First draft of dietician notes extraction schema (#288)

src/ontogpt/templates/dietician_notes.py

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+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, field_validator
+import re
+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 ClinicalObservationSet(ConfiguredBaseModel):
+    """
+    A set of sets of clinical observations.
+    """
+    observations: Optional[List[str]] = Field(default_factory=list)
+
+
+
+class MalnutritionObservations(ConfiguredBaseModel):
+
+    malnutrition_presence: Optional[str] = Field(None, description="""True if the patient is malnourished, False otherwise.""")
+    severity: Optional[str] = Field(None, description="""The severity of the patient's malnutrition, if present.""")
+    diagnosis: Optional[str] = Field(None, description="""The patient's malnutrition diagnosis, if present.""")
+
+
+
+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 ClinicalObservations(NamedEntity):
+    """
+    A set of clinical observations about a single patient at a single time.
+    """
+    is_pediatric: Optional[str] = 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, description="""A semicolon-separated list of the patient's diet supplementation therapies.""")
+    nutrition_support: Optional[List[str]] = Field(default_factory=list, description="""A semicolon-separated list of the patient's nutrition support therapies, usually enteral or parenteral nutrition.""")
+    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):
+    """
+    A diet supplementation therapy.
+    """
+    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):
+    """
+    A nutrition support therapy used to treat or prevent malnutrition.
+    """
+    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[float] = Field(None, description="""The value of the quantity.""")
+    unit: Optional[str] = Field(None, description="""The unit of the quantity.""")
+
+
+
+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
+ClinicalObservationSet.model_rebuild()
+MalnutritionObservations.model_rebuild()
+ExtractionResult.model_rebuild()
+NamedEntity.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

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+id: http://w3id.org/ontogpt/dietician_notes
+name: dietician_notes
+title: Dietician Notes Extraction Template
+description: >-
+  A template for extracting clinical observations from dietician notes
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  linkml: https://w3id.org/linkml/
+  dietician_notes: http://w3id.org/ontogpt/dietician_notes
+  HP: http://purl.obolibrary.org/obo/HP_
+
+default_prefix: dietician_notes
+default_range: string
+
+imports:
+  - linkml:types
+  - core
+
+classes:
+  ClinicalObservationSet:
+    description: >-
+      A set of sets of clinical observations.
+    attributes:
+      observations:
+        range: ClinicalObservations
+        multivalued: true
+
+  ClinicalObservations:
+    tree_root: true
+    description: >-
+      A set of clinical observations about a single patient at a single time.
+    is_a: NamedEntity
+    attributes:
+      is_pediatric:
+        annotations:
+          prompt: >-
+            True if the patient is a child, False otherwise.
+        range: string
+      patient_height:
+        annotations:
+          prompt: >-
+            The value and units of the patient's height.
+        range: QuantitativeValue
+      patient_weight:
+        annotations:
+          prompt: >-
+            The value and units of the patient's weight.
+        range: QuantitativeValue
+      malnutrition_status:
+        annotations:
+          prompt: >-
+            Observations of the patient's malnutrition status.
+        range: MalnutritionObservations
+      diet_supplementation:
+        description: >-
+          A semicolon-separated list of the patient's diet supplementation
+          therapies.
+        range: DietSupplementation
+        multivalued: true
+      nutrition_support:
+        description: >-
+          A semicolon-separated list of the patient's nutrition support
+          therapies, usually enteral or parenteral nutrition.
+        range: NutritionSupport
+        multivalued: true
+
+  # TODO: Resolve validation errors if the values can't be parsed as floats
+  #       This may happen if no value is provided.
+  QuantitativeValue:
+    is_a: CompoundExpression
+    annotations:
+      owl: IntersectionOf
+    attributes:
+      value:
+        description: The value of the quantity.
+        range: float
+        annotations:
+          owl: DataProperty, DataHasValue
+      unit:
+        description: The unit of the quantity.
+        range: Unit
+        slot_uri: qudt:unit
+        annotations:
+          owl: ObjectProperty, ObjectSomeValuesFrom
+
+  MalnutritionObservations:
+    attributes:
+      malnutrition_presence:
+        description: True if the patient is malnourished, False otherwise.
+        range: string
+      severity:
+        description: >-
+          The severity of the patient's malnutrition, if present.
+        range: string
+      diagnosis:
+        description: >-
+          The patient's malnutrition diagnosis, if present.
+        range: Disease
+
+  # TODO: distinguish whether this is currently active therapy
+  #       or a reccomendation for future therapy (but not yet started)
+  DietSupplementation:
+    description: >-
+      A diet supplementation therapy.
+    is_a: NamedEntity
+    id_prefixes:
+      - FOODON
+      - MAXO
+    annotations:
+      annotators: "sqlite:obo:foodon, sqlite:obo:chebi, sqlite:obo:maxo"
+      prompt.examples: >-
+        single vitamin supplement, ginkgo biloba supplement,
+        multi-mineral supplement, biotin supplementation,
+        glucosamine supplement
+
+  # TODO: consider limiting to children of MAXO:0000009
+  #       or a more specific group of terms
+  NutritionSupport:
+    description: >-
+      A nutrition support therapy used to treat or prevent malnutrition.
+    is_a: NamedEntity
+    id_prefixes:
+      - MAXO
+    annotations:
+      annotators: sqlite:obo:maxo
+      prompt.examples: >-
+        enteral nutrition intake, gavage nutrition intake,
+        parenteral nutrition intake, partial parenteral nutrition intake
+
+  Disease:
+    is_a: NamedEntity
+    id_prefixes:
+      - MONDO
+    annotations:
+      annotators: sqlite:obo:mondo
+      prompt.examples: cardiac asystole, COVID-19, Headache, cancer
+
+  Unit:
+    is_a: NamedEntity
+    id_prefixes:
+      - UO
+      - NCIT
+      - dbpediaont
+    annotations:
+      annotators: sqlite:obo:uo, sqlite:obo:dbpediaont, sqlite:obo:foodon