Template for extraction of knowledge from literature to go into RNA KG

src/ontogpt/evaluation/rna_kg/abstract1.txt

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+Abstract
+One challenge in miRNA–genes–diseases interaction studies is that it is challenging to
+find labeled data that indicate a positive or negative relationship between miRNA and
+genes. The use of one-class classification methods shows a promising path for validating
+them. We have applied two one-class classification methods, Isolation Forest and
+One-class SVM, to validate miRNAs interactions with the ERBB2 gene present in breast
+cancer scenarios using features extracted via sequence-binding. We found that the
+One-class SVM outperforms the Isolation Forest model, with values of sensitivity of
+80.49% and a specificity of 86.49% showing results that are comparable to previous studies.
+Additionally, we have demonstrated that the use of features extracted from a
+sequence-based approach (considering miRNA and gene sequence binding characteristics)
+and one-class models have proven to be a feasible method for validating these genetic
+molecule interactions.

src/ontogpt/evaluation/rna_kg/abstract2.txt

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+MicroRNA (miRNA)–gene interactions are well-recognized as involved in the progression
+of almost all cancer types including prostate cancer, which is one of the most common
+cancers in men. This study explored the significantly dysregulated genes and miRNAs and
+elucidated the potential miRNA–gene regulatory network in prostate cancer. Integrative
+analysis of prostate cancer and normal prostate transcriptomic data in The Cancer Genome
+Atlas dataset was conducted using both differential expression analysis and weighted
+correlation network analysis (WGCNA). Thirteen genes (RRM2, ORC6, CDC45, CDKN2A, E2F2,
+MYBL2, CCNB2, PLK1, FOXM1, CDC25C, PKMYT1, GTSE1, and CDC20) were potentially
+correlated with prostate cancer based on functional enrichment analyses. MiRNAs
+targeting these genes were predicted and eight miRNAs were intersections between
+those miRNAs and the hub miRNAs obtained from miRNA WGCNA analysis. Three genes
+(E2F2, RRM2, and PKMYT1) and four miRNAs (hsa-mir-17-5p, hsa-mir-20a-5p, hsa-mir-92a-3p,
+and hsa-mir-93-5p) were key factors according to the interaction network. RRM2 and
+PKMYT1 were significantly related to survival. These findings partially elucidated
+the dysregulation of gene expressions in prostate cancer. Efficient manipulations of
+the miRNA–gene interactions in prostate cancer may be exploited as promising therapeutics.

src/ontogpt/templates/composite_disease.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, Literal
+from pydantic import BaseModel as BaseModel, Field
+from linkml_runtime.linkml_model import Decimal
+
+metamodel_version = "None"
+version = "None"
+
+class WeakRefShimBaseModel(BaseModel):
+   __slots__ = '__weakref__'
+
+class ConfiguredBaseModel(WeakRefShimBaseModel,
+                validate_assignment = True, 
+                validate_all = True, 
+                underscore_attrs_are_private = True, 
+                extra = 'forbid', 
+                arbitrary_types_allowed = True):
+    pass                    
+
+
+class NCITDrugType(str, Enum):
+
+
+    dummy = "dummy"
+
+
+class NCITTreatmentType(str, Enum):
+
+
+    dummy = "dummy"
+
+
+class NCITTActivityType(str, Enum):
+
+
+    dummy = "dummy"
+
+
+class MAXOActionType(str, Enum):
+
+
+    dummy = "dummy"
+
+
+class MESHTherapeuticType(str, Enum):
+
+
+    dummy = "dummy"
+
+
+class CHEBIDrugType(str, Enum):
+
+
+    dummy = "dummy"
+
+
+class NullDataOptions(str, Enum):
+
+    UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION"
+    NOT_APPLICABLE = "NOT_APPLICABLE"
+    NOT_MENTIONED = "NOT_MENTIONED"
+
+
+
+class CompositeDisease(ConfiguredBaseModel):
+
+    main_disease: Optional[str] = Field(None, description="""the name of the disease that is treated.""")
+    drugs: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of named small molecule drugs""")
+    treatments: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of therapies and treatments are indicated for treating the disease.""")
+    contraindications: Optional[List[str]] = Field(default_factory=list, description="""semicolon-separated list of therapies and treatments that are contra-indicated for the disease, and should not be used, due to risk of adverse effects.""")
+    treatment_mechanisms: Optional[List[TreatmentMechanism]] = Field(default_factory=list, description="""semicolon-separated list of treatment to asterisk-separated mechanism associations""")
+    treatment_efficacies: Optional[List[TreatmentEfficacy]] = Field(default_factory=list, description="""semicolon-separated list of treatment to efficacy associations, e.g. Imatinib*effective""")
+    treatment_adverse_effects: Optional[List[TreatmentAdverseEffect]] = Field(default_factory=list, description="""semicolon-separated list of treatment to adverse effect associations, e.g. Imatinib*nausea""")
+
+
+
+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: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+
+class Gene(NamedEntity):
+
+    id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+
+class Symptom(NamedEntity):
+
+    id: Optional[str] = Field(None, 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: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+
+class AdverseEffect(NamedEntity):
+
+    id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+
+class Treatment(NamedEntity):
+
+    id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+
+class Mechanism(NamedEntity):
+
+    id: Optional[str] = Field(None, description="""A unique identifier for the named entity""")
+    label: Optional[str] = Field(None, description="""The label (name) of the named thing""")
+
+
+
+class Drug(NamedEntity):
+
+    id: Optional[str] = Field(None, 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 TreatmentMechanism(CompoundExpression):
+
+    treatment: Optional[str] = Field(None)
+    mechanism: Optional[str] = Field(None)
+
+
+
+class TreatmentAdverseEffect(CompoundExpression):
+
+    treatment: Optional[str] = Field(None)
+    adverse_effects: Optional[List[str]] = Field(default_factory=list)
+
+
+
+class TreatmentEfficacy(CompoundExpression):
+
+    treatment: Optional[str] = Field(None)
+    efficacy: Optional[str] = Field(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 TextWithTriples(ConfiguredBaseModel):
+
+    publication: Optional[Publication] = Field(None)
+    triples: Optional[List[Triple]] = Field(default_factory=list)
+
+
+
+class RelationshipType(NamedEntity):
+
+    id: Optional[str] = Field(None, 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)
+
+
+
+
+# Update forward refs
+# see https://pydantic-docs.helpmanual.io/usage/postponed_annotations/
+CompositeDisease.update_forward_refs()
+ExtractionResult.update_forward_refs()
+NamedEntity.update_forward_refs()
+Gene.update_forward_refs()
+Symptom.update_forward_refs()
+Disease.update_forward_refs()
+AdverseEffect.update_forward_refs()
+Treatment.update_forward_refs()
+Mechanism.update_forward_refs()
+Drug.update_forward_refs()
+CompoundExpression.update_forward_refs()
+TreatmentMechanism.update_forward_refs()
+TreatmentAdverseEffect.update_forward_refs()
+TreatmentEfficacy.update_forward_refs()
+Triple.update_forward_refs()
+TextWithTriples.update_forward_refs()
+RelationshipType.update_forward_refs()
+Publication.update_forward_refs()
+AnnotatorResult.update_forward_refs()
+