Create utils/preprocess_umls_data.py

utils/preprocess_umls_data.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+"""
+Preprocess raw UMLS RRF/TSV into a simple CSV for indexing.
+"""
+import argparse
+import pandas as pd
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument('--input', required=True)
+    p.add_argument('--output', required=True)
+    p.add_argument('--sep', default='\t')
+    args = p.parse_args()
+
+    df = pd.read_csv(args.input, sep=args.sep, dtype=str)
+    df = df.rename(columns={'CUI':'cui','STR':'name','DEF':'definition','SAB':'source'})
+    df = df.dropna(subset=['cui','name'])
+    df['definition'] = df['definition'].fillna('')
+    df['source'] = df['source'].fillna('')
+    df = df.drop_duplicates(subset=['cui','name'])
+    df.to_csv(args.output, index=False)
+    print(f'Wrote {len(df)} concepts to {args.output}')
+
+if __name__ == '__main__':
+    main()