This video demonstrates exporting reference sets in the SNOMED CT release file formats (RF2 and the discontinued RF1). It explains the differences between the standard delta, snapshot, and full release formats with examples from a simple B2i reference set that has undergone three publications.

This is the second video of a two part-series about exporting reference sets. You can find the previous video at

Once you’ve seen the video, you can find additional documentiation at:

 

Transcript

This is the second video about exporting reference sets.

In the previous video I exported this reference set to delimiter separated values format and today we will create an RF1 (SNOMED CT Release Format 1) and RF2 (SNOMED CT Release Format 2) file, which are the official SNOMED CT release formats.

When you’re exporting in RF2 you can choose a publication format that contains the history of the reference set. This is called the Full export. The history of a reference set reflects what happened to the different components during the previous publications. We can see the history of a reference set or also of a concept down here in the history view: Whenever a component is active up here in the editor, the history is displayed down here in this view.

Let’s just maximize this view to get a better look. You can see the date when something was changed, the number of changes, who changed it, and some information about the kind of change. When you click a component, you can see down here what exactly happened.

This is a reference set that I created for demonstration purposes. Let’s see what happened to this reference set.

First, the reference set called “Continents” was created, then different members were added: Africa, Antarctica, Asia and so on. And then this reference set was published: I created version on the 24th of July and we can see what happened to the different components during this publication: the different members were published and an effective time was attributed to each of them on the 24th of July.

After that I made some more changes. I added a new reference set member, a concept I created myself: Arctica. I also inactivated Africa, another reference set member and published these two changes. Here’s the new reference set member and here’s the effective time that changed for Arctica, for the new member and this one is Africa which was inactivated. The status change also got a tag for effective time. This is the second version; it had one member inactivated and one new member.

Then I changed the status of Africa from inactive to active again and also published these changes on 28th. You see there’s only the effective time for this status change that was recorded here. So that’s the history of this reference set and if you recall the previous video, what was exported was only the most recent version of the reference set. We exported only what we see here, we could select different attributes for the export, but it was not possible to export the history of a reference set.

Now let’s start the export. First we need to specify a name, I’m going to call it “Continents RF2”, export to the desktop. Here are the three publication formats:

  • There is the Full export, which contains every version of every component ever released. This is the full historical information of the reference set. This is what I just showed, so everything that we just looked at in Snow Owl can be included in the export if you’re doing the Full export.
  • There’s also something called Snapshot, which is the most recent version of the reference set. If you don’t work with historical information, the Snapshot release might be sufficient for your needs; it’s just the most recent version.
  • The last one is the Delta, which contains only components that were changed or added since the last release. For example, if you exported the first version and you just want to export the update from the first to the second version, so only the components that were changed, you would choose the Delta export.

For Delta it’s also possible to specify a time range down here, which means you can only include components that were changed during a certain period of time. For example, if you wanted to export only components that were changed within the last six months, you would select the beginning date here and the end date here. This way you can limit your Delta export even further.

But what we want to do today is the Full export with all the historical information that I showed you. If you need an RF1 file, you have to check this box here. As RF1 is an obsolete format that is being phased out internationally, it’s not possible to export only in RF1; you’re always generating an RF2 file as well and you will see there will be two separate export folders. Let’s do this.

I’ll check this box and now on the next page we need to select the modules for export. For me this would be the SNOMED CT B2i extension. Modules can be dependent upon other modules and it’s possible to show the dependencies here, so you don’t need to figure them out yourself. Just click this button and we see that my extension is dependent on the SNOMED CT core and on the SNOMED CT model component modules. Clicking this button automatically adds the required modules, it’s quite convenient.

Let’s start the export and review the file. You can see this is a zip file. Let’s open it. We have an RF1 export which is this one here. It contains these two text files and this is the RF2 export and you see this looks very different from the text file that we exported in the first video. So it’s a more complicated, standardized structure that these formats require. We cannot look at the whole thing, this is actually machine readable, which is used to exchange information and not really something that you would normally read, but we can still take a look at it. I’ll make this a bit bigger.

You see it’s a Tab separated file. This is why this header goes with this column here. In the last column we have the SNOMED CT concepts: This is Arctica, this is the one that I created myself, we can instantly identify it because this has a much longer concept ID (because it’s in the B2i namespace). This is the reference set ID. Here’s the module ID. This is interesting because it’s the status and here is the effective time (this is just a unique identifier) but with these two columns we can actually deduce the history of this reference set:

If you recall we had three publications, you see we have three different effective times: 24th, 26th and then the 28th. These are the first seven reference set members.

Then with the second release, there was one reference set member, this one here, with this ID that was inactivated. If I enter this ID in Snow Owl we can see that this was Africa. Here’s the concept ID and the status was changed to inactive. There was also a new reference set member; this was Arctica that was the one that I added.

Then in the last release on the 28th there was a reference set member that was activated again. We can see here that the concept ID is the same, so this is again Africa. There’s no Preferred Term, you cannot really read it, only if you look up the IDs.

OK, that’s all I wanted to show about exporting. I hope you enjoyed both videos.