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
python3is 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