BRAinS-Graph/src/postprocessing/README.md

postprocessing

postprocess.py executes Cypher queries to create mappings between MeSH, UMLS, MDM, and ClinicalTrials.gov data in a Neo4j graph database.

The main script postprocess.py runs a set of predefined Cypher queries for:

• mapping MeSH terms to UMLS concepts
• mapping MDM Portal aliases to UMLS concepts
• mapping ClinicalTrials.gov studies to MeSH terms
• mapping ClinicalTrials.gov studies to MDM Portal entries

Quickstart

Create a configuration file with your Neo4j connection details.
For example, save it as postprocess.conf:

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

Run the postprocessing by providing the configuration file:

python3 src/postprocess.py --conf ~/postprocess.conf

Requirements

• make sure python3 is installed
• have a running Neo4j instance (version 5)
• the Neo4j instance must have the APOC plugin installed
• create the configuration file as described in the Quickstart section