This is an adaptation of SETH

• Forked at: https://github.com/rockt/SETH

• Documentation: See http://rockt.github.com/SETH/

  Contributors

  • Philippe Thomas
  • Tim Rocktäschel
  • Yvonne Mayer
  • Johannes Kirschnick
  • Eugene Brevdo

Installation (Linux)

Install scala version 2.11.7 and add its location to $PATH

You could either download scala binaries from https://www.scala-lang.org/download/2.11.7.html

tar -zxf scala-2.11.7.tgz

export PATH=$PATH:~/blabla/scala-2.11.7/bin

Or install scala easily with

sudo apt install scala

Install Java development Kit (JDK v8)

You also need to install JDK (version 8) using

sudo apt install openjdk-8-jdk

You could check your installation with java -version.

Usage

To start, clone this repository

git clone https://github.com/helmersl/SETH.git
cd SETH

Extract NER muation using the following CLI, note that you need to specify your input data (with PubTator format) into txt file

java -cp seth.jar seth.ner.wrapper.SETHNERAppMut test_input.txt    

The results will be wriiten into muts_extr_seth.txt file.