Create UMLS parser for Entrez genes

Convert Entrez gene ids into UMLS CUIs using the mapping provided
by HGNC.

src/dataload/sources/umls/umls_parser.py

@@ -0,0 +1,61 @@
+# Determine UMLS CUI to Entrez Gene id mappings for genes
+# 1. Parse UMLS to determine HGNC ids for each CUI
+# 2. Use HGNC to convert HGNC ids to Entrez Gene ids
+
+from collections import defaultdict
+
+import pandas as pd
+
+def parse_hgnc():
+    """Determine HGNC to Entrez gene id mapping.
+
+    Drops all genes without Entrez Gene ids.
+    """
+
+    file_url = "ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt"
+
+    # drops any HGNC genes with missing Entrez ids
+    return (pd
+        .read_csv(file_url, sep='\t', low_memory=False)
+        [["hgnc_id", "symbol", "status", "entrez_id"]]
+        .dropna(axis=0, how="any", subset=["entrez_id"])
+        .assign(entrez_id = lambda df: df["entrez_id"].astype(int))
+    )
+
+def parse_umls():
+    """Parse the UMLS to determine the HGNC identifier of each gene CUI.
+
+    The relevant files are in the archive <version>-1-meta.nlm (a zip file)
+    within <version>/META/MRCONSO.RRF.*.gz
+
+    Concatenate the unzipped versions of the MRCONSO files together to get the
+    final MRCONSO.RRF file, which is a | delimited text file without a header.
+    """
+
+    res = defaultdict(list)
+    with open("MRCONSO.RRF", "r") as fin:
+        for line in fin:
+            if "HGNC:" in line:
+                vals = line.rstrip("\n").split("|")
+
+                cui = vals[0]
+                for val in vals[1:]:
+                    if val.startswith("HGNC:"):
+                        res["cui"].append(cui)
+                        res["hgnc_id"].append(val)
+
+    return pd.DataFrame(res).drop_duplicates()
+
+def load_data():
+    hgnc_map = parse_hgnc()
+    cui_map = parse_umls()
+
+    res = hgnc_map.merge(cui_map, how="inner", on="hgnc_id")
+
+    for idx, row in res.iterrows():
+        yield {
+            "_id": row["entrez_id"],
+            "umls": {
+                "cui": row["cui"]
+            }
+        }