Bring in similarty through copy & paste instead of import

backend/src/monarch_py/cli.py

@@ -275,7 +275,7 @@ def compare(
     """Compare two entities using semantic similarity via OAK"""
     subjects = subjects.split(",")
     objects = objects.split(",")
-    response = oak.compare(subjects, objects)
+    response = oak().compare(subjects, objects)
     format_output(fmt, response, output)
 
 

backend/src/monarch_py/datamodels/model.py

@@ -47,13 +47,19 @@ class Association(ConfiguredBaseModel):
     id: str = Field(...)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
-    subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
-    subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
+    subject_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the subject entity"""
+    )
+    subject_category: Optional[str] = Field(
+        None, description="""The category of the subject entity"""
+    )
     subject_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject id and the ids of all of it's ancestors""",
     )
-    subject_label: Optional[str] = Field(None, description="""the label or name for the first entity""")
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
     subject_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
@@ -63,13 +69,19 @@ class Association(ConfiguredBaseModel):
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
-    object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
-    object_category: Optional[str] = Field(None, description="""The category of the object entity""")
+    object_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the object entity"""
+    )
+    object_category: Optional[str] = Field(
+        None, description="""The category of the object entity"""
+    )
     object_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object id and the ids of all of it's ancestors""",
     )
-    object_label: Optional[str] = Field(None, description="""the label or name for the second entity""")
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
     object_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
@@ -97,7 +109,9 @@ class Association(ConfiguredBaseModel):
         description="""count of supporting documents, evidence codes, and sources supplying evidence""",
     )
     pathway: Optional[str] = Field(None)
-    frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
+    frequency_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the frequency_qualifier entity"""
+    )
     frequency_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
@@ -112,11 +126,15 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
+    onset_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the onset_qualifier entity"""
+    )
     onset_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the onset_qualifier entity"""
     )
-    onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
+    onset_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the onset_qualifier entity"""
+    )
     onset_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
@@ -125,11 +143,15 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
     )
-    sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
+    sex_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the sex_qualifier entity"""
+    )
     sex_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the sex_qualifier entity"""
     )
-    sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
+    sex_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the sex_qualifier entity"""
+    )
     sex_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
@@ -138,11 +160,15 @@ class Association(ConfiguredBaseModel):
         default_factory=list,
         description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
     )
-    stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
+    stage_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the stage_qualifier entity"""
+    )
     stage_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the stage_qualifier entity"""
     )
-    stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
+    stage_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the stage_qualifier entity"""
+    )
     stage_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
@@ -199,13 +225,19 @@ class DirectionalAssociation(Association):
     id: str = Field(...)
     subject: str = Field(...)
     original_subject: Optional[str] = Field(None)
-    subject_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the subject entity""")
-    subject_category: Optional[str] = Field(None, description="""The category of the subject entity""")
+    subject_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the subject entity"""
+    )
+    subject_category: Optional[str] = Field(
+        None, description="""The category of the subject entity"""
+    )
     subject_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject id and the ids of all of it's ancestors""",
     )
-    subject_label: Optional[str] = Field(None, description="""the label or name for the first entity""")
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
     subject_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing subject name and the names of all of it's ancestors""",
@@ -215,13 +247,19 @@ class DirectionalAssociation(Association):
     predicate: str = Field(...)
     object: str = Field(...)
     original_object: Optional[str] = Field(None)
-    object_namespace: Optional[str] = Field(None, description="""The namespace/prefix of the object entity""")
-    object_category: Optional[str] = Field(None, description="""The category of the object entity""")
+    object_namespace: Optional[str] = Field(
+        None, description="""The namespace/prefix of the object entity"""
+    )
+    object_category: Optional[str] = Field(
+        None, description="""The category of the object entity"""
+    )
     object_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object id and the ids of all of it's ancestors""",
     )
-    object_label: Optional[str] = Field(None, description="""the label or name for the second entity""")
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
     object_closure_label: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing object name and the names of all of it's ancestors""",
@@ -249,7 +287,9 @@ class DirectionalAssociation(Association):
         description="""count of supporting documents, evidence codes, and sources supplying evidence""",
     )
     pathway: Optional[str] = Field(None)
-    frequency_qualifier_label: Optional[str] = Field(None, description="""The name of the frequency_qualifier entity""")
+    frequency_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the frequency_qualifier entity"""
+    )
     frequency_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the frequency_qualifier entity"""
     )
@@ -264,11 +304,15 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing frequency_qualifier name and the names of all of it's ancestors""",
     )
-    onset_qualifier_label: Optional[str] = Field(None, description="""The name of the onset_qualifier entity""")
+    onset_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the onset_qualifier entity"""
+    )
     onset_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the onset_qualifier entity"""
     )
-    onset_qualifier_category: Optional[str] = Field(None, description="""The category of the onset_qualifier entity""")
+    onset_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the onset_qualifier entity"""
+    )
     onset_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing onset_qualifier id and the ids of all of it's ancestors""",
@@ -277,11 +321,15 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing onset_qualifier name and the names of all of it's ancestors""",
     )
-    sex_qualifier_label: Optional[str] = Field(None, description="""The name of the sex_qualifier entity""")
+    sex_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the sex_qualifier entity"""
+    )
     sex_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the sex_qualifier entity"""
     )
-    sex_qualifier_category: Optional[str] = Field(None, description="""The category of the sex_qualifier entity""")
+    sex_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the sex_qualifier entity"""
+    )
     sex_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing sex_qualifier id and the ids of all of it's ancestors""",
@@ -290,11 +338,15 @@ class DirectionalAssociation(Association):
         default_factory=list,
         description="""Field containing sex_qualifier name and the names of all of it's ancestors""",
     )
-    stage_qualifier_label: Optional[str] = Field(None, description="""The name of the stage_qualifier entity""")
+    stage_qualifier_label: Optional[str] = Field(
+        None, description="""The name of the stage_qualifier entity"""
+    )
     stage_qualifier_namespace: Optional[str] = Field(
         None, description="""The namespace/prefix of the stage_qualifier entity"""
     )
-    stage_qualifier_category: Optional[str] = Field(None, description="""The category of the stage_qualifier entity""")
+    stage_qualifier_category: Optional[str] = Field(
+        None, description="""The category of the stage_qualifier entity"""
+    )
     stage_qualifier_closure: Optional[List[str]] = Field(
         default_factory=list,
         description="""Field containing stage_qualifier id and the ids of all of it's ancestors""",
@@ -322,11 +374,15 @@ class Entity(ConfiguredBaseModel):
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
-    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    full_name: Optional[str] = Field(
+        None, description="""The long form name of an entity"""
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
-    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
+    in_taxon: Optional[str] = Field(
+        None, description="""The biolink taxon that the entity is in the closure of."""
+    )
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -378,7 +434,9 @@ class Node(Entity):
     UI container class extending Entity with additional information
     """
 
-    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
+    in_taxon: Optional[str] = Field(
+        None, description="""The biolink taxon that the entity is in the closure of."""
+    )
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -404,7 +462,9 @@ class Node(Entity):
     id: str = Field(...)
     category: Optional[str] = Field(None)
     name: Optional[str] = Field(None)
-    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    full_name: Optional[str] = Field(
+        None, description="""The long form name of an entity"""
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
@@ -460,16 +520,22 @@ class EntityResults(Results):
 
 class SearchResult(Entity):
 
-    highlight: Optional[str] = Field(None, description="""matching text snippet containing html tags""")
-    score: Optional[str] = Field(None, description="""Abstract base slot for different kinds of scores""")
+    highlight: Optional[str] = Field(
+        None, description="""matching text snippet containing html tags"""
+    )
+    score: Optional[float] = Field(None)
     id: str = Field(...)
     category: str = Field(...)
     name: str = Field(...)
-    full_name: Optional[str] = Field(None, description="""The long form name of an entity""")
+    full_name: Optional[str] = Field(
+        None, description="""The long form name of an entity"""
+    )
     description: Optional[str] = Field(None)
     xref: Optional[List[str]] = Field(default_factory=list)
     provided_by: Optional[str] = Field(None)
-    in_taxon: Optional[str] = Field(None, description="""The biolink taxon that the entity is in the closure of.""")
+    in_taxon: Optional[str] = Field(
+        None, description="""The biolink taxon that the entity is in the closure of."""
+    )
     in_taxon_label: Optional[str] = Field(
         None,
         description="""The label of the biolink taxon that the entity is in the closure of.""",
@@ -510,21 +576,41 @@ class TermPairwiseSimilarity(PairwiseSimilarity):
     A simple pairwise similarity between two atomic concepts/terms
     """
 
-    subject_id: str = Field(..., description="""The first of the two entities being compared""")
-    subject_label: Optional[str] = Field(None, description="""the label or name for the first entity""")
-    subject_source: Optional[str] = Field(None, description="""the source for the first entity""")
-    object_id: Optional[str] = Field(None, description="""The second of the two entities being compared""")
-    object_label: Optional[str] = Field(None, description="""the label or name for the second entity""")
-    object_source: Optional[str] = Field(None, description="""the source for the second entity""")
+    subject_id: str = Field(
+        ..., description="""The first of the two entities being compared"""
+    )
+    subject_label: Optional[str] = Field(
+        None, description="""The name of the subject entity"""
+    )
+    subject_source: Optional[str] = Field(
+        None, description="""the source for the first entity"""
+    )
+    object_id: Optional[str] = Field(
+        None, description="""The second of the two entities being compared"""
+    )
+    object_label: Optional[str] = Field(
+        None, description="""The name of the object entity"""
+    )
+    object_source: Optional[str] = Field(
+        None, description="""the source for the second entity"""
+    )
     ancestor_id: Optional[str] = Field(
         None,
         description="""the most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected""",
     )
-    ancestor_label: Optional[str] = Field(None, description="""the name or label of the ancestor concept""")
+    ancestor_label: Optional[str] = Field(
+        None, description="""the name or label of the ancestor concept"""
+    )
     ancestor_source: Optional[str] = Field(None)
-    object_information_content: Optional[float] = Field(None, description="""The IC of the object""")
-    subject_information_content: Optional[float] = Field(None, description="""The IC of the subject""")
-    ancestor_information_content: Optional[float] = Field(None, description="""The IC of the object""")
+    object_information_content: Optional[float] = Field(
+        None, description="""The IC of the object"""
+    )
+    subject_information_content: Optional[float] = Field(
+        None, description="""The IC of the subject"""
+    )
+    ancestor_information_content: Optional[float] = Field(
+        None, description="""The IC of the object"""
+    )
     jaccard_similarity: Optional[float] = Field(
         None,
         description="""The number of concepts in the intersection divided by the number in the union""",

backend/src/monarch_py/datamodels/model.yaml

@@ -4,10 +4,9 @@ description: Data models for the Monarch Initiative data access library
 prefixes:
   linkml: https://w3id.org/linkml/
   biolink: https://w3id.org/biolink/vocab/
-  oak: https://w3id.org/oak/
 imports:
   - linkml:types
-  - oak:similarity
+  - similarity
 default_range: string
 
 
@@ -239,7 +238,6 @@ classes:
         items:
           range: SearchResult
 
-
 slots:
   aggregator_knowledge_source:
     multivalued: true