Correctly type drugs and nucleic acids in IntAct ingest

Knowledge-Graph-Hub · Jun 11, 2020 · 1620843 · 1620843
1 parent 145c7bb
commit 1620843
Showing 1 changed file with 10 additions and 2 deletions.
diff --git a/kg_covid_19/transform_utils/intact/intact.py b/kg_covid_19/transform_utils/intact/intact.py
@@ -33,12 +33,18 @@ def __init__(self, input_dir: str = None, output_dir: str = None) -> None:
         source_name = "intact"
         super().__init__(source_name, input_dir, output_dir)
         # interactor type to biolink category
+        bl_protein_cat = 'biolink:Protein'
         bl_rna_cat = 'biolink:RNA'
+        bl_nucleic_acid = 'biolink:MolecularEntity'
+        bl_drug_cat = 'biolink:Drug'
         self.type_to_biolink_category = {
-            'protein': 'biolink:Protein',
+            'protein': bl_protein_cat,
+            'peptide': bl_protein_cat,
             'rna': bl_rna_cat,
             'mrna': bl_rna_cat,
-            'snrna': bl_rna_cat
+            'snrna': bl_rna_cat,
+            'nucleic acid': bl_nucleic_acid,
+            'small molecule': bl_drug_cat
         }
         self.db_to_prefix = {
             'uniprot': 'UniProtKB',
@@ -255,6 +261,8 @@ def interactor_to_node(self, interactor) -> List[Union[int, list]]:
             interactor.getElementsByTagName('interactorType')[0].getElementsByTagName(
                 'shortLabel')[0].childNodes[0].data
             type = type.lower()
+            if type == 'small molecule':
+                pass
             if type in self.type_to_biolink_category:
                 category = self.type_to_biolink_category[type]
         except (KeyError, IndexError, AttributeError) as e: