diff --git a/tools/schemacode/bidsschematools/data/tests/test_rules.py b/tools/schemacode/bidsschematools/data/tests/test_rules.py
index 6c46a5da5d..39fce83a3a 100644
--- a/tools/schemacode/bidsschematools/data/tests/test_rules.py
+++ b/tools/schemacode/bidsschematools/data/tests/test_rules.py
@@ -87,6 +87,11 @@ def test_rule_objects(schema_obj):
 
                 # Build a list of items mentioned in rules, but not found in objects.
                 if use not in object_values:
+                    if (use, object_type) == ("phenotype", "datatypes"):
+                        # Special case: phenotype is a top-level directory
+                        # that acts like a datatype, but we don't want to
+                        # define it that way in the glossary, currently.
+                        continue
                     temp_path = path[:]
                     if is_list:
                         temp_path[-1] += f"[{i_use}]"