pulling in changes from JM - adding a few edge types

parsers/biolink/src/loadBL.py

@@ -41,7 +41,7 @@ class BLLoader(SourceDataLoader):
     source_data_url = "https://api.monarchinitiative.org/api/"
     license = "https://monarchinitiative.org/about/licensing"
     attribution = "https://monarchinitiative.org/about/monarch"
-    parsing_version: str = '1.2'
+    parsing_version: str = '1.3'
 
     def __init__(self, test_mode: bool = False, source_data_dir: str = None):
         """
@@ -163,11 +163,43 @@ def passes_qc_filter(line: list):
     'biolink:treats'
 }
 
+PREDICATES_WITH_DISEASE_SUBJECT = {
+    'biolink:disrupts',
+    'biolink:caused_by',
+    'biolink:causes',
+    'biolink:has_participant'
+}
+
+ALLOWABLE_DISEASE_PHENOTYPE_PREFIXES = {
+    'MONDO:',
+    'UMLS:',
+    'OMIA:',
+    'OMIM:',
+    'OMIMPS:',
+    'MESH:',
+    'KEGG-ds:',
+    'HP:',
+    'DOID:',
+    'HGNC:',
+    'GeneReviews:',
+    'ORPHA:',
+    'EFO:',
+    'MP:'
+}
+
 
 def get_bl_edge_predicate(line: list):
     predicate = line[EDGESDATACOLS.PREDICATE.value]
     if predicate == 'biolink:biomarker_for' and not passes_qc_filter(line):
         return None
+    elif predicate in PREDICATES_WITH_DISEASE_SUBJECT:
+        subject = line[EDGESDATACOLS.SUBJECT.value]
+        for prefix in ALLOWABLE_DISEASE_PHENOTYPE_PREFIXES:
+            if prefix in subject:
+                return predicate
+            else:
+                continue
+        return None
     else:
         return predicate if predicate in DESIRED_BL_PREDICATES else None