Merge pull request #234 from Knowledge-Graph-Hub/issue-233

Added NCBITaxon:XX edge to strain
Knowledge-Graph-Hub · Aug 26, 2024 · 05ee4b3 · 05ee4b3
2 parents 4094a65 + a11eed0
commit 05ee4b3
Showing 1 changed file with 14 additions and 1 deletion.
diff --git a/kg_microbe/transform_utils/mediadive/mediadive.py b/kg_microbe/transform_utils/mediadive/mediadive.py
@@ -84,6 +84,7 @@
     NCBI_CATEGORY,
     NCBI_TO_MEDIUM_EDGE,
     NCBITAXON_ID_COLUMN,
+    NCBITAXON_PREFIX,
     OBJECT_ID_COLUMN,
     PUBCHEM_KEY,
     PUBCHEM_PREFIX,
@@ -387,9 +388,21 @@ def run(self, data_file: Union[Optional[Path], Optional[str]] = None, show_statu
                                                 medium_id,
                                                 IS_GROWN_IN,
                                                 strain_id,
-                                            ]
+                                            ],
                                         ]
                                     )
+                                    if strain.get(ID_COLUMN):
+                                        medium_strain_edge.extend(
+                                            [
+                                                [
+                                                    ncbi_strain_id,
+                                                    SUBCLASS_PREDICATE,
+                                                    NCBITAXON_PREFIX+str(strain.get(ID_COLUMN)),
+                                                    RDFS_SUBCLASS_OF,
+                                                    strain_id
+                                                ],
+                                            ]
+                                        )
                                     edge_writer.writerows(medium_strain_edge)
 
                     if SOLUTIONS_KEY not in json_obj: