EBIvariation · apriltuesday · Mar 30, 2026 · Mar 25, 2026 · Mar 25, 2026 · Mar 26, 2026
diff --git a/OT_SCHEMA_VERSION b/OT_SCHEMA_VERSION
@@ -1 +1 @@
-917e836
+v26.03.0
diff --git a/cmat/output_generation/clinvar_to_evidence_strings.py b/cmat/output_generation/clinvar_to_evidence_strings.py
@@ -47,7 +47,8 @@ def validate_evidence_string(ev_string, ot_schema_contents):
 def launch_pipeline(clinvar_xml_file, efo_mapping_file, gene_mapping_file, ot_schema_file, dir_out, start, end):
     os.makedirs(dir_out, exist_ok=True)
     ot_schema_contents = json.loads(open(ot_schema_file).read())
-    string_to_efo_mappings, _, nonmatching_mappings = load_ontology_mapping(efo_mapping_file, ot_schema_contents)
+    ontology_id_regex = ot_schema_contents['definitions']['diseaseFromSourceMappedId']['pattern']
+    string_to_efo_mappings, _, nonmatching_mappings = load_ontology_mapping(efo_mapping_file, ontology_id_regex)
     variant_to_gene_mappings = CT.process_consequence_type_file(gene_mapping_file)
 
     # Output mappings that don't conform to the schema in a separate file

diff --git a/cmat/trait_mapping/utils.py b/cmat/trait_mapping/utils.py
@@ -35,7 +35,7 @@ def string_to_preferred_ontologies(ontology_string, target_ontology):
     return preferred_ontologies
 
 
-def load_ontology_mapping(trait_mapping_file, schema=None):
+def load_ontology_mapping(trait_mapping_file, ontology_id_regex='.*'):
     """
     Load ontology mappings from a TSV file.
 
@@ -50,9 +50,6 @@ def load_ontology_mapping(trait_mapping_file, schema=None):
     target_ontology = 'EFO'
     n_ontology_mappings = 0
     in_header = True
-    ontology_id_regex = '.*'
-    if schema:
-        ontology_id_regex = schema['definitions']['diseaseFromSourceMappedId']['pattern']
     nonmatching_mappings = []
 
     with open(trait_mapping_file, 'rt') as f:

diff --git a/tests/output_generation/evaluation/test_ols_utils.py b/tests/output_generation/evaluation/test_ols_utils.py
@@ -9,7 +9,7 @@ def test_fetch_eval_data():
 
 def test_fetch_eval_data_include_neighbors():
     expected = ('MONDO:0004975', False, {'MONDO:0004975'},
-                {'EFO:0005815', 'MONDO:0001627'},
+                {'MONDO:0005574', 'MONDO:0001627'},
                 {'MONDO:0010422', 'MONDO:0014036', 'MONDO:0014265', 'MONDO:0014316', 'MONDO:0100087'})
     assert fetch_eval_data(db_iden=('MONDO', 'MONDO:0004975'), include_neighbors=True) == expected
 

diff --git a/tests/output_generation/test_clinvar_to_evidence_strings.py b/tests/output_generation/test_clinvar_to_evidence_strings.py
@@ -38,17 +38,8 @@ def test_efo_mapping(self):
             ('http://www.ebi.ac.uk/efo/EFO_0001645', 'coronary heart disease')]
 
     def test_efo_mapping_with_schema(self):
-        schema = {
-            "definitions": {
-                "diseaseFromSourceMappedId": {
-                    "type": "string",
-                    "description": "Identifier of the disease in the EFO ontology",
-                    "pattern": "(^NCIT_|^Orphanet_|^GO_|^HP_|^EFO_|^MONDO_|^DOID_|^MP_|^OTAR_|^PATO_|^OBI_|^OBA_|^OGMS_|^GSSO_|^UBERON_)",
-                    "examples": ["EFO_0005537"]
-                }
-            }
-        }
-        mappings, _, nonmatching_mappings = load_ontology_mapping(config.efo_mapping_file, schema)
+        ontology_id_regex = "(^NCIT_|^Orphanet_|^GO_|^HP_|^EFO_|^MONDO_|^DOID_|^MP_|^OTAR_|^PATO_|^OBI_|^OBA_|^OGMS_|^GSSO_|^UBERON_)"
+        mappings, _, nonmatching_mappings = load_ontology_mapping(config.efo_mapping_file, ontology_id_regex)
         assert len(mappings) == 10
         assert 'tbc1 domain family member 24' not in mappings
         assert len(nonmatching_mappings) == 1

diff --git a/tests/trait_mapping/resources/string_to_ontology_mappings.tsv b/tests/trait_mapping/resources/string_to_ontology_mappings.tsv
@@ -1,8 +1,8 @@
 #clinvar_trait_name	uri	label
 11p partial monosomy syndrome	http://purl.obolibrary.org/obo/MONDO_0008681	WAGR syndrome
 3 beta-hydroxysteroid dehydrogenase deficiency	http://www.orpha.net/ORDO/Orphanet_90791	Congenital adrenal hyperplasia due to 3-beta-hydroxysteroid dehydrogenase deficiency
-coronary artery disease/myocardial infarction	http://www.ebi.ac.uk/efo/EFO_0000612	myocardial infarction
-coronary artery disease/myocardial infarction	http://www.ebi.ac.uk/efo/EFO_0001645	coronary heart disease
+coronary artery disease/myocardial infarction	http://purl.obolibrary.org/obo/MONDO_0005068	myocardial infarction
+coronary artery disease/myocardial infarction	http://purl.obolibrary.org/obo/MONDO_0005010	coronary heart disease
 frontotemporal dementia, ubiquitin-positive	http://www.orpha.net/ORDO/Orphanet_282	Frontotemporal dementia
 meckel syndrome, type 3	http://purl.obolibrary.org/obo/MONDO_0018921	Meckel syndrome
 renal-hepatic-pancreatic dysplasia 2	http://www.orpha.net/ORDO/Orphanet_294415	Renal-hepatic-pancreatic dysplasia

diff --git a/tests/trait_mapping/test_output.py b/tests/trait_mapping/test_output.py
@@ -105,7 +105,7 @@ def test_find_replacement_mapping():
     # Deprecated in EFO but replacement is also deprecated, so use its replacement
     assert find_replacement_mapping(
         trait_name, 'http://www.orpha.net/ORDO/Orphanet_226316', target_ontology, preferred_ontologies
-    ) == 'http://purl.obolibrary.org/obo/MONDO_0011792|thyroid dyshormonogenesis 6|TOKEN_MATCH_SYNONYM|MONDO_HP_NOT_EFO'
+    ) == 'http://purl.obolibrary.org/obo/MONDO_0011792|thyroid dyshormonogenesis 6|TOKEN_MATCH_SYNONYM|EFO_CURRENT'
 
 
 def test_to_mapping_string():

diff --git a/tests/trait_mapping/test_trait_processing.py b/tests/trait_mapping/test_trait_processing.py
@@ -56,9 +56,9 @@ def test_ols_exact_ascii_match(self):
         # Search should be agnostic to accents and other non-ASCII characters
         trait = Trait('pelger-huët anomaly', None, None)
         processed_trait = self.run_process_trait(trait)
-        assert len(processed_trait.ols_result_list) == 11
+        assert len(processed_trait.ols_result_list) == 10
         assert processed_trait.is_finished
-        assert {m.uri for m in processed_trait.finished_mapping_set} == {'http://www.ebi.ac.uk/efo/EFO_1001093'}
+        assert {m.uri for m in processed_trait.finished_mapping_set} == {'http://purl.obolibrary.org/obo/MONDO_0008214'}
 
     def test_multiple_mappings(self):
         # Multiple mappings from OLS