Jena UMLS Filter - filters and enhances UMLS Files
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README.md

JuFiT - Jena UMLS Filter

This is the Jena UMLS Filter Tool (JuFiT), a rule-based open-source tool to filter and enhance entries of the Unified Medical Language System (UMLS). JuFiT uses rules similar to those in MetaMap and Casper, but extends these by adding support for multiple languages and their language-specific phenomena, e.g., German compounds. We provide rules for English, Spanish, French, German, and Dutch, yet the declarative implementation of these rules makes it possible to add support for further languages without changing JuFiT’s source code.

Note before usage

Input

You need files from the UMLS. After registration at [UTS] (https:/uts.nlm.nih.gov), you can download the UMLS files from the [U.S. National Library of Medicine (NIH)] (https://www.nlm.nih.gov/research/umls/). Unpack the ZIP file of a UMLS version (e.g. umls-2017AA-full.zip). Unpack the files MRCONSO.RRF.aa and MRCONSO.RRF.ab (files of Concept Names and Sources), concatenate these both to one file and unpack MRSTY.RFF (Semantic Types). Use this files for the input of JuFiT.

Gazetteer format

Further information

Usage

java -jar <JuFiT-JAR> <MODE> <PARAMETERS>

Additional hit, update your Java VM arguments with -Xmx512M

Need at least 2 arguments, got

  • 1: MRCONSO file
  • 2: MRSTY file
  • 3: language to process, 3 letter code (ENG, GER, SPA, FRE, DUT)
  • 4: optional json rule file used instead of the default configuration

Modes

  • mr - filter UMLS, output MRCONSO
  • ga - generate gazetteer file (idiosyncratic format), without any filtering
  • gf - generate gazetteer file (idiosyncratic format), applying filter

Example Usage

ga MRCONSO.RRF MRSTY.RRF GER

Parameters

Depend on mode, call a mode to see its parameters as a help message.