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 |
|---|---|