This section assumes using UNIX-based system for setting-up and configuring the Bio-Yodie. These steps should be also possible to accomplish on a Windows OS with UNIX environments installed such as Cygwin, MinGW or Windows Subsystem for Linux.
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.
Bio-Yodie has been primarily tested using Unified Medical Language System (UMLS), a medical concepts resources database. However, distribution, usage and access to UMLS requires obtaining a special license to use, followed by 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).
Please note that two different versions of GATE are being used – one to prepare UMLS resources and one to run Bio-Yodie.
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, an additional GATE installation needs to be present in the system.
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, the one meant to be used.
Bio-Yodie can be downloaded from the official GitHub repository: https://github.com/GateNLP/Bio-YODIE
The configuration guide and scripts are provided on the GitHub. The configuration of Bio-Yodie should boil down to running in the main Bio-Yodie directory:
The script will take care of downloading all the prerequisites for Bio-Yodie, including external plugins and compiling them. After that, one can proceed to UMLS resources preparation.
The generated UMLS resources for Bio-Yodie should be placed in directory
bio-yodie-resources (or sym-linked as) inside the main Bio-Yodie directory.