This video demonstrates exporting SNOMED CT reference sets to delimiter separated value file that you can use with a spreadsheet. We’ll see how the export wizard walks you through selecting different description types and properties.
This video is the first of two videos about exporting reference sets. You can find the second video at
Once you’ve seen the video, you can find additional documentiation at:
- Getting started with reference sets
- User guide documentation about reference sets, subsets and value sets
- Importing and exporting reference sets
This is the first of two videos about exporting reference sets.
Snow Owl supports two different export formats. Today I will demonstrate how to export a reference set to a delimiter separated value file or a “DSV” file. You would choose this format if you need a text file that can be used in other applications, for example, in Microsoft Excel.
The other option – which I will show in the next video – is an export to the SNOMED CT release file formats RF1 and RF2.
There are two ways of starting an export. You can either do it from the reference set view by right-clicking the reference set that you would like to export and selecting “Export reference set” (and here are the two options).
Or if your reference set editor is already open – like for example this one which is a reference set called “Continents” a very small one, it has only eight members – you can just use this button up here.
OK, let’s start the export. First, we need to specify the file name and location I will just call it “Continents” and export it to the desktop. We also need to indicate which character should be used to separate the different fields of information in the export file. We could use comma or space, but let’s stick with Tab and proceed.
What we can see here is a list of the attributes for the export items. The icons indicate what kind of attribute it is. So this tag here indicates that these are descriptions, for example Preferred Term, the flag indicates this is a relationship and these here are different properties such as Status or Module. This list was calculated based upon the attributes of the reference set members. That means that at least one concept in this reference set has this attribute. The reference set I selected is a fairly simple and small one, this is why we just have a short list here but I will show another example later where have a reference set with a lot more attributes and then the list is longer.
For the export we need to select which export items should be exported. We can do this by moving the items from the left side to the box on the right side. If you wanted to export all attributes, you would just use this double arrow and move them all over at once. It goes both ways. You can also select just a single one by using these arrows or you can also hold down the CTRL button or CMD on Mac and then select multiple attributes. I would like to export the Fully Specified Name, the Preferred Term, and the Status. I just move them over.
These arrows here can be used to change the order. Since this is going to be a spreadsheet that should start with the Fully Specified Name, followed by the Preferred Term, I can change the order here like this.
It’s also possible to export the description ID and the relationship ID just by checking these boxes, but let’s not do this. Let’s just export these three and run the export.
It was very fast, it was a very small reference set, and now follow the link to the export file. Here it is. It’s a text file but I will open it with Excel, this is just easier to look at and let me just format it so it’s a bit better to see and change the column size, get it bigger. Here we go.
You can see that the concept ID was automatically exported. It is always in the first column, you don’t need to indicate this in the wizard. One concept ID is a lot longer because this is a concept I created in the B2i namespace. The other ones are all SNOMED CT core concepts. Here is the Fully Specified Name with the semantic tag, the Preferred Term and all of the concepts are active. Now I close it and go back to Snow Owl.
Let me show another example of a reference set that has a lot more members. This has over 600 members and you can see if I open one of the members, that we have a lot more attributes that were specified here so we have several synonyms, Product Term, Short Name, Administration Method, a Product hierarchy level. You see it’s a lot more complicated. All of these attributes will show up on the list, which means you can export them. Here we go.
Here we have the Dose Form reference set. Let’s just export this: I’m going to call it call it “Dose Form”, keep Tabs. It already calculated the list and you can see that we have additional description types: the Product Term, the Short Name. We have additional relationship types such as the Delivery device, the Administration method and we also have datatype properties like numerical values, for example for drug ingredient strengths.
I would like to export the Preferred Term and the Short Name and the Administration method. Let’s run the export. It takes a bit longer, because we have a lot more members, and let’s just take a quick look.
You can see the Concept ID, the Preferred Term, the Short Name where some of the members don’t have attributes defined, this is why the cells are empty. We have different property groups for the Administration method and depending on which property group it is in there were different columns created here for this. So this is what it looks like for a bit more complicated reference set.
OK, some so much about exporting DSV files. In the next video I will show the other option, which is SNOMED CT release file formats RF1 and RF2.