I open one in the editor - you remember double-clicking a concept will open the editor - let's do "puffer fish", you will see this icon is here and you can see instantly if you know your icons that this is an organism. And if I open another one, it has the icon here as well. The icon will also show up in your search results. if I do a quick search up here - this is kind of like our internet Google search text field - and then I type in "puffer fish" it will show the search results as well as the dedicated icons. So it's quite useful to know these icons because wherever you are within Snow Owl they will show up and they will help you identify the type of concept that you are working with.

Let's go to the parent view that we haven't talked about. "Fugu poisoning" is actually a nice example. The parent view displays the parent or the parents of a concept. This concept here - fugu poisoning - actually has multiple parents so let me just maximize it and it's in contrast to the SNOMED CT view the child is on top and then the parents are at the bottom.

If you open them - and it works exactly the same way as the the SNOMED CT view that I've just showed you - you should eventually reach the end of the line and here is the root concept but you see it's all the heart symbol which stands for "Clinical Findings." So much about parent concept.

The parents view is linked to the concept view so when you click a concept here it will show up as you can see down here in the parents view. I click another one so whatever concept is activated in this concept view, will be in the parents view.

This works as well for the other terminologies. We haven't talked about them but they work exactly the same so these concept views, we also call them concept navigators because you navigate through a hierarchy. They can be opened by clicking the little triangle and closed again.

You can set it as a root concept, can go back, and you can collapse all the nodes and you see down here I'll go further down in the hiearchy. If I click this, it will show its parents so it works exactly the same and of course if you double-click this, you can open an editor here as well.

There is also the option to link the editor to the concept navigator. It's this button, it says "Link concept editor to navigator." The Navigator is the same as the concept view and if I activate it, just by clicking it - now you see it's activated, it has a little border and changed its colour then when I have an active editor here, let me go to fugu poisoning and now it shows up in the hierarchy so this way you can see the concept editor with all the information and will have a separate video about how to use this and what exactly it shows you but you can also see where your concept is located within the hierarchy.

If I maximize this, there is fugu poisoning, or the puffer fish. You see now it went into a different sub-hierarchy into the organisms to puffer fish and the same with the parents view so the parent view follows as well.

Of course this works for other terminologies, so I have this one and let's unlink this so you link it by activating the button by pressing it and then if this is up, it's not linked anymore. So if I go to this one, and I link it - let's open a new one - now it's linked. You see now it goes back.


This link button, by the way works also down here in this view for the history for instance. So if you have the history view and you have a concept then it will show the history of the active concepts of the puffer fish here or the fugu poisoning here. If I inactivate it, then it's not going to change anymore so you see now fugu poisoning is still here. So this is the link button which is quite useful.

There's a little help symbol that opens up a menu on the side that talks about this part of the platform that you're using and it also gives you links to our user guide so this is a concept navigator and it shows you what it is.

So much about navigating and using the navigator for browsing SNOMED CT and if you're wandering what actually is in the terminology, you can watch the next video. We will take a closer look at each of these top-level concepts. I will talk a little bit more about the dediated icons.

If you're already familiar with SNOMED CT you might want to skip this video and just go right to the video about doing searches.