Overview

In this section are described useful third-party applications that

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have been used or that can be integrated with CogStack platform

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Overview

Bio-Yodie is a GATE application (stored as xgapp application) that can be used to extract medical concepts from the free-text documents. It is also a core component of SemEHR.

Downloading

Bio-Yodie can be downloaded from the official GitHub repository: https://github.com/GateNLP/Bio-YODIE

Prerequisites

JAVA Runtime Environment

As a primary prerequisite Java JRE is required in version >= 8.0.

Either the official Java JRE from Oracle or OpenJDK can be used.

UMLS

Bio-Yodie has been primarily tested using Unified Medical Language System (UMLS), a medical concepts resources database. However, the distribution, usage and access to UMLS requires special license and acceptance of terms and conditions. Hence, Bio-Yodie resources need to be compiled manually using provided scripts after obtaining UMLS (see below).

UMLS dataset can be downloaded from the official website: https://www.nlm.nih.gov/research/umls/

The dataset is downloaded as compressed file umls-*-full.zip which should occupy > 4 GB (compressed) and 9.1 GB (uncompressed).

GATE Developer

Bio-Yodie requires GATE Developer to be installed on the system to run. The required GATE version is >= 8.5.

However, when generating UMLS resources locally for BIo-Yodie (see below), the provided scripts are compatible with GATE in version prior to 8.5. Therefore, additional GATE installation need to be present in the system for that.

This implies that, when running the resources generation scripts, the environment variable $GATE_HOME needs to point to the older GATE installation directory.

After that, when running Bio-Yodie, $GATE_HOME should point to the newer installation of GATE.

Bio-Yodie

Bio-Yodie can be downloaded from the official GitHub repository: https://github.com/GateNLP/Bio-YODIE

The Bio-Yodie configuration guide is provided on the GitHub.

The configuration of Bio-Yodie should boil down to running in the main Bio-Yodie directorty:

bash update.sh

After downloading all the prerequisites for Bio-Yodie, including external plugins and compiling them, one should proceed to UMLS resources preparation.

Preparing the Bio-Yodie resources

UMLS MetamorphoSys tool

After downloading and extracting UMLS dataset it needs to be pre-processed for Bio-Yodie by running MetamorphoSys tool. MetamorphoSys is the UMLS installation wizard and Metathesaurus customization tool included in each UMLS release. MetamorphoSys is included in mmsys.zip file inside the decompressed UMLS package.

In the next step, one should decompress mmsys.zip file so that mmsys application will reside in the same directory as all the decompressed UMLS files.

To run mmsys one should run appropriate run_* script. The wizard MetamorphoSys wizard will appear in which will allow for customising the UMLS resources to be exported. After following the wizard and selecting the appropriate configuration, the exported UMLS resources will be available in the specified output directory. The resources from the output directory will be later used to generate the resources for Bio-Yodie.

More information with a detailed description of MetamorphoSys tool can be found on the official website: https://www.nlm.nih.gov/research/umls/implementation_resources/metamorphosys/help.html

Preparing UMLS resources for BIo-Yodie

The scripts to generate Bio-Yodie resources are provided in separate GitHub repository: https://github.com/GateNLP/bio-yodie-resource-prep

The official GitHub page covers the topic of setting up the environment, downloading the dependencies, linking the UMLS input and output resources, etc.

After downloading the required dependences and linking the input UMLS resources, one should be able to generate the resources for Bio-Yodie by running in the main directory:

bash bin/all.sh

Running Bio-Yodie

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Integrating with CogStack

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