Metamap Installation (Linux)

metamap_installation.md

MetaMap Installation Tutorial

MetaMap is a tool developed by the National Library of Medicine for analyzing biomedical texts. Follow these steps to install and set up MetaMap on a Linux system.

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Prerequisites

1. Java Installation:

   • Ensure Java is installed:

     which java
     java -version

     The expected output should confirm an OpenJDK version, such as:

     openjdk version "1.8.0_275"
     OpenJDK Runtime Environment (build 1.8.0_275-b01)
     OpenJDK 64-Bit Server VM (build 25.275-b01, mixed mode)
     

   • If Java is not installed, install OpenJDK:

     sudo apt update
     sudo apt install openjdk-8-jdk

2. Set the JAVA_HOME Environment Variable:

   • Find the Java path (if not already done):

     which java

   • Export the JAVA_HOME variable:

     export JAVA_HOME=/usr/bin/java

   • Verify:

     echo $JAVA_HOME

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Step 1: Download MetaMap Files

• Download the following files from the official MetaMap repository:
  1. public_mm_data_lite_usabase_2022aa.zip (data file)
  2. public_mm_linux_main_2020.tar.bz2 (main installation)
  3. public_mm_lite_3.6.2rc8_binaryonly.zip (optional MetaMap Lite)

Place the downloaded files in a directory of your choice, e.g., ~/metamap.

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Step 2: Extract Files

1. Extract Main Installation:

   bunzip2 -c public_mm_linux_main_2020.tar.bz2 | tar xvf -

2. Extract Data Files: If needed, unzip the data files:

   unzip public_mm_data_lite_usabase_2022aa.zip

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Step 3: Install MetaMap

• Navigate to the bin directory of the extracted MetaMap files:

  cd ./bin

• Run the installation script:

  ./install.sh

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Step 4: Start Required Servers

MetaMap requires the following servers to run in the background:

1. Start SKR/MedPost Part-of-Speech Tagger Server:

   ./bin/skrmedpostctl start

   Expected output:

   Starting skrmedpostctl:
   started.
   

2. (Optional) Start the Word Sense Disambiguation (WSD) Server: If you plan to use the WSD feature (-y flag):

   ./bin/wsdserverctl start

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Step 5: Verify the Installation

• Run the following command to check if MetaMap is working:

  ./bin/metamap -V

  You should see the version details of MetaMap.

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Step 6: Using MetaMap

MetaMap can now be used for text processing. For example:

./bin/metamap input.txt output.txt

• Replace input.txt with your input file.
• The results will be saved in output.txt.

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Stopping the Servers

To stop the servers when done:

1. Stop the SKR/MedPost Part-of-Speech Tagger Server:

   ./bin/skrmedpostctl stop

2. Stop the WSD Server (if started):

   ./bin/wsdserverctl stop

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Optional: Python Integration

For Python integration, you can follow this guide to interact with MetaMap through Python.

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