mdm2neo4j

mdm2neo4j imports ODM-XML-files into a Neo4j graph database.

Quickstart

Create a configuration file, storing your details for the database-connection. E.g. in your home-directory with the name mdm.conf.

[neo4j]
uri = bolt://localhost:7687
username = neo4j
password = myfancypassword

Start the program by providing the location of your configuration-file and the location of the XML-files.

python3 src/run.py --conf ~/mdm.conf --files ~/Desktop/datasource

Requirements

make sure, python3 is installed
install the required libraries with pip install -r requirements.txt
download all ODM-XML-files from the MDM portal and place all XML-files you want to load in one folder
have a running Neo4j DB (Neo4j version 5)
create the configuration-file as described in the Quickstart section

General Structure of Repo

The two main scripts that do things are database_connector.py and xml_processor.py. run.py is the "main" script where everything comes together and that is responsible for running everything.

Detailled Infos

The mapping of the odm-xml files to Neo4j is based on specification for ODM version 1.3.2. The specification document is available on the CDISC website http://www.cdisc.org/odm.

The mapping includes 18 of 39 elements of the "Study" section (section 3.1.1) of the "General Elements" (section 3) of the ODM specification. The Neo4j graph has eleven labels:

Study
StudyEvent
Form
ItemGroup
Item
RangeCheck
CodeList
CodeListItem
BasicDefinitions
MeasurementUnit
Alias

Tech Docu

Find the technical documentation in the docs-folder.

Licence

This program is released under Version 3 of the GPL or any later version.

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