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Dietitian Notes Extraction Template

A template for extracting clinical observations from dietitian notes. Developed with guidance from Lauren Chan, PhD, RD and Alyson Lawrence, RD, CNSC

URI: http://w3id.org/ontogpt/dietician_notes

Name: dietitian_notes

Schema Diagram

erDiagram ClinicalObservations { string is_pediatric string is_preterm string nil_per_os string id string label } DrugTherapy { string route_of_administration } QuantitativeValue { string value } Unit { string id string label } QuantitativeValueWithFrequency { string frequency string value } Drug { string id string label } NutritionSupport { } NutritionSupportComponent { } TherapeuticMaterial { string id string label } NutritionSupportMethod { string id string label } DietSupplementation { string route_of_administration } MalnutritionObservations { string malnutrition_presence string malnutrition_risk string severity string acute_or_chronic string risk_for_refeeding_syndrome } Disease { string id string label } QuantitativeValueWithMetric { string percentile string zscore string value } ClinicalObservations ||--|o QuantitativeValue : "patient_age" ClinicalObservations ||--|o QuantitativeValueWithMetric : "patient_height" ClinicalObservations ||--|o QuantitativeValueWithMetric : "current_patient_weight" ClinicalObservations ||--|o QuantitativeValueWithMetric : "usual_patient_weight" ClinicalObservations ||--|o QuantitativeValueWithMetric : "head_circumference" ClinicalObservations ||--|o MalnutritionObservations : "malnutrition_status" ClinicalObservations ||--}o DietSupplementation : "diet_supplementation" ClinicalObservations ||--}o NutritionSupport : "nutrition_support" ClinicalObservations ||--}o DrugTherapy : "medications" DrugTherapy ||--|o Drug : "drug" DrugTherapy ||--|o QuantitativeValueWithFrequency : "amount" DrugTherapy ||--|o Unit : "dosage_by_unit" DrugTherapy ||--|o QuantitativeValue : "duration" QuantitativeValue ||--|o Unit : "unit" QuantitativeValueWithFrequency ||--|o Unit : "unit" NutritionSupport ||--|o NutritionSupportMethod : "method" NutritionSupport ||--}o NutritionSupportComponent : "components" NutritionSupportComponent ||--|o TherapeuticMaterial : "material" NutritionSupportComponent ||--|o QuantitativeValueWithFrequency : "amount" NutritionSupportComponent ||--|o Unit : "dosage_by_unit" NutritionSupportComponent ||--|o QuantitativeValue : "duration" DietSupplementation ||--|o TherapeuticMaterial : "supplement" DietSupplementation ||--|o QuantitativeValueWithFrequency : "amount" DietSupplementation ||--|o Unit : "dosage_by_unit" DietSupplementation ||--|o QuantitativeValue : "duration" MalnutritionObservations ||--|o Disease : "diagnosis" MalnutritionObservations ||--|o Disease : "etiology" QuantitativeValueWithMetric ||--|o Unit : "unit"

Classes

Class Description
AnnotatorResult None
Any None
ClinicalObservationSet A set of sets of clinical observations.
CompoundExpression None
        DietSupplementation None
        DrugTherapy None
        NutritionSupport None
        NutritionSupportComponent None
        QuantitativeValue None
                QuantitativeValueWithFrequency None
                QuantitativeValueWithMetric None
        Triple Abstract parent for Relation Extraction tasks
ExtractionResult A result of extracting knowledge on text
MalnutritionObservations None
NamedEntity None
        ClinicalObservations A set of clinical observations about a single patient at a single time.
        Disease None
        Drug None
        NutritionSupportMethod A method of nutrition support therapy used to treat or prevent malnutrition. This includes any method of feeding intended to replace or support oral feeding.
        RelationshipType None
        TherapeuticMaterial A specific material added to a patient's diet or included as part of a nutritional plan.
        Unit None
Publication None
TextWithEntity A text containing one or more instances of a single type of entity.
TextWithTriples A text containing one or more relations of the Triple type.

Slots

Slot Description
abstract The abstract of the publication
acute_or_chronic The duration of the patient's malnutrition, if present
amount The quantity or dosage of the therapy, if provided
combined_text
components The names of specific components included in a patient's diet
current_patient_weight
diagnosis The patient's malnutrition diagnosis, if present
diet_supplementation A semicolon-separated list of the patient's diet supplementation therapies
dosage_by_unit The unit of a patient's properties used to determine supplement dosage
drug The name of a specific drug for a patient's preventative or therapeutic treat...
duration The duration of the supplementation, if provided
entities
etiology The cause of the patient's malnutrition, if known
extracted_object The complex objects extracted from the text
frequency A phrase describing how often an event or procedure should happen
full_text The full text of the publication
head_circumference
id A unique identifier for the named entity
input_id
input_text
input_title
is_pediatric
is_preterm
label The label (name) of the named thing
malnutrition_presence True if the patient is malnourished, False otherwise
malnutrition_risk True if the patient has a demonstrable risk for malnutrition, False otherwise
malnutrition_status
material The name of a specific material included in a patient's diet
medications A semicolon-separated list of the patient's medications
method The name of a method used to provide nutritional support
named_entities Named entities extracted from the text
nil_per_os True if the patient is not receiving any oral nutrition, False otherwise
nutrition_support A semicolon-separated list of the patient's nutrition support therapies, usua...
object
object_id
object_qualifier An optional qualifier or modifier for the object of the statement, e
object_text
observations
patient_age
patient_height
percentile The reported percentile of the value, as compared to a reference patient popu...
predicate
prompt
publication
qualifier A qualifier for the statements, e
raw_completion_output
risk_for_refeeding_syndrome True if the patient is at risk for refeeding syndrome, False otherwise
route_of_administration The route of administration for the supplementation, if provided
severity The severity of the patient's malnutrition, if present
subject
subject_qualifier An optional qualifier or modifier for the subject of the statement, e
subject_text
supplement The name of a specific material added to a patient's diet
title The title of the publication
triples
unit The unit of the quantity, or N/A if not provided
usual_patient_weight
value The value of the quantity, or N/A if not provided
zscore The relative standard deviation of the value, as a function of the percentile

Enumerations

Enumeration Description
NullDataOptions

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE

Subsets

Subset Description