UMLS Metathesaurs Tool – Part 2 (Browsing the datasets)by Nadeem Nazeer
In the previous post we went through installing the UMLS® Metathesaurus tool itself and validating the installation.
In this post we will go through loading and setting up the tool for browsing the UMLS using a built-in Java Browser and exploring the data files which we may import to other database systems for use in our own apps as needed. One of such Apps here at “Applied” is our Health Vocabulary Rest API, one of our open source projects that you may check out via git here.
To get started, the first thing is installing the data-set and writing out the database load scripts:
1. After validating and launching the tool, the initial screen will appear as shown below; click on “Install UMLS” to proceed.
2. A new screen will appear, allowing you to choose:
- source: location where the tool and its data files reside.
- destination: location where we want the tool to put files at.
- and some options for selecting which UMLS Knowledge sources you want to install.
3. On clicking “OK”, you will be allowed to create the new configuration file or choose an existing one, which is needed to customize the things you want or don’t want to install.
4. On clicking “New Configuration”, the system will prompt you to accept the license agreement.
5. Next, you will be allowed to select the subset of metathesaurus vocabularies. The default is “Level 0” for which no additional license agreements are necessary.
6. Now the window for choosing the various input and output options will appear. Click on “output options” tab, and here we see the section with a heading “Write Database Load Scripts”. Choose the database you want the scripts for.
7. In the top menu go to “File” => “Save configuration”, and then click on “Done” => “Start Subset”. This will start the process of extraction of the needed files in the “destination location”(selected in step 2) for browsing and generating the scripts to load them in the database.
8. After completion of process, you may click on “Browse Subset” in the main initial window, to browse and search the vocabularies.
In this post we set up the UMLS® Metathesaurus tool and the installation/extraction files needed to use the built-in Java Browser for exploring and searching the UMLS files. In the next part we will start using the extracted “Database Load Scripts” from step 7 to load loading them up in our own database systems.
For any queries shoot me an email at firstname.lastname@example.org.