NamedThing -> NamedEntity

src/ontogpt/templates/dietician_notes.py

@@ -0,0 +1,186 @@
+from __future__ import annotations
+from datetime import datetime, date
+from enum import Enum
+from typing import List, Dict, Optional, Any, Union
+from pydantic import BaseModel as BaseModel, ConfigDict, Field
+import sys
+if sys.version_info >= (3, 8):
+    from typing import Literal
+else:
+    from typing_extensions import Literal
+
+
+metamodel_version = "None"
+version = "None"
+
+class ConfiguredBaseModel(BaseModel):
+    model_config = ConfigDict(
+        validate_assignment=True,
+        validate_default=True,
+        extra='forbid',
+        arbitrary_types_allowed=True,
+        use_enum_values = True)
+
+
+class NullDataOptions(str, Enum):
+
+
+    UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION"
+
+    NOT_APPLICABLE = "NOT_APPLICABLE"
+
+    NOT_MENTIONED = "NOT_MENTIONED"
+
+
+
+class MalnutritionObservations(ConfiguredBaseModel):
+
+    malnutrition_presence: Optional[bool] = Field(None)
+    severity: Optional[str] = Field(None)
+    diagnosis: Optional[str] = Field(None)
+
+
+class ExtractionResult(ConfiguredBaseModel):
+    """
+    A result of extracting knowledge on text
+    """
+    input_id: Optional[str] = Field(None)
+    input_title: Optional[str] = Field(None)
+    input_text: Optional[str] = Field(None)
+    raw_completion_output: Optional[str] = Field(None)
+    prompt: Optional[str] = Field(None)
+    extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""")
+    named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""")
+
+
+class NamedEntity(ConfiguredBaseModel):
+
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class ClinicalObservationSet(NamedEntity):
+
+    observations: Optional[List[str]] = Field(default_factory=list)
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class ClinicalObservations(NamedEntity):
+
+    is_pediatric: Optional[bool] = Field(None)
+    patient_height: Optional[QuantitativeValue] = Field(None)
+    patient_weight: Optional[QuantitativeValue] = Field(None)
+    malnutrition_status: Optional[MalnutritionObservations] = Field(None)
+    diet_supplementation: Optional[List[str]] = Field(default_factory=list)
+    nutrition_support: Optional[List[str]] = Field(default_factory=list)
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class DietSupplementation(NamedEntity):
+
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class NutritionSupport(NamedEntity):
+
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class Disease(NamedEntity):
+
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class Unit(NamedEntity):
+
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class CompoundExpression(ConfiguredBaseModel):
+
+    None
+
+
+class QuantitativeValue(CompoundExpression):
+
+    value: Optional[str] = Field(None, description="""the value of the quantity""")
+    unit: Optional[str] = Field(None, description="""the unit of the quantity, e.g. grams, cups, etc.""")
+
+
+class Triple(CompoundExpression):
+    """
+    Abstract parent for Relation Extraction tasks
+    """
+    subject: Optional[str] = Field(None)
+    predicate: Optional[str] = Field(None)
+    object: Optional[str] = Field(None)
+    qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""")
+    subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""")
+    object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""")
+
+
+class TextWithTriples(ConfiguredBaseModel):
+    """
+    A text containing one or more relations of the Triple type.
+    """
+    publication: Optional[Publication] = Field(None)
+    triples: Optional[List[Triple]] = Field(default_factory=list)
+
+
+class TextWithEntity(ConfiguredBaseModel):
+    """
+    A text containing one or more instances of a single type of entity.
+    """
+    publication: Optional[Publication] = Field(None)
+    entities: Optional[List[str]] = Field(default_factory=list)
+
+
+class RelationshipType(NamedEntity):
+
+    id: str = Field(..., description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+class Publication(ConfiguredBaseModel):
+
+    id: Optional[str] = Field(None, description="""The publication identifier""")
+    title: Optional[str] = Field(None, description="""The title of the publication""")
+    abstract: Optional[str] = Field(None, description="""The abstract of the publication""")
+    combined_text: Optional[str] = Field(None)
+    full_text: Optional[str] = Field(None, description="""The full text of the publication""")
+
+
+class AnnotatorResult(ConfiguredBaseModel):
+
+    subject_text: Optional[str] = Field(None)
+    object_id: Optional[str] = Field(None)
+    object_text: Optional[str] = Field(None)
+
+
+
+# Model rebuild
+# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model
+MalnutritionObservations.model_rebuild()
+ExtractionResult.model_rebuild()
+NamedEntity.model_rebuild()
+ClinicalObservationSet.model_rebuild()
+ClinicalObservations.model_rebuild()
+DietSupplementation.model_rebuild()
+NutritionSupport.model_rebuild()
+Disease.model_rebuild()
+Unit.model_rebuild()
+CompoundExpression.model_rebuild()
+QuantitativeValue.model_rebuild()
+Triple.model_rebuild()
+TextWithTriples.model_rebuild()
+TextWithEntity.model_rebuild()
+RelationshipType.model_rebuild()
+Publication.model_rebuild()
+AnnotatorResult.model_rebuild()
+

src/ontogpt/templates/dietician_notes.yaml

@@ -26,6 +26,7 @@ classes:
         multivalued: true
 
   ClinicalObservations:
+    is_a: NamedEntity
     attributes:
       is_pediatric:
         range: boolean
@@ -70,15 +71,15 @@ classes:
 
   # TODO: consider MAXO terms; children of MAXO:0000009
   DietSupplementation:
-    is_a: NamedThing
+    is_a: NamedEntity
     id_prefixes:
       - FOODON
     annotations:
       annotators: sqlite:obo:foodon
 
   # TODO: consider MAXO terms; children of MAXO:0000009
   NutritionSupport:
-    is_a: NamedThing
+    is_a: NamedEntity
     id_prefixes:
       - MAXO
     annotations: