Installing Terminology Validators
In order to validate terminologies Inferno can be loaded with files generated from the Unified Medical Language System (UMLS). The UMLS is distributed by the National Library of Medicine (NLM) and requires an account to access.
Inferno provides some rake tasks which may make this process easier.
Downloading the UMLS
Inferno provides a task which attempts to download the UMLS for you:
bundle exec rake terminology:download_umls[username, password]
Note: username and passwords should be entered as strings to avoid issues with special characters. For example
bundle exec rake terminology:download_umls['jsmith','hunter2!']
This command requires a valid UMLS
password. Inferno does not store this information and
only uses it to download the necessary files during this step.
If this command fails, or you do not have a UMLS account, the file can be downloaded directly from the UMLS website.
Unzipping the UMLS files
The UMLS files should be decompressed for processing and use. The metamorphoSys utility provided within the UMLS distribution must be unzipped as well.
Inferno provides a task which will attempt to unzip the files into the correct location for further operation:
bundle exec rake terminology:unzip_umls
Users can also manually unzip the files. The mmsys.zip file should be unzipped to the same directory as the other downloaded files.
Creating a UMLS Subset
The metamorphoSys tool can customize and install UMLS sources. Inferno provides a configuration file and a task to help run the metamorphoSys tool.
bundle exec rake terminology:run_umls
The UMLS tool can also be manually executed.
Note: This step can take a while to finish
Loading the subset
Inferno loads the UMLS subset into a SQLite database for executing the queries which support creating the terminology validators. A shell script is provided at the root of the project to automatically create the database
Creating the Terminology Validators
Once the UMLS database has been created the terminology validators can be created for Inferno's use.
bundle exec rake terminology:create_vs_validators
The UMLS distribution is large and no longer required by Inferno after processing.
Inferno provides a utility which removes the umls.zip file, the unzipped distribution, and the installed subset
bundle exec rake terminology:cleanup_umls