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 |
---|---|