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MEDDOCAN: Format Converter Script

Digital Object Identifier (DOI)

Introduction

This script is distributed as apart of the Medical Document Anonymization (MEDDOCAN) task. It is intended to be used via command line:

$> python converter.py -i input_folder/ -o output_folder/

It converts files between MEDDOCAN-Brat, MEDDOCAN-XML, and i2b2 formats. The mapping between the different formats is defined in the files in the mappings/ folders. See below for further information.

Input and target directories, as well as source and target formats can be chosen via command line.

Prerequisites

This software requires to have Python 3 installed on your system.

Directory structure

input/
This directory contains sample input  files with annotations in `MEDDOCAN-Brat`, 
`MEDDOCAN-XML`, and `i2b2` annotation formats.

mapping/
This folder contains the files defining the mapping between the different formats.
Files ending with `map_categories.csv` define the mapping of the categories defined 
in the i2b2 2014 Personal Health-care Information (PHI) task, and files ending with 
`map_types.csv` define the mapping of the sub-categories defined in the same task.
This files are loaded into dictionaries to map the categories/sub-categories. If you
wish to change the mapping, do not change the script, just change the mapping in these
files.

output/
This directory contains sample output files with annotations in `MEDDOCAN-Brat`, 
`MEDDOCAN-XML`, and `i2b2` annotation formats.

Usage

It is possible to configure the behavior of this software using the different options.

  • The -i/--input_dir and -o/--output_dir options allow to select the input and output directories.

  • The -s/--source option allows to select the source format of the input files.

  • The -t/--target option allows to select the target format of the output files.

  • verbose and quiet options allow to control the verbosity level.

The user can select the different options using the command line:

usage: converter.py [-h] [-i INPUT_DIR] [-o OUTPUT_DIR] [-s {brat,xml,i2b2}]
                    [-t {brat,xml,i2b2}] [-v | -q]

Script to convert between MEDDOCAN-BRAT/MEDDOCAN-XML/i2b2 formats.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_DIR, --input_dir INPUT_DIR
                        Folder with the original input files
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                        Folder to store the output converted files
  -s {brat,xml,i2b2}, --source {brat,xml,i2b2}
                        Format of source files
  -t {brat,xml,i2b2}, --target {brat,xml,i2b2}
                        Format of target files
  -v, --verbose         Increase output verbosity
  -q, --quiet           Do not print anything

Examples

Basic Examples:

Convert all files in input/brat/sample/ from MEDDOCAN-Brat format (default source format) into MEDDOCAN-XML (default target format) and store output files in output/xml/sample/:

$> python converter.py -i input/brat/sample/ -o output/xml/sample/

Convert all files in input/xml/sample/ from MEDDOCAN-XML format into i2b2 formatand store output files in output/i2b2/sample/:

$> python converter.py -i input/xml/sample/ -o output/i2b2/sample/ -s xml -t i2b2

Contact

Aitor Gonzalez-Agirre ([email protected])

License

Copyright (c) 2019 Secretaría de Estado para el Avance Digital (SEAD)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.