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
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.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.
- [UMLS® Reference Manual (https://www.ncbi.nlm.nih.gov/books/NBK9676/)]
- publication [JuFiT: A Configurable Rule Engine for Filtering and Generating New Multilingual UMLS Terms (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765630/)]
java -jar <JuFiT-JAR> <MODE> <PARAMETERS>
Additional hit, update your Java VM arguments with
Need at least 2 arguments, got
- 1: MRCONSO file
- 2: MRSTY file
- 3: language to process, 3 letter code (
- 4: optional json rule file used instead of the default configuration
mr- filter UMLS, output MRCONSO
ga- generate gazetteer file (idiosyncratic format), without any filtering
gf- generate gazetteer file (idiosyncratic format), applying filter
ga MRCONSO.RRF MRSTY.RRF GER
Depend on mode, call a mode to see its parameters as a help message.