Builds i2b2 tranSMART ontology from an dbGaP study
This python script queries dbGaP projects web pages base on a phs (study id) in order to retrieve contextual information for dbGaP phv (variables id).
Using these information it builds a set of i2b2 ontology paths for each phv. These informations are stored in a file (leafFilePath). These file is then used to create a new mappig file for the i2b2/tranSMART etl pipeline (based on a pre-existing one)
python 2 (should work with python 3)
git clone https://github.com/vianneyJouhet/dbGaP-i2b2Tm-TreeBuilder.gitCopy properties.json from template to the root of the project
- study_id ==> dgGap study id (phs that includes version and p)
- current_object_id ==> dbGap object id (number within the phs)
- retrievePaths ==> do you want yo retrieve path from dbGap (can be set to "N" in order to skip this part)
- buildMappingFile ==> do you want to build a mapping file (needs sourceMappingFile and targetMappingFile to be set)
- leafFilePath ==> Target file for tree building (will replace file if exists)
- sourceMappingFile ==> Pre-existing Mapping file as defiend in i2b2 TranSMART ETL)
- targetMappingFile ==> Mapping File that will be created
python main.py