Use all_categories (with ancestors) as labels

code/kg2c/README.md

@@ -41,7 +41,7 @@ KG2canonicalized (KG2c) is a lightweight version of KG2 in which synonymous node
 ```
 The node `id` is the 'preferred' curie for the group of synonymous nodes this KG2c node represents (according to the ARAX `NodeSynonymizer`). Similarly, the node `category` and `name` are the 'preferred' category/name, according to the `NodeSynonymizer`.
 
-In the Neo4j instantiation of KG2c (see [below section](#host-kg2canonicalized-in-neo4j) for how to host KG2c in Neo4j), nodes are labeled with their `expanded_categories`.
+In the Neo4j instantiation of KG2c (see [below section](#host-kg2canonicalized-in-neo4j) for how to host KG2c in Neo4j), nodes are labeled with their `all_categories` and ancestors of those categories.
 
 ###### Example KG2c edge:
 ```

code/kg2c/create_kg2c_files.py

@@ -28,6 +28,8 @@
 from RTXConfiguration import RTXConfiguration
 sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/../ARAX/NodeSynonymizer/")
 from node_synonymizer import NodeSynonymizer
+sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/../ARAX/BiolinkHelper/")
+from biolink_helper import BiolinkHelper
 
 ARRAY_NODE_PROPERTIES = ["all_categories", "publications", "equivalent_curies", "all_names", "expanded_categories"]
 ARRAY_EDGE_PROPERTIES = ["provided_by", "publications", "kg2_ids"]
@@ -194,7 +196,7 @@ def create_kg2c_lite_json_file(canonicalized_nodes_dict: Dict[str, Dict[str, any
                                meta_info_dict: Dict[str, str], is_test: bool):
     logging.info(f" Creating KG2c lite JSON file..")
     # Filter out all except these properties so we create a lightweight KG
-    node_lite_properties = ["id", "name", "category", "expanded_categories"]
+    node_lite_properties = ["id", "name", "category", "all_categories"]
     edge_lite_properties = ["id", "predicate", "subject", "object", "provided_by", "publications"]
     lite_kg = {"nodes": [], "edges": []}
     for node in canonicalized_nodes_dict.values():
@@ -235,12 +237,14 @@ def create_kg2c_sqlite_db(canonicalized_nodes_dict: Dict[str, Dict[str, any]], i
 
 
 def create_kg2c_tsv_files(canonicalized_nodes_dict: Dict[str, Dict[str, any]],
-                          canonicalized_edges_dict: Dict[str, Dict[str, any]], is_test: bool):
+                          canonicalized_edges_dict: Dict[str, Dict[str, any]],
+                          biolink_version: str, is_test: bool):
+    bh = BiolinkHelper(biolink_version)
     # Convert array fields into the format neo4j wants and do some final processing
     for canonicalized_node in canonicalized_nodes_dict.values():
         for list_node_property in ARRAY_NODE_PROPERTIES:
             canonicalized_node[list_node_property] = _convert_list_to_string_encoded_format(canonicalized_node[list_node_property])
-        canonicalized_node['node_labels'] = canonicalized_node['expanded_categories']
+        canonicalized_node['node_labels'] = bh.get_ancestors(canonicalized_node['all_categories'])
     for canonicalized_edge in canonicalized_edges_dict.values():
         if not is_test:  # Make sure we don't have any orphan edges
             assert canonicalized_edge['subject'] in canonicalized_nodes_dict
@@ -439,7 +443,7 @@ def create_kg2c_files(is_test=False):
     meta_info_dict = {"kg2_version": kg2_version, "biolink_version": biolink_version}
     create_kg2c_lite_json_file(canonicalized_nodes_dict, canonicalized_edges_dict, meta_info_dict, is_test)
     create_kg2c_sqlite_db(canonicalized_nodes_dict, is_test)
-    create_kg2c_tsv_files(canonicalized_nodes_dict, canonicalized_edges_dict, is_test)
+    create_kg2c_tsv_files(canonicalized_nodes_dict, canonicalized_edges_dict, biolink_version, is_test)
 
 
 def main():

code/kg2c/record_kg2c_meta_info.py

@@ -43,8 +43,8 @@ def build_meta_kg(nodes_by_id: Dict[str, Dict[str, any]], edges_by_id: Dict[str,
         if not is_test or (subject_node_id in nodes_by_id and object_node_id in nodes_by_id):
             subject_node = nodes_by_id[subject_node_id]
             object_node = nodes_by_id[object_node_id]
-            subject_categories = biolink_helper.add_conflations(subject_node["category"])
-            object_categories = biolink_helper.add_conflations(object_node["category"])
+            subject_categories = biolink_helper.add_conflations(subject_node["all_categories"])
+            object_categories = biolink_helper.add_conflations(object_node["all_categories"])
             predicate = edge["predicate"]
             for subject_category in subject_categories:
                 for object_category in object_categories:
@@ -67,7 +67,7 @@ def build_meta_kg(nodes_by_id: Dict[str, Dict[str, any]], edges_by_id: Dict[str,
     logging.info("Saving meta KG to JSON file..")
     meta_kg = {"nodes": meta_nodes, "edges": meta_edges}
     with open(f"{KG2C_DIR}/{meta_kg_file_name}", "w+") as meta_kg_file:
-        json.dump(meta_kg, meta_kg_file, default=serialize_with_sets)
+        json.dump(meta_kg, meta_kg_file, default=serialize_with_sets, indent=2)
 
 
 def add_neighbor_counts_to_sqlite(nodes_by_id: Dict[str, Dict[str, any]], edges_by_id: Dict[str, Dict[str, any]],
@@ -151,7 +151,7 @@ def record_meta_kg_info(is_test: bool):
     meta_kg_file_name = f"kg2c_meta_kg{'_test' if is_test else ''}.json"
     sqlite_file_name = f"kg2c{'_test' if is_test else ''}.sqlite"
     fda_approved_file_name = f"fda_approved_drugs{'_test' if is_test else ''}.pickle"
-    label_property_name = "expanded_categories"
+    label_property_name = "all_categories"
 
     start = time.time()
     with open(f"{KG2C_DIR}/{input_kg_file_name}", "r") as input_kg_file: