diff --git a/src/sssom/util.py b/src/sssom/util.py
index fc7249b0..9491d0a1 100644
--- a/src/sssom/util.py
+++ b/src/sssom/util.py
@@ -155,7 +155,13 @@ def clean_prefix_map(self, strict: bool = True) -> None:
         if self.metadata:
             prefixes_in_table.update(get_prefixes_used_in_metadata(self.metadata))
 
-        missing_prefixes = prefixes_in_table - self.converter.get_prefixes()
+        # Convert prefixes_in_table to lowercase
+        prefixes_in_table_lower = {prefix.lower() for prefix in prefixes_in_table}
+        # Convert self.converter.get_prefixes() to lowercase
+        converter_prefixes_lower = {prefix.lower() for prefix in self.converter.get_prefixes()}
+        missing_prefixes = prefixes_in_table_lower - converter_prefixes_lower
+        # missing_prefixes = prefixes_in_table - self.converter.get_prefixes()
+
         if missing_prefixes and strict:
             raise ValueError(
                 f"{missing_prefixes} are used in the SSSOM mapping set but it does not exist in the prefix map"
diff --git a/tests/data/sample1.sssom.tsv b/tests/data/sample1.sssom.tsv
new file mode 100644
index 00000000..fc256028
--- /dev/null
+++ b/tests/data/sample1.sssom.tsv
@@ -0,0 +1,8 @@
+#curie_map:
+#  FBbt: "http://purl.obolibrary.org/obo/FBbt_"
+#  ORCID: "https://orcid.org/"
+#  UBERON: "http://purl.obolibrary.org/obo/UBERON_"
+#creator_id:
+#  - "ORCID:0000-0002-6095-8718"
+subject_id	subject_label	predicate_id	object_id	mapping_justification
+FBbt:00000001	organism	semapv:crossSpeciesExactMatch	UBERON:0000468	semapv:ManualMappingCuration
\ No newline at end of file