Add medical action extraction template (#208)

src/ontogpt/templates/maxo.py

@@ -0,0 +1,174 @@
+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, 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,
+                validate_assignment = True,
+                validate_default = True,
+                extra = 'forbid',
+                arbitrary_types_allowed = True,
+                use_enum_values = True):
+    pass
+
+
+class NullDataOptions(str, Enum):
+
+
+    UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION"
+
+    NOT_APPLICABLE = "NOT_APPLICABLE"
+
+    NOT_MENTIONED = "NOT_MENTIONED"
+
+
+
+class MaxoAnnotations(ConfiguredBaseModel):
+
+    action: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of medical actions.""")
+    disease: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of diseases.""")
+    symptom: Optional[List[str]] = Field(default_factory=list, description="""Semicolon-separated list of symptoms.""")
+    action_to_disease: Optional[List[ActionToDiseaseRelationship]] = Field(default_factory=list)
+    action_to_symptom: Optional[List[ActionToSymptomRelationship]] = Field(default_factory=list)
+
+
+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 Action(NamedEntity):
+    """
+    A clinically prescribed procedure, therapy, intervention, or recommendation.
+    """
+    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):
+    """
+    A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.
+    """
+    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 Symptom(NamedEntity):
+    """
+    A condition or phenotype resulting from an abnormal health state.
+    """
+    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 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 ActionToDiseaseRelationship(Triple):
+    """
+    A triple representing a relationship between a medical action  (A clinically prescribed procedure, therapy, intervention, or recommendation) and a disease, for example, radiation therapy TREATS cancer, or PET scan IS USED TO DIAGNOSE myocarditis.
+    """
+    subject: Optional[str] = Field(None)
+    predicate: Optional[str] = Field(None, description="""The relationship type, usually TREATS or IS USED TO DIAGNOSE""")
+    object: Optional[List[str]] = Field(default_factory=list)
+    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 medical action.""")
+    object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the disease.""")
+
+
+class ActionToSymptomRelationship(Triple):
+    """
+    A triple representing a relationship between a medical action  (A clinically prescribed procedure, therapy, intervention, or recommendation) and a symptom, for example, a chest X-ray IS USED TO DIAGNOSE pleural effusion.
+    """
+    subject: Optional[str] = Field(None)
+    predicate: Optional[str] = Field(None, description="""The relationship type, usually IS USED TO DIAGNOSE""")
+    object: Optional[List[str]] = Field(default_factory=list)
+    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 medical action.""")
+    object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the symptom.""")
+
+
+class TextWithTriples(ConfiguredBaseModel):
+
+    publication: Optional[Publication] = Field(None)
+    triples: Optional[List[Triple]] = 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
+MaxoAnnotations.model_rebuild()
+ExtractionResult.model_rebuild()
+NamedEntity.model_rebuild()
+Action.model_rebuild()
+Disease.model_rebuild()
+Symptom.model_rebuild()
+CompoundExpression.model_rebuild()
+Triple.model_rebuild()
+ActionToDiseaseRelationship.model_rebuild()
+ActionToSymptomRelationship.model_rebuild()
+TextWithTriples.model_rebuild()
+RelationshipType.model_rebuild()
+Publication.model_rebuild()
+AnnotatorResult.model_rebuild()
+

src/ontogpt/templates/maxo.yaml

@@ -0,0 +1,142 @@
+id: http://w3id.org/ontogpt/maxo
+name: maxo
+title: Template for Medical Action Extraction
+description: >-
+  A template for extracting relationships relevant to the
+  MAXO medical action ontology.
+license: https://creativecommons.org/publicdomain/zero/1.0/
+prefixes:
+  linkml: https://w3id.org/linkml/
+  maxo_extract: http://w3id.org/ontogpt/maxo
+  MAXO: http://purl.obolibrary.org/obo/MAXO_
+  MONDO: http://purl.obolibrary.org/obo/MONDO_
+  HP: http://purl.obolibrary.org/obo/HP_
+  RO: http://purl.obolibrary.org/obo/RO_
+  OBA: http://purl.obolibrary.org/obo/OBA_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  biolink: https://w3id.org/biolink/vocab/
+
+default_prefix: maxo_extract
+default_range: string
+
+imports:
+  - linkml:types
+  - core
+
+classes:
+
+  MaxoAnnotations:
+    tree_root: true
+    attributes:
+      action:
+        annotations:
+          prompt: >-
+            Semicolon-separated list of medical actions, where each is a
+            clinically prescribed procedure, therapy, intervention, or recommendation.
+        description: Semicolon-separated list of medical actions.
+        multivalued: true
+        range: Action
+      disease:
+        description: Semicolon-separated list of diseases.
+        multivalued: true
+        range: Disease
+      symptom:
+        description: Semicolon-separated list of symptoms.
+        multivalued: true
+        range: Symptom
+      action_to_disease:
+        annotations:
+          prompt: >-
+            Semicolon-separated list of medical action to disease relationships, where
+            each is a triple representing a relationship between a medical action 
+            and a disease, for example, radiation therapy TREATS cancer,
+            or PET scan IS USED TO DIAGNOSE myocarditis.
+        multivalued: true
+        range: ActionToDiseaseRelationship
+      action_to_symptom:
+        annotations:
+          prompt: >-
+            A triple representing a relationship between a medical action 
+            (A clinically prescribed procedure, therapy, intervention, or recommendation)
+            and a symptom, for example,
+            a chest X-ray IS USED TO DIAGNOSE pleural effusion.
+        multivalued: true
+        range: ActionToSymptomRelationship
+
+  ActionToDiseaseRelationship:
+    is_a: Triple
+    description: >- 
+      A triple representing a relationship between a medical action 
+      (A clinically prescribed procedure, therapy, intervention, or recommendation)
+      and a disease, for example, radiation therapy TREATS cancer,
+      or PET scan IS USED TO DIAGNOSE myocarditis.
+    slot_usage:
+      subject:
+        range: Action
+      object:
+        range: Disease
+        multivalued: true
+      predicate:
+        range: NamedEntity
+        description: The relationship type, usually TREATS or IS USED TO DIAGNOSE
+      subject_qualifier:
+        range: NamedEntity
+        description: >-
+          An optional qualifier or modifier for the medical action.
+      object_qualifier:
+        range: NamedEntity
+        description: >-
+          An optional qualifier or modifier for the disease.
+
+  ActionToSymptomRelationship:
+    is_a: Triple
+    description: >- 
+      A triple representing a relationship between a medical action 
+      (A clinically prescribed procedure, therapy, intervention, or recommendation)
+      and a symptom, for example,
+      a chest X-ray IS USED TO DIAGNOSE pleural effusion.
+    slot_usage:
+      subject:
+        range: Action
+      object:
+        range: Symptom
+        multivalued: true
+      predicate:
+        range: NamedEntity
+        description: The relationship type, usually IS USED TO DIAGNOSE
+      subject_qualifier:
+        range: NamedEntity
+        description: >-
+          An optional qualifier or modifier for the medical action.
+      object_qualifier:
+        range: NamedEntity
+        description: >-
+          An optional qualifier or modifier for the symptom.
+
+  Action:
+    is_a: NamedEntity
+    description: >-
+      A clinically prescribed procedure, therapy, intervention, or recommendation.
+    annotations:
+      annotators: sqlite:obo:maxo, sqlite:obo:ogms, sqlite:obo:ncit
+    id_prefixes:
+      - MAXO
+
+  Disease:
+    is_a: NamedEntity
+    description: >-
+      A disposition to undergo pathological processes that exists in an organism
+      because of one or more disorders in that organism.
+    annotations:
+      annotators: sqlite:obo:mondo
+    id_prefixes:
+      - MONDO
+
+  Symptom:
+    is_a: NamedEntity
+    description: >-
+      A condition or phenotype resulting from an abnormal health state.
+    annotations:
+      annotators: sqlite:obo:hp
+    id_prefixes:
+      - HP