In this video we will use the editor to take a closer look at SNOMED CT concepts. We’ll introduce the three main editor sections: Descriptions, Properties, and SNOMED CT Properties.
This is the first of a two videos about working with the Snow Owl editor. You can find the subsequent video at:
Once you’ve seen the video, you can find additional documentation at:
- Getting started with the concept editor
- User guide documentation about editing and authoring SNOMED CT content
In this video I will introduce you to working with the editor. We will perform different changes such as adding descriptions, changing the preferred term, and adding relationships to a concept.
We will start with adding a new synonym. I’ve already prepared a concept for you here. If you click the blue triangle, a list with actions will come up that you can perform and what we’re going to do is — we will just clone the synonym. I just click > Clone here and — you see — the system creates an identical copy of the previous synonym here, the one that I chose. And it copies also all of the settings, for instance the case sensitivity it’s the same as here above. Case sensitive and this one is case sensitive as well. And you see now here a little asterisk indicates that we have made a change that hasn’t been safed. You can also see an informational message displayed: “Concept contains unpublished changes” and a little icon here next to the icon for organism appears that indicates also that there are unpublished changes.
Now all you have to do it is type in your new synonym. I will type “Hantavirus” and hit the save button and now you can enter the a commit comment. I will just write “Added Hantavirus synonym” and click “OK.” Now it’s saved and now that new description appears here.
It has a box around the term, this is because it’s an unpublished change. This means the change has been saved in the repository but not formally published, not been formally published yet. Once a concept has been published only the text appears so he won’t see this box anymore.
You can also see my change here and the commit information view. You can see the date, when it was changed, you can see my user ID and my commit comment that I typed is also displayed here and the same in the history view: you can see here — I’m the author, my comment and the date when it was changed. And down here you can see here that’s a new synonym hantavirus that was added.
You can use the clone function whenever you have a description type that is already there — like synonym in this case and what is actually displayed here is specified by the concept model — I will talk a little bit more about this in the properties section.
You also have the option to add an unsanctioned description. Unsanctioned means that it’s not been sanctioned by the concept model, but you can add it nevertheless and this is with this little icon here in the toolbar. If I click it two entry boxes will appear: one for the description type. and one for the description term and if I click into this Snow Owl will automatically give me valid description types that I can you use. So in this case it’s definition, fully specified name, or synonym. If you’re wondering what these are. They are in the description format here, this is actually what triggers this so that they come up.
So you see here there are three different options, the description format is defined as plain text and the maximum characters that you can
enter for a definition are characters and for fully specified name and for synonym there are less characters, so they are shorter.
Let’s go back and I want to add a definition so you just click it and I actually already copied something from Wikipedia that I will just paste in here for Hantavirus so you see it’s that’s quite a long definition and then it’s again like before, you just click the save button and you can enter a commit comment again like Added definition from Wikipedia and you hit OK and it saves it to the repository.
Again you can’t see the two boxes around it that indicate that it’s an unpublished change. So this is unpublished the description type is unpublished and also the definition and the synonym that I saved earlier. If I hover over it the tooltip appears that you might remember from the previous video. It shows the effect time and it says “unpublished” because the description has not been published yet. So it’s actually not the time from the commit information view which is when I actually make the change this would be the time of the publication as you can see with the published concepts here and something that is also different is the module it’s the SNOMED CT B2i extension versus here it was the SNOMED CT core module and you can also see the description is case insensitive which is the default setting for unsanctioned descriptions. If I copy a synonym then it will take the case sensitivity. This is case sensitive and if a copy this, it’s case insensitive this is why it’s different. You can change it very easily if you want that by going to this context menu so you can set it to “case sensitive” or “initial character case insensitive” whatever you’d like.
Now I would like to show you how to change the preferred term of a concept. This is quite easy. Let’s go to a different concept, to this one the preferred term is indicated by the little rosette icon so wherever this is, this is the preferred term. If you hover over it you will also see “preferred term” displayed and we want to change it from “Calcific tendinitis of shoulder” to “Milwaukee shoulder.” All you have to do is click here the blue triangle again and then there’s an option that is set to Great Britain preferred. This means that to you set the selected description as the preferred description for the currently active language dialect.
This is indicated that it’s Great Britain by the British flag so if this was Australia than it would have the Australian flag here and so on. So if I click this you see then the rosette icon changed down here to Milwaukee shoulder and its not saved yet. There is again a little asterisk here. And if I save it I can enter a comment which i’m not going to do now and now it saves it as the new preferred term. You can see here in the editor, it’s not “Calcific tendinitis of shoulder” anymore but it’s “Milwaukee shoulder” and it also changed here in my SNOMED CT hierarchy. Now it’s “Milwaukee shoulder” so both of the terms changed.
You might have already noticed that some of the actions here are disabled for instance for the fully specified name I cannot “Clone” or “Retire” I can only “Clone and retire” This is because it’s restricted by the concept model. So it will only enable actions that are actually allowed by the concept model. For the fully specified name the IHTSDO editorial guide defines that a concept has one — and only one — fully specified name, one or more synonyms, and one preferred term and we implemented this rule in our Snow Owl concept model and therefore you will always have only one fully specified name, at least one synonym, and one preferred term. This is the reason why you can’t retire a fully specified name because there has to be at least one, has to be only one and not two and you can’t clone it because there can’t be two fully specified names and this is why you can only “clone and retire” it there. This means that a new copy will be created of the description and it retires the previously published description.
We already talked about this bottom part of the menu where you can see which case sensitivity is set. This is indicated by the little box around it here, so you can see here “Initial character case sensitive” which means it doesn’t matter if the first letter is upper or lower case but the rest of that description is case sensitive. So much about the description section. I’m just going to close it and let’s go to the properties section.
We call this properties section and not relationships sections because it includes not only SNOMED CT relationships but also datatypes like 500 in a 500 mg capsule for instance. And when we designed Snow Owl we wanted to make it easy for you to do editing and for this reason you see all of these empty text fields here. They are automatically created because they’re specified by the concept model. This has the advantage that you don’t have to find out which properties are appropriate for your selected concept because the mandatory and the optional properties are already displayed in this section.
Okay, now let’s see how that works — actually of course the concept model can be customized for your particular organization and the values that you can enter here are also restricted. So the results that will come up are like in the quick search, it’s the quick search feature that you already know from up here but the results are restricted to valid values that actually make sense to enter and I’ll show you what this looks like. Let’s add the severity. If I click into this field, it will bring up the quick search and there are only seven different options here for severity because the results are constrained to the values that are valid for this particular property and I’m just going to pick one of them. Let’s use “mild” and then you can save it again with the save button, you have a comment and you can see now it has the box around it. It’s been committed to the repository. Let’s do it for something else, for instance, “finding method.” If I click this field here, it will give me a lot more options over 53.000 — so there are a lot of procedures here so now it makes sense to use the quick search. If I look for “radiography of the shoulder” and I just type in a few words, it will give me this option and I can click it and now I can save it as well. So this is when the quick search comes in handy. Your previous choices and bookmarks also displayed in this field. The actions available are same as in the descriptions section. You don’t have the “case sensitivity” options because you have to use existing concept so you won’t be able to type in new terms but you can also clone and retire.
Let’s go to the last section which is the “SNOMED CT properties.” There are just a few options here. There’s the “status”, it can either be inactivated or deleted. You can only delete concepts that haven’t been published yet so if I try to delete this concept, I get this dialogue: “The requested component cannot be deleted”. So it has been releasing cannot be deleted. So I can’t do this. What I can do is inactivate it and here it presents the inactivation plan which shows all the different components that will be inactivated it: So the concept itself, the descriptions, the relationships and so on and you can also choose the reason for inactivation, or the target component, but I’m not going to do this now. I’m just going to hit cancel. You can also change the “definition status” from primitive to defined or the “subclass definitions” but those are more advanced topics and I just wanted to give you the basics of editing here in this video.