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xpmkg cui-umls

Annotates MeSH nodes in the knowledge graph with their corresponding UMLS Concept Unique Identifiers (CUIs), sourced from the UMLS Metathesaurus.

Overview

This subcommand reads the MRCONSO.RRF file from a local UMLS release, builds a mapping from every MeSH UI to the set of CUIs that reference it, and appends a new UMLSConceptsUI column to the following CSV files produced by pm2kg:

  • MeSHConcept.csv
  • MeSHDescriptor.csv
  • MeSHQualifier.csv
  • MeSHSupplemental.csv

Each node is matched by its MeSH UI. When multiple CUIs map to the same UI, they are stored as a semicolon-separated list, compatible with Neo4j's array property import format (string[]).

To ensure data integrity, each file is first written to a .tmp sibling, then atomically renamed to replace the original only on success. A partial failure therefore never corrupts existing data.

License requirement — access to UMLS data requires a UMLS Metathesaurus License from the NLM. The tool operates on a locally extracted UMLS release; it does not download data automatically.

Requirements

  • Output CSVs produced by pm2kg
  • A locally extracted UMLS release containing META/MRCONSO.RRF

Usage

xpmkg cui-umls --umls <PATH> --output <PATH>
Flag Short Description
--umls <PATH> -u Root directory of the extracted UMLS release (must contain META/MRCONSO.RRF)
--output <PATH> -o Directory containing the pm2kg output CSV files to be annotated

Example

xpmkg cui-umls \
  --umls /data/umls_2026 \
  --output /data/pm2kg-output/

Output

The four MeSH CSV files are updated in place. A new column is appended to each:

Column Neo4j type Description
UMLSConceptsUI:string[] string[] Semicolon-separated list of UMLS CUIs mapping to this MeSH UI

Nodes with no CUI mapping receive an empty string for that field.

Example — before / after

Before (MeSHDescriptor.csv, partial):

:ID(MeSH),name,...
D000001,Calcimycin,...

After:

:ID(MeSH),name,...,UMLSConceptsUI:string[]
D000001,Calcimycin,...,C0006611