UMLS Source Vocabularies (#25)

examples/conf/meddra_german.yaml

@@ -0,0 +1,8 @@
+name: meddra_german
+
+dict:
+  custom:    
+    umls_meta_path: ${oc.env:UMLS_HOME}/2023AA/META
+    sabs:
+        - MDR
+        - MDRGER

examples/dicts/umls_source.py

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+from tqdm.auto import tqdm
+from xmen.umls import read_umls_file_headers
+
+
+def get_concept_details(cfg):
+    mrconso = "MRCONSO.RRF"
+    concept_details = {}
+    meta_path = cfg.dict.custom.umls_meta_path
+    sabs = cfg.dict.custom.sabs
+
+    headers = read_umls_file_headers(meta_path, mrconso)
+
+    with open(f"{meta_path}/{mrconso}") as fin:
+        for line in tqdm(fin.readlines()):
+            splits = line.strip().split("|")
+            assert len(headers) == len(splits)
+            concept = dict(zip(headers, splits))
+            if concept["SAB"] in sabs:
+                sid = concept["SDUI"]
+                name = concept["STR"]
+                if sid in concept_details:
+                    concept_details[sid]["aliases"].append(name)
+                else:
+                    concept_details[sid] = {"concept_id": sid, "canonical_name": name, "types": [], "aliases": []}
+    return concept_details