From 9e034ad679961381154afb2dec23b990ab4c30d7 Mon Sep 17 00:00:00 2001 From: Christina Lohr Date: Fri, 28 Feb 2020 15:39:55 +0100 Subject: [PATCH] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index ca4ee32..adf0b34 100644 --- a/README.md +++ b/README.md @@ -5,11 +5,12 @@ ## UMLS * Register at NIV and download the UMLS from https://www.nlm.nih.gov/research/umls/index.html -* 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`). +* 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-2019AB-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 these files for the input of JuFiT. * More information on the UMLS can be found in the [UMLS® Reference Manual](https://www.ncbi.nlm.nih.gov/books/NBK9676/). -# JuFit +# JuFiT: filtered dictionaries from UMLS * Download JuFit from https://github.com/JULIELab/jufit and create the jar file by maven +* run `java -jar JenaUmlsFilter-1.1-jar-with-dependencies.jar MRCONSO.RRF MRSTY.RRF GER --grounded > UMLS_dict.txt`