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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
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. So 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 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 basically all I wanted to show you
about
SNOMED CT reference sets
and in
the next video we will talk about mapping.