add attributes regarding biolink:knowledge_level and biolink:agent_ty…

…pe for xDTD/xCRG edges
RTXteam · Nov 19, 2024 · 1efa3d1 · 1efa3d1
1 parent a050c2c
commit 1efa3d1
Showing 1 changed file with 18 additions and 8 deletions.
diff --git a/code/ARAX/ARAXQuery/Infer/scripts/infer_utilities.py b/code/ARAX/ARAXQuery/Infer/scripts/infer_utilities.py
@@ -223,8 +223,9 @@ def genrete_treat_subgraphs(self, response: ARAXResponse, top_scores: pd.DataFra
                                     attribute_source="infores:arax", value_type_id="metatype:Boolean",
                                     value_url=None,
                                     description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
-                    Attribute(attribute_type_id="EDAM-DATA:0951", original_attribute_name="probability_treats",
-                                    value=str(treat_score))
+                    Attribute(attribute_type_id="EDAM-DATA:0951", original_attribute_name="probability_treats", value=str(treat_score)),
+                    Attribute(attribute_source="infores:arax", attribute_type_id="biolink:agent_type", value="computational_model"),
+                    Attribute(attribute_source="infores:arax", attribute_type_id="biolink:knowledge_level", value="prediction")
                 ]
                 retrieval_source = [
                                     RetrievalSource(resource_id="infores:arax", resource_role="primary_knowledge_source")
@@ -339,7 +340,9 @@ def genrete_treat_subgraphs(self, response: ARAXResponse, top_scores: pd.DataFra
                         new_edge = Edge(subject=subject_curie, object=object_curie, predicate=predicate, attributes=[], sources=[])
                         ## add attributes to the path-based edge
                         edge_attribute_list = [
-                            Attribute(original_attribute_name="defined_datetime", value=datetime.now().strftime("%Y-%m-%d %H:%M:%S"), attribute_type_id="metatype:Datetime")
+                            Attribute(original_attribute_name="defined_datetime", value=datetime.now().strftime("%Y-%m-%d %H:%M:%S"), attribute_type_id="metatype:Datetime"),
+                            Attribute(attribute_source="infores:arax", attribute_type_id="biolink:agent_type", value="computational_model"),
+                            Attribute(attribute_source="infores:arax", attribute_type_id="biolink:knowledge_level", value="prediction")
                         ]
                         if predicate == "biolink:self_loop_relation":
                             edge_attribute_list += [
@@ -373,7 +376,9 @@ def genrete_treat_subgraphs(self, response: ARAXResponse, top_scores: pd.DataFra
                 edge_attribute_list = [
                     Attribute(original_attribute_name="defined_datetime", value=datetime.now().strftime("%Y-%m-%d %H:%M:%S"), attribute_type_id="metatype:Datetime"),
                     Attribute(original_attribute_name=None, value=True, attribute_type_id="EDAM-DATA:1772", attribute_source="infores:arax", value_type_id="metatype:Boolean", value_url=None, description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
-                    Attribute(attribute_type_id="EDAM-DATA:0951", original_attribute_name="probability_treats", value=str(treat_score))
+                    Attribute(attribute_type_id="EDAM-DATA:0951", original_attribute_name="probability_treats", value=str(treat_score)),
+                    Attribute(attribute_source="infores:arax", attribute_type_id="biolink:agent_type", value="computational_model"),
+                    Attribute(attribute_source="infores:arax", attribute_type_id="biolink:knowledge_level", value="prediction")
                 ]
                 retrieval_source = [
                         RetrievalSource(resource_id="infores:arax", resource_role="primary_knowledge_source")
@@ -605,8 +610,9 @@ def genrete_regulate_subgraphs(self, response: ARAXResponse, query_chemical: Opt
                                     attribute_source="infores:arax", value_type_id="metatype:Boolean",
                                     value_url=None,
                                     description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
-                        Attribute(attribute_type_id="EDAM-OPERATION:2434", original_attribute_name=f"probably_{model_type}_activity",
-                                    value=str(prob_score))
+                        Attribute(attribute_type_id="EDAM-OPERATION:2434", original_attribute_name=f"probably_{model_type}_activity", value=str(prob_score)),
+                        Attribute(attribute_source="infores:arax", attribute_type_id="biolink:agent_type", value="computational_model"),
+                        Attribute(attribute_source="infores:arax", attribute_type_id="biolink:knowledge_level", value="prediction")
                     ]
                     retrieval_source = [
                                     RetrievalSource(resource_id="infores:arax", resource_role="primary_knowledge_source")
@@ -655,7 +661,9 @@ def genrete_regulate_subgraphs(self, response: ARAXResponse, query_chemical: Opt
                                     attribute_source="infores:arax", value_type_id="metatype:Boolean",
                                     value_url=None,
                                     description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
-                        Attribute(attribute_type_id="EDAM-OPERATION:2434", original_attribute_name=f"probably_{model_type}_activity", value=str(prob_score))
+                        Attribute(attribute_type_id="EDAM-OPERATION:2434", original_attribute_name=f"probably_{model_type}_activity", value=str(prob_score)),
+                        Attribute(attribute_source="infores:arax", attribute_type_id="biolink:agent_type", value="computational_model"),
+                        Attribute(attribute_source="infores:arax", attribute_type_id="biolink:knowledge_level", value="prediction")
                     ]
                     if model_type == 'increase':
                         edge_qualifier_direction = 'increased'
@@ -769,7 +777,9 @@ def genrete_regulate_subgraphs(self, response: ARAXResponse, query_chemical: Opt
                 edge_attribute_list = [
                     Attribute(original_attribute_name="defined_datetime", value=datetime.now().strftime("%Y-%m-%d %H:%M:%S"), attribute_type_id="metatype:Datetime"),
                     Attribute(original_attribute_name=None, value=True, attribute_type_id="EDAM-DATA:1772", attribute_source="infores:arax", value_type_id="metatype:Boolean", value_url=None, description="This edge is a container for a computed value between two nodes that is not directly attachable to other edges."),
-                    Attribute(attribute_type_id="EDAM-OPERATION:2434", original_attribute_name=f"probably_{model_type}_activity", value=str(regulate_score))
+                    Attribute(attribute_type_id="EDAM-OPERATION:2434", original_attribute_name=f"probably_{model_type}_activity", value=str(regulate_score)),
+                    Attribute(attribute_source="infores:arax", attribute_type_id="biolink:agent_type", value="computational_model"),
+                    Attribute(attribute_source="infores:arax", attribute_type_id="biolink:knowledge_level", value="prediction")
                 ]
                 retrieval_source = [
                                         RetrievalSource(resource_id="infores:arax", resource_role="primary_knowledge_source")