Unified Medical Language System.
MetamorphoSys:
Creating Subsets.
In this Tutorial, we will show how to create a subset of the UMLS
that contains data of your choice.
Load MetamorphoSys by launching
the appropriate run file for your operating system
from the folder where you downloaded
and extracted the UMLS release files.
In the Welcome window, click “Install UMLS”
to start creating a subset.
On the Install UMLS screen,
the Source box indicates the directory
where the UMLS files reside.
In this example, the files reside on the local hard drive.
Remember that your MetamorphoSys files should
reside in the same directory as UMLS source files.
The destination indicates the directory
where the UMLS subset will be installed.
Click “Browse” to select a destination directory.
If you wish you can create a new folder
for the subset. Click
“Open” when done.
The UMLS consists of three Knowledge Sources – the Metathesaurus,
the Semantic Network, and
the SPECIALIST Lexicon and Lexical Tools.
The default settings include all three Knowledge Sources;
however, we will only be creating a Metathesaurus subset in this example
so we will uncheck the other two Knowledge Sources.
Now click “OK” to begin configuring your subset.
Two windows - a Progress window,
and the Configuration window will open.
We will proceed with setting up a new configuration,
however, note that you can choose to
open an existing configuration
from a local file if you have saved
such a file previously or received it
from a colleague.
Click the “New Configuration” button to
create a new configuration.
The License Agreement Notice that appears
on the screen explains that the
Metathesaurus contains source vocabularies
produced by many different copyright holders,
and some of the vocabularies
have additional restrictions on their usage.
Read the Notice, and click “Accept” to continue.
The Select Default Subset Configuration window
that appears offers to select from
4 pre-defined configurations.
The first configuration is the Active Subset of UMLS.
This subset contains UMLS data
from sources that are actively updated
in the Metathesaurus.
The second option called “Level 0” includes
only Category 0 sources
that have no additional restrictions in the UMLS Metathesaurus License Agreement.
You can also select “Level 0 + SNOMED CT,”
which includes sources in the “Level 0” configuration,
plus SNOMED CT.
Finally, you can choose the SNOMEDCT_US
configuration that includes data
from the US Edition of SNOMED CT.
Technically, you can choose
any of these configurations and then
customize by including or excluding
specific vocabularies and choosing
other options in subsequent steps.
The predefined configurations
are provided for convenience.
In this demonstration, I will select the
“Active Subset” configuration
and click “OK.” If the active
subset is what you need,
then you don’t need to change the default configuration any further
and can simply proceed to creating the dataset by selecting
“Begin Subset” from the “Done” menu.
In this demo, we will examine several
other configuration options.
The first set of options is in this Input Options tab.
Here you can change the default
Input format and the location or
source files used to create your subset.
The Output Options tab
allows to change the format of output
from the default, and recommended,
Rich Release Format, or RRF
to the Original Metathesaurus Release format, or ORF,
as well as to change the destination folder
and a few other output options.
You can read in detail about
these options by clicking on the
Help button on the right upper corner of this window.
Even more details are available in the web-based Metathesaurus
documentation that you can access by clicking
on the link at the bottom of every built-in help page in
the MetamorphoSys interface.
To add or remove terminology sources
from your subset,
click on the Source List tab.
Here you can either select sources to include in your subset,
or to exclude from it.
We will keep the default list of sources to exclude
from our demo subset.
Another important set of options is
under File menu.
This menu selection is called “Enable/Disable Filters.”
The first filter we will apply is the Language filter.
Select the Languages List check box and click OK.
Select languages to exclude.
We will keep all languages, except English,
excluded.
This will result in our subset containing only terms in the English language.
Go back to “Enable/Disable Filters” and
select Semantic Types check box.
Click OK to review the list of Semantic Types.
Click on the radio button for “Select semantic types to
INCLUDE in subset”
then select Semantic Type
T047, Disease or Syndrome.
Once you made your selection,
MetamorphoSys offers to include 2 related
semantic types, Mental or Behavioral Dysfunction
and Neoplastic Process.
Click Cancel to keep only the
Disease or Syndrome Semantic Type.
To summarize, we have finished
configuring a subset based on the
Active UMLS sources, with
English language content,
and further limited our data to the
concepts assigned the semantic type “Disease or Syndrome”.
You can now save your configuration settings
in a local file that you can keep
for your records or share with your colleagues.
For that, select “Save Configuration”
from the File menu and browse to the folder where you
would like to save your configuration file.
Click Save to save the file.
Now select Begin Subset from
Done menu to start creating the subset.
After your subset completes processing, a
window with the subset process log will be displayed.
This log is saved for your reference in the
mmsys.log file in folder
META in your subset output folder.
The same folder also contains all files
comprising your subset.
These files can be used outside of the
MetamorphoSys for text manipulation
and extraction in your custom applications.
To browse your subset, click on the Browse Subset
button in the Log window.
Otherwise, you can click OK and close the window.
You can now click the “Browse my Subset” button
in the Welcome window to find the
newly created subset.
Your subset will reside in the /META sub-folder.
For more information about the UMLS,
go to the UMLS Home page
where you can access and search UMLS data,
review help documentation and tutorials,
and access related terminology resources.
Thank you for watching!