Import DrugBank-DrugCentral mappings

scripts/import_drugcentral_mappings.py

@@ -0,0 +1,77 @@
+"""This script imports Harry Caufield's mappings from DrugCentral to various resources."""
+
+import bioregistry
+import click
+import pandas as pd
+import pyobo
+from tqdm import tqdm
+
+from biomappings.resources import append_true_mappings
+
+URL = "http://kg-hub-public-data.s3.amazonaws.com/frozen_incoming_data/drug-id-maps-0.2.sssom.tsv"
+
+
+@click.command()
+def main():
+    """Import DrugCentral mappings from Harry Caufield into Biomappings."""
+    df = pd.read_csv(URL, sep="\t", skiprows=11)
+    del df["author_id"]
+    del df["comment"]
+    del df["mapping_justification"]
+    df = df.rename(
+        columns={
+            "predicate_id": "relation",
+            "subject_label": "source name",
+            "object_label": "target name",
+            "reviewer_id": "source",
+        }
+    )
+    df["type"] = "manually_reviewed"
+
+    drugcentral_drugbank_mappings = pyobo.get_filtered_xrefs("drugcentral", "drugbank")
+
+    mappings = df.iterrows()
+    mappings = [
+        row
+        for _, row in tqdm(
+            mappings, unit="mapping", unit_scale=True, total=len(df.index), desc="Pre-Filtering"
+        )
+        if (
+            row["subject_id"].startswith("DRUGBANK:")
+            and row["object_id"].startswith("DrugCentral:")
+            and row["object_id"].removeprefix("DrugCentral:") not in drugcentral_drugbank_mappings
+        )
+    ]
+    mappings = (
+        _prepare_mapping(row)
+        for row in tqdm(mappings, unit="mapping", unit_scale=True, desc="Mapping")
+    )
+    # Filter mappings with missing values
+    mappings = (mapping for mapping in mappings if mapping)
+    append_true_mappings(mappings)
+
+
+def _prepare_mapping(row):
+    row = row.to_dict()
+    subject_prefix, subject_id = bioregistry.parse_curie(row.pop("subject_id"))
+    target_prefix, target_id = bioregistry.parse_curie(row.pop("object_id"))
+    row["source prefix"] = subject_prefix
+    row["source identifier"] = (
+        bioregistry.miriam_standardize_identifier(subject_prefix, subject_id) or subject_id
+    )
+    row["target prefix"] = target_prefix
+    row["target identifier"] = (
+        bioregistry.miriam_standardize_identifier(target_prefix, target_id) or subject_id
+    )
+    if pd.isna(row["source name"]):
+        row["source name"] = pyobo.get_name(subject_prefix, subject_id)
+    if pd.isna(row["target name"]):
+        row["target name"] = pyobo.get_name(target_prefix, target_id)
+    if not all(value and pd.notna(value) for value in row.values()):
+        tqdm.write(str(row))
+        return None
+    return row
+
+
+if __name__ == "__main__":
+    main()

src/biomappings/resources/curators.tsv

@@ -5,3 +5,4 @@ hoytfamily	0000-0003-1307-2508	Amelia Hoyt
 ddomingof	0000-0002-2046-6145	Daniel Domingo-Fernandez
 cmungall	0000-0002-6601-2165	Christopher Mungall
 KrishnaTO	0000-0002-2627-0696	Krishna Udaiwal
+caufieldjh	0000-0001-5705-7831	Harry Caufield