ontology2transmart 0.1.0

Example ontology to TranSMART loader

This package contains a mapper that reads ontologies from DIMDI (Deutsche Institut für Medizinische Dokumentation und Information) and translates them to the data model of the TranSMART platform, an open source data sharing and analytics platform for translational biomedical research.

It also provides a utility that applies the mapper and writes the translated data to tab-separated files that can be loaded into a TranSMART database using the transmart-copy tool.

⚠️ Note: this is a very preliminary version, still under development. Issues can be reported at https://github.com/thehyve/python_ontology2transmart/issues.

Installation

The package requires Python 3.6.

To install ontology2transmart, do:

pip install ontology2transmart

Or from source:

git clone https://github.com/thehyve/python_ontology2transmart.git
cd python_ontology2transmart
pip install .

Run tests (including coverage) with:

python setup.py test

Usage

Read ontology from a collection of TSV files from DIMDI and write the output in transmart-copy format to /path/to/output. The output directory should be empty of not existing (then it will be created).

ontology2transmart <system> <chapters> <groups> <codes> /path/to/output

Parameters:

system:

Unique identifier for the ontology

chapters:

Semicolon-separated file with chapters

groups:

Semicolon-separated file with groups

codes:

Semicolon-separated file with codes

/path/to/output:

Output directory

Example: the ICD-10-GM (German modification of ICD-10) is available at icd10gm2019syst-meta.zip.

# Unzip and navigate to the classification directory
mkdir icd10gm2019
cd icd10gm2019
unzip ../icd10gm2019syst-meta.zip
cd Klassifikationsdateien
# create an output directory
mkdir output
# apply the mapping
ontology2transmart http://dimdi.de/icd10gm2019 icd10gm2019syst_kapitel.txt icd10gm2019syst_gruppen.txt icd10gm2019syst_kodes.txt output

This generates the directories i2b2metadata and i2b2demodata in the output directory. The generated data can be loaded using transmart-copy:

# Download transmart-copy:
curl -f -L https://repo.thehyve.nl/service/local/repositories/releases/content/org/transmartproject/transmart-copy/17.1-HYVE-5.9-RC3/transmart-copy-17.1-HYVE-5.9-RC3.jar -o transmart-copy.jar
# Load data
PGUSER=tm_cz PGPASSWORD=tm_cz java -jar transmart-copy.jar -d output

License

Copyright (c) 2019, The Hyve

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.