From 6f9586ed297ff6c80825cf0024df6b971d937084 Mon Sep 17 00:00:00 2001
From: EddieLF <eddieformaini@gmail.com>
Date: Mon, 15 Jun 2026 13:12:05 +1000
Subject: [PATCH 1/6] Update HPO term parsing for new OBO release format

---
 .../management/commands/update_human_phenotype_ontology.py    | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/reference_data/management/commands/update_human_phenotype_ontology.py b/reference_data/management/commands/update_human_phenotype_ontology.py
index 76f50893bc..5e9c3537ed 100644
--- a/reference_data/management/commands/update_human_phenotype_ontology.py
+++ b/reference_data/management/commands/update_human_phenotype_ontology.py
@@ -1,5 +1,6 @@
 import logging
 import os
+import re
 from tqdm import tqdm
 
 from django.db import transaction
@@ -79,7 +80,8 @@ def parse_obo_file(file_iterator):
                 'is_category': False,
             }
         elif line.startswith("is_a: "):
-            is_a = value.split(" ! ")[0]
+            # OBO format: "<id>" optionally followed by " ! <label>" and/or trailing " {<modifiers>}"
+            is_a = re.sub(r'\s*\{[^}]*\}\s*$', '', value).split(' ! ')[0].strip()
             if is_a == "HP:0000118":
                 hpo_id_to_record[hpo_id]['is_category'] = True
             hpo_id_to_record[hpo_id]['parent_id'] = is_a

From b2f8f08672b0d44bdfb0860347ec4a4721c428c1 Mon Sep 17 00:00:00 2001
From: EddieLF <eddieformaini@gmail.com>
Date: Mon, 15 Jun 2026 13:43:54 +1000
Subject: [PATCH 2/6] Update HPO term parsing test with new OBO formatting

---
 reference_data/management/tests/update_hpo_tests.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/reference_data/management/tests/update_hpo_tests.py b/reference_data/management/tests/update_hpo_tests.py
index e3cf107312..c836299070 100644
--- a/reference_data/management/tests/update_hpo_tests.py
+++ b/reference_data/management/tests/update_hpo_tests.py
@@ -81,6 +81,16 @@
     'synonym: "Head and neck abnormality" EXACT layperson []\n',
     'xref: UMLS:C4021817\n',
     'is_a: HP:0000118 ! Phenotypic abnormality\n',
+    '[Term]\n', # is_a with xref and no label
+    'id: HP:9999001\n',
+    'name: trailer with xref only\n',
+    'is_a: HP:0000118 {xref="PMID:31677808"}\n',
+    '\n',
+    '[Term]\n', # is_a with label and xref
+    'id: HP:9999002\n',
+    'name: trailer with label and xref\n',
+    'is_a: HP:0000118 ! Phenotypic abnormality {xref="PMID:31677808"}\n',
+    '\n',
 ]
 
 EXPECTED_DB_DATA = {

From 7908feeafcdc70860ef87fa45ac0dbe0137792ed Mon Sep 17 00:00:00 2001
From: EddieLF <eddieformaini@gmail.com>
Date: Mon, 15 Jun 2026 13:46:07 +1000
Subject: [PATCH 3/6] Update HPO term parsing test with new OBO formatting
 again

---
 .../management/tests/update_hpo_tests.py      | 20 +++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/reference_data/management/tests/update_hpo_tests.py b/reference_data/management/tests/update_hpo_tests.py
index c836299070..5379ee8559 100644
--- a/reference_data/management/tests/update_hpo_tests.py
+++ b/reference_data/management/tests/update_hpo_tests.py
@@ -81,6 +81,7 @@
     'synonym: "Head and neck abnormality" EXACT layperson []\n',
     'xref: UMLS:C4021817\n',
     'is_a: HP:0000118 ! Phenotypic abnormality\n',
+    '\n',
     '[Term]\n', # is_a with xref and no label
     'id: HP:9999001\n',
     'name: trailer with xref only\n',
@@ -90,7 +91,6 @@
     'id: HP:9999002\n',
     'name: trailer with label and xref\n',
     'is_a: HP:0000118 ! Phenotypic abnormality {xref="PMID:31677808"}\n',
-    '\n',
 ]
 
 EXPECTED_DB_DATA = {
@@ -133,7 +133,23 @@
         'parent_id': 'HP:0000001',
         'hpo_id': 'HP:0000003',
         'category_id': None
-    }
+    },
+    'HP:9999001': {
+        'is_category': False,
+        'definition': None,
+        'name': 'trailer with xref only',
+        'parent_id': 'HP:0000118',
+        'hpo_id': 'HP:9999001',
+        'category_id': None,
+    },
+    'HP:9999002': {
+        'is_category': False,
+        'definition': None,
+        'name': 'trailer with label and xref',
+        'parent_id': 'HP:0000118',
+        'hpo_id': 'HP:9999002',
+        'category_id': None,
+    },
 }
 
 class UpdateHpoTest(TestCase):

From 6e6c501769f0e207a246c97a69d4d007f3dc64d2 Mon Sep 17 00:00:00 2001
From: EddieLF <eddieformaini@gmail.com>
Date: Mon, 15 Jun 2026 14:05:22 +1000
Subject: [PATCH 4/6] Fix HPO test

---
 reference_data/management/tests/update_hpo_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reference_data/management/tests/update_hpo_tests.py b/reference_data/management/tests/update_hpo_tests.py
index 5379ee8559..5833af25ab 100644
--- a/reference_data/management/tests/update_hpo_tests.py
+++ b/reference_data/management/tests/update_hpo_tests.py
@@ -178,7 +178,7 @@ def test_update_hpo_command(self, mock_tempfile, mock_logger):
         call_command('update_human_phenotype_ontology')
 
         calls = [
-            mock.call('Deleting HumanPhenotypeOntology table with 12 records and creating new table with 5 records'),
+            mock.call('Deleting HumanPhenotypeOntology table with 12 records and creating new table with 7 records'),
             mock.call('Done'),
         ]
         mock_logger.info.assert_has_calls(calls)

From 24206ae414e4b9bb2e63e070435056439e38d1d3 Mon Sep 17 00:00:00 2001
From: EddieLF <eddieformaini@gmail.com>
Date: Mon, 15 Jun 2026 14:27:23 +1000
Subject: [PATCH 5/6] Fix HPO test 2

---
 reference_data/management/tests/update_hpo_tests.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reference_data/management/tests/update_hpo_tests.py b/reference_data/management/tests/update_hpo_tests.py
index 5833af25ab..8340ff1e7a 100644
--- a/reference_data/management/tests/update_hpo_tests.py
+++ b/reference_data/management/tests/update_hpo_tests.py
@@ -189,7 +189,7 @@ def test_update_hpo_command(self, mock_tempfile, mock_logger):
         call_command('update_human_phenotype_ontology', tmp_file)
 
         calls = [
-            mock.call('Deleting HumanPhenotypeOntology table with 5 records and creating new table with 5 records'),
+            mock.call('Deleting HumanPhenotypeOntology table with 7 records and creating new table with 7 records'),
             mock.call('Done'),
         ]
         mock_logger.info.assert_has_calls(calls)

From eb0c57c1b2d2db2670f46d639d26e83eb003f9f1 Mon Sep 17 00:00:00 2001
From: EddieLF <eddieformaini@gmail.com>
Date: Mon, 15 Jun 2026 14:59:05 +1000
Subject: [PATCH 6/6] Fix HPO test 3

---
 reference_data/management/tests/update_hpo_tests.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/reference_data/management/tests/update_hpo_tests.py b/reference_data/management/tests/update_hpo_tests.py
index 8340ff1e7a..5cf8b55bb7 100644
--- a/reference_data/management/tests/update_hpo_tests.py
+++ b/reference_data/management/tests/update_hpo_tests.py
@@ -135,20 +135,20 @@
         'category_id': None
     },
     'HP:9999001': {
-        'is_category': False,
+        'is_category': True,
         'definition': None,
         'name': 'trailer with xref only',
         'parent_id': 'HP:0000118',
         'hpo_id': 'HP:9999001',
-        'category_id': None,
+        'category_id': 'HP:9999001',
     },
     'HP:9999002': {
-        'is_category': False,
+        'is_category': True,
         'definition': None,
         'name': 'trailer with label and xref',
         'parent_id': 'HP:0000118',
         'hpo_id': 'HP:9999002',
-        'category_id': None,
+        'category_id': 'HP:9999002',
     },
 }