Merge pull request #477 from Knowledge-Graph-Hub/ontology-case

Fix NCBITaxon nodes filename case mismatch in bacdive transform

Author: realmarcin

download.yaml

@@ -77,6 +77,20 @@
   url: https://purl.obolibrary.org/obo/hp/hp.json
   local_name: hp.json
 
+#
+# UBERON (Uber Anatomy Ontology)
+#
+-
+  url: https://purl.obolibrary.org/obo/uberon.owl
+  local_name: uberon.owl
+
+#
+# FOODON
+#
+-
+  url: https://purl.obolibrary.org/obo/foodon.owl
+  local_name: foodon.owl
+
 # **** Data sources ****
 
 # BacDive

kg_microbe/transform_utils/bacdive/bacdive.py

@@ -226,7 +226,7 @@ def _load_ncbitaxon_labels(self):
         This is much faster than querying the NCBITaxon SQLite database via OakLib
         for each record. Creates both id->label and label->id mappings.
         """
-        ncbitaxon_nodes_file = Path("data/transformed/ontologies/NCBITaxon_nodes.tsv")
+        ncbitaxon_nodes_file = Path("data/transformed/ontologies/ncbitaxon_nodes.tsv")
 
         if ncbitaxon_nodes_file.exists():
             try:

kg_microbe/transform_utils/ontologies/ontologies_transform.py

@@ -79,6 +79,8 @@
     "mondo": "mondo.json",
     "hp": "hp.json",
     "metpo": "metpo.owl",
+    "uberon": "uberon.owl",
+    "foodon": "foodon.owl",
 }