From ea258a9478eeef43fe31b75eb33c5c92744e5ce6 Mon Sep 17 00:00:00 2001 From: ktwaco Date: Thu, 12 Nov 2015 15:08:59 -0500 Subject: [PATCH] updated readme to include instructors how to get umls tables --- README.rst | 20 +++++++++++++++++--- 1 file changed, 17 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index 10af2c2..736e78d 100644 --- a/README.rst +++ b/README.rst @@ -211,7 +211,7 @@ Please email wboag@cs.uml.edu with your installation questions. http://www.nlm.nih.gov/databases/umls.html - You will need to get following tables: **MRREL, MRCON, MRSTY** + You will need to get following tables: **MRREL.RRF, MRCONSO.RRF, MRSTY.RRF** **Put these tables in the $CLINER_DIR/umls_tables directory.** @@ -219,6 +219,20 @@ Please email wboag@cs.uml.edu with your installation questions. **The database will be built from the tables when CliNER is run for the first time.** + How to obtain UMLS tables: + + 1. download all the files from https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html + 2. unzip mmsys.zip into a folder + 3. put all other files downloaded into that folder + 4. execute run_linux.sh + 5. select install UMLS on gui + 6. choose destination for umls directory + 7. hit ok + 8. hit new config + 9. accept agreement + 10. select only active UMLS sources as your default subset + 11. select at top of gui pane, done and then select begin subset. + 12. the destination folder should contain the necessary files needed. (7) Create 'cliner' executable script for command-line use @@ -245,10 +259,10 @@ Deploying with Vagrant With Vagrant and a type-2 hypervisor (such as the free VirtualBox) installed on the system, running "vagrant up" will deploy a virtual machine and painlessly -install/build CliNER. +install/build CliNER. The access ip is listed during deployment (usually 127.0.0.1:2222). -The username/password is vagrant/vagrant. +The username/password is vagrant/vagrant. Usage Examples --------