Extract required info from the DrugBank XML file

drugbank.py

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+# To run:
+# PYTHONIOENCODING=UTF-8 python3 drugbank.py
+
+import xml.etree.ElementTree as ET
+
+xml_file = "raw_data/drugbank/full_database.xml"
+tag_prefix = "{http://www.drugbank.ca}"
+
+def find_tag(obj, tag):
+  return obj.find(tag_prefix + tag)
+
+def findall_tag(obj, tag):
+  return obj.findall(tag_prefix + tag)
+
+def get_child_tag_text(obj, tag):
+  return find_tag(obj, tag).text
+
+for drug in ET.parse(xml_file).getroot():
+  drugbank_id = get_child_tag_text(drug, "drugbank-id")
+  name = get_child_tag_text(drug, "name")
+  description = get_child_tag_text(drug, "description")
+  for group in findall_tag(find_tag(drug, "groups"), "group"):
+    drug_group = group.text
+  for article in findall_tag(find_tag(find_tag(drug, "general-references"), "articles"), "article"):
+    pubmed_id = get_child_tag_text(article, "pubmed-id")
+  for other_drug in findall_tag(find_tag(drug, "drug-interactions"), "drug-interaction"):
+    # TODO: Need to get ChEBI ID for other_drug
+    other_drug = get_child_tag_text(other_drug, "drugbank-id")
+  for pathway in findall_tag(find_tag(drug, "pathways"), "pathway"):
+    smpdb_id = get_child_tag_text(pathway, "smpdb-id")
+    for involved_drug in findall_tag(find_tag(pathway, "drugs"), "drug"):
+      # TODO: Need to get ChEBI ID for involved_drug
+      involved_drug = get_child_tag_text(involved_drug, "drugbank-id")
+    for uniprot_id in findall_tag(find_tag(pathway, "enzymes"), "uniprot-id"):
+      uniprot_id = uniprot_id.text