disorder-normalizer

A sieve-based system for normalizing disorder mentions in biomedical data.

The disorder-normalizer tool has been written in Java and is released as free software.

You can find more explanation about our normalization system here.

Usage:

1. If using the source code available in "src" folder. First, copy the "resources" folder into the "src" folder, then run the program as below.

   java tool.Main <terminology/ontology-file> max-sieve-level

   Sieve levels:
   1 for exact match
   2 for abbreviation expansion
   3 for subject<->object conversion
   4 for numbers replacement
   5 for hyphenation
   6 for affixation
   7 for disorder synonyms replacement
   8 for stemming
   9 for composite disorder mentions
   10 for partial match

An example execution using the "training", "test", and ontology "TERMINOLOGY.txt" files provided in the "ncbi-data" folder is shown below.

C:\disorder-normalizer\src>java tool.Main ..\ncbi-data\training\ ..\ncbi-data\test\ ..\ncbi-data\TERMINOLOGY.txt 10

2. If using the executable jar file "disorder-normalizer.jar". First, copy the "resources" folder into the same folder as the jar file, then run the program as show in example below.

   C:\disorder-normalizer>java -jar disorder-normalizer.jar ..\ncbi-data\training\ ..\ncbi-data\test\ ..\ncbi-data\TERMINOLOGY.txt 10

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On executing the program, a new folder called "output" will be automatically created in the same folder as the <test-data-dir> to which the result from normalizing the test mentions will be written. In addition, the system performance on normalizing the test disorder mentions will be printed to the terminal.

Please Note:
* In order to run the tool on new data, please ensure that your training, test, and terminology files are in the same format as the data provided in the "ncbi-data" folder.
* The training data files are used to train the normalizer. However, since disorder-normalizer is not a learning-based system, this folder can be empty.
* The tool will attempt to normalize the mentions in the test data folder files to the terminology.
* The TERMINOLOGY file is the ontology/knowledge-base used to which the test data mentions are normalized.

Detailed explanation about our normalization system can be found on webpage here.