Add phenio

bionty/_phenotype/_core.py

@@ -9,17 +9,21 @@
 
 FILENAMES = {
     "human_hp": "phenotype_lookup.parquet",
+    "all_phenio": "phenio_lookup.parquet",
 }
 
 
 class Phenotype(EntityTable):
-    """Phenotype.
-
-    Args:
-        species: `name` of `Species` entity EntityTable.
+    """Phenotype ontology.
 
+    1. Human phenotype ontology
     Edits of terms are coordinated and reviewed on:
     https://hpo.jax.org/app/
+
+    2. Phenomics Integrated Ontology (PHENIO)
+    Edits of terms are coordinated and reviewed on:
+    https://github.com/monarch-initiative/phenio
+    Set species to "all" to use it.
     """
 
     def __init__(

bionty/_table.py

@@ -52,7 +52,9 @@ def __init__(
                     "Check active databases using `bionty.display_active_versions`."
                 )
 
-            database = br.normalize_prefix(database)
+            normalized_database = br.normalize_prefix(database)
+            if normalized_database:
+                database = normalized_database
         self._set_attributes(database=database, version=version)
 
     @property

bionty/versions/versions.yaml

@@ -45,3 +45,6 @@ Phenotype:
   hp:
     versions:
       2023-01-27: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-01-27/hp.owl
+  phenio:
+    versions:
+      2022-12-13: https://github.com/monarch-initiative/phenio/releases/download/2022-12-13/phenio.owl