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Scripts to prepare the informational resources required by GATE Bio-YODIE.
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Scripts to prepare the informational resources required by GATE Bio-YODIE.

Running the Bio-YODIE preparation

The Bio-YODIE preparation does all the preparation that can be done in advance in order to minimize the calculation being done at runtime. This includes creating the gazetteer, creating a minimal database containing everything that needs to go onto disambiguation candidates, and assigning information to these candidates. It also includes creating scoring resources that will be used at runtime.


  • JAVA 8

    • for ubuntu user
      • sudo add-apt-repository ppa:webupd8team/java
      • sudo apt-get update
      • sudo apt-get install oracle-java8-installer
  • Gate8.4 or below - Gate can be downloaded from

  • Groovy

Environment setting


Download scala 2.11.7 to scala folder and compile scripts

You will need the following directory symbolic links:

  • mkdir databases
  • mkdir output
  • mkdir tmpdata

databases -> should point to the directory where you will store your new UMLS H2 database.

output -> this is the directory that will be populated with the new Bio-YODIE resources, that then needs to be copied into yodie-pipeline in order for it to work. (Note that yodie-pipeline/bin/ is a script that gets it from a hardcoded location on GS8.)

tmpdata -> this is a temporary space for intermediate files, and just needs to be somewhere you have space.

You will need a downloaded UMLS from After install umls, you should have a folder called 2017AB (folder name depends on release year and version) in your umls installation directory

Link (or move) the umls to srcs folder

  • cd srcs
  • mkdir umls
  • ln -s /umls/install/path/2017AB umls/2015AB
  • cd ..

srcs -> should point to where you have your UMLS download. You will receive a srcs directory in the prep distribution. You may put your UMLS in here, or move the contents to the directory containing UMLS, alongside it, and make a symbolic link. It expects a directory called "umls" containing "2015AB" (this is hardcoded in bin/

You can then run bin/

  • bin/

If you want to run the prep for a language other than English, you can set the environment variable LANGS to the appropriate two letter code, for example "fr". It will default to English. If you want to do multiple languages, separate them with a space. Be sure to put inverted commas around the string, for example export LANGS="en fr".

A benchmarking file is automatically produced in the parent directory. To stop this, comment out the relevant lines in bin/

In the "scala" directory, the symbolic link "scala-latest-version" should point to a scala installation.

Change output semantic types

You can subselect the semantic by editing config/, Change line STYCLASSES='KCX' to the list you wish to output The style list can be found at: config/styclasses.lst You can also create a new semantic types in the file

Copy output to Bio-YODIE

Once you finish the data preparation, you can copy the output to main Bio-YODIE (

First, you need to create an empty folder under Bio-YODIE root directory called "bio-yodie-resources"

  • mkdir bio-yodie-resources

Then, copy all data in output to the "bio-yodie-resources"

  • cp path/to/output/* path/to/bio-yodie/bio-yodie-resources/
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