Sub-Term Mapping Tools

Synonym Mapping Tool (smt)

- Introduction
- Set Up
- Test Run
- Input
- Output
- Options

Introduction

Smt (Synonym Mapping Tool) applies STMT APIs with a preloaded corpus (UMLS-Core Synonyms) to find:

• CUIs with synonym substitutions

Set Up

Follow the installation instructions to install and run the smt program. Check on the following items only if you don't use the provided script to install Sub-Term Mapping Tools.

• CLASSPATH:
  1. include the STMT distribution jar file, ${STMT_DIR}/lib/stmt${YEAR}dist.jar, in your CLASSPATH.
  2. include the stmt top directory in your CLASSPATH.

• Configuration File: assign the full path of the top directory of stmt${YEAR} to a variable named ROOT_DIR in the configuration file, data/Config/smt.properties.

• Lvg Configuration File: set the lvg configuration file (LVG_CONFIG_FILE) to the default (data/Config/lvg.properties) or your installed lvg directory in the smt configuration file.

Test Run

• Run java program

  Enter the command:

  > smt -p -pt
  - Please input a term (type "Ctl-d" to quit) >
  Cold
  Cold|cold|C0009264|Cold Temperature|0
  Cold|cold|C0009443|Common Cold|0
  Cold|cold|C0010412|Cold Therapy|0
  Cold|cold|C0024117|Chronic Obstructive Airway Disease|0
  Cold|cold|C0234192|Cold Sensation|0
  Cold|cold|C0719425|Cold brand of chlorpheniramine-phenylpropanolamine|0
  Cold|cold|C1949981|Colds homeopathic medication|0
  

  where:

  • smt: smt script to run smt Java class
  • -p: set smt system option to show prompt (try -h option!)
  • -pt: show the preferred term of the CUI

Input

Free text (a word or term)

Output

Normalized term with CUI, Number of synonym substitution, and preferred term

Input Term	Normalized Term	CUI	Preferred term	Number of synonym substitution

Options

Please refer to design document