Merge remote-tracking branch 'origin/kg2.10.1c' into main

RTXteam · Oct 11, 2024 · a11d884 · a11d884
2 parents 4331e9b + 9d689ab
commit a11d884
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Showing 2 changed files with 23 additions and 11 deletions.
diff --git a/app/app/plover.py b/app/app/plover.py
@@ -156,12 +156,16 @@ def build_indexes(self):
                 if "qualified_object_aspect" in edge:
                     edge[self.graph_object_aspect_property] = edge["qualified_object_aspect"]
                     del edge["qualified_object_aspect"]
+                # TODO: Remove this patch after these KG2.10.1pre issues are fixed in future KG2pre versions
+                edge["predicate"] = edge["predicate"].replace("biolink:biolink_", "biolink:")
+                if edge["primary_knowledge_source"] == "infores:biothings-multiomics-clinicaltrials":
+                    edge["primary_knowledge_source"] = "infores:multiomics-clinicaltrials"
 
         # Zip up specified 'zip' columns to form a list of dicts (e.g., list of supporting studies)
         if self.kg_config.get("zip"):
             for zipped_prop_name, zipped_prop_info in self.kg_config["zip"].items():
                 for edge in edges:
-                    # TODO: Remove this patch after CTKP TSVs are fixed..
+                    # TODO: Add generalized way of handling this situation (not CTKP-specific)
                     if "tested_intervention" in zipped_prop_info["properties"]:
                         edge["tested_intervention"] = edge["tested_intervention"] * len(edge["nctid"])
                     zip_cols = [edge[property_name] for property_name in zipped_prop_info["properties"]]

diff --git a/app/config_kg2c.json b/app/config_kg2c.json
@@ -1,6 +1,6 @@
 {
-  "nodes_file": "https://kg2webhost.rtx.ai/kg2c-2.10.0-v1.0-nodes.jsonl.gz",
-  "edges_file": "https://kg2webhost.rtx.ai/kg2c-2.10.0-v1.0-edges.jsonl.gz",
+  "nodes_file": "https://kg2webhost.rtx.ai/kg2c-2.10.1-v1.0-nodes.jsonl.gz",
+  "edges_file": "https://kg2webhost.rtx.ai/kg2c-2.10.1-v1.0-edges.jsonl.gz",
   "biolink_version": "4.2.1",
   "kp_infores_curie": "infores:rtx-kg2",
   "endpoint_name": "kg2c",
@@ -30,38 +30,46 @@
     },
     "iri": {
       "attribute_type_id": "biolink:IriType",
-      "value_type_id": "metatype:Uri"
+      "value_type_id": "metatype:Uri",
+      "attribute_source": "{kp_infores_curie}"
     },
     "description": {
       "attribute_type_id": "biolink:description",
-      "value_type_id": "metatype:String"
+      "value_type_id": "metatype:String",
+      "attribute_source": "{kp_infores_curie}"
     },
     "all_categories": {
       "attribute_type_id": "biolink:category",
       "value_type_id": "metatype:Uriorcurie",
-      "description": "Categories of all nodes in this synonym set in RTX-KG2."
+      "description": "Categories of all nodes in this synonym set in RTX-KG2.",
+      "attribute_source": "{kp_infores_curie}"
     },
     "all_names": {
       "attribute_type_id": "biolink:synonym",
       "value_type_id": "metatype:String",
-      "description": "Names of all nodes in this synonym set in RTX-KG2."
+      "description": "Names of all nodes in this synonym set in RTX-KG2.",
+      "attribute_source": "{kp_infores_curie}"
     },
     "equivalent_curies": {
       "attribute_type_id": "biolink:xref",
       "value_type_id": "metatype:Nodeidentifier",
-      "description": "Identifiers of all nodes in this synonym set in RTX-KG2."
+      "description": "Identifiers of all nodes in this synonym set in RTX-KG2.",
+      "attribute_source": "{kp_infores_curie}"
     },
     "publications": {
       "attribute_type_id": "biolink:publications",
-      "value_type_id": "biolink:Uriorcurie"
+      "value_type_id": "biolink:Uriorcurie",
+      "attribute_source": "{kp_infores_curie}"
     },
     "kg2_ids": {
       "attribute_type_id": "biolink:original_predicate",
       "value_type_id": "metatype:String",
-      "description": "The IDs of the original RTX-KG2pre edge(s) corresponding to this edge prior to any synonymization or remapping."
+      "description": "The IDs of the original RTX-KG2pre edge(s) corresponding to this edge prior to any synonymization or remapping.",
+      "attribute_source": "{kp_infores_curie}"
     },
     "publications_info": {
-      "attribute_type_id": "bts:sentence"
+      "attribute_type_id": "bts:sentence",
+      "attribute_source": "{kp_infores_curie}"
     }
   },
   "sources_template": {}