Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Structured Representation of Disorders of the Newborn Infant

Andrew James MBChB MBI

The Hospital for Sick Children, Toronto

Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Canadian Neonatal Network . . . Enables and promotes evidence-based intensive care in all neonatal intensive care units within Canada

Clinical, epidemiological, outcome and health services research aimed at improving both the efficacy and efficiency of neonatal care

ICD-9-CM for the representation of disorders of the newborn infant

Canada Health Infoway: SNOMED CT as pan-Canadian standard [ICD-10 also].

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Disorders of the newborn infant . . .

Perinatal events [labour and delivery, postnatal transition to extrauterine environment]

Immaturity

Respiratory disorders

Jaundice

Infection

Low birth weight [preterm infant, small mature infant ]

Congenital malformations

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Representation of Disorders . . .

Aetiology

Pathology [abnormal morphology, location]

Pathophysiology [disturbance of biological process, abnormal function]

Clinical features [symptoms, signs]

Investigations [laboratory, imaging, other . . . ]

Natural history [duration, progression …]

Interventions [physical, pharmacological, biological, behavioural . . . ]

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Challenges for representation . . .

Origin in embryonic, fetal, perinatal or neonatal period

Transient disturbances of function

Predisposition to a disorder

Outcome of a disorder that no longer exists

Resolution of disorder but persistence of consequences into infancy, childhood, and beyond

Congenital malformations may not be detectable

Genetically determined conditions asymptomatic

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Representation by SNOMED CT . . .

Systematic examination of SNOMED CT July 2006 release to determine whether 434 terms for disorders of the newborn infant are represented SNOMED CT

Complete representation 90.8%

Partial representation 6.4%

No representation 2.8%

Nearly 40% fully defined, nearly 50% have synonyms

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Respiratory distress . . . Commonest presenting problem in neonatal period

Constellation of respiratory signs

• tachypnoea

• grunting

• chest wall indrawing [subcostal, intercostal . . .]

• cyanosis

Abnormal CXR

Respiratory distress syndrome . . . three distinct causes

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Respiratory distress . . . Primary surfactant deficiency

Developmental, functional disorder associated with immaturity

Genetically determined disorder

Secondary surfactant deficiency

Inhibition of surfactant function by protein [albumin, meconium and blood]

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009 9

SCT’s representation of RDS . . .

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009 10

Ontological anomalies . . .

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Temporal environment . . .

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

The neonatal periods . . .

LateEarly

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009 13

The root anomaly . . .

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

RefSet for Respiratory Disorders Three neonatologists identified 348 candidate disorders for inclusion in a RefSet for structured representation of respiratory disorders of the newborn infant

Criteria for inclusion included congenital, perinatal and neonatal disorders

348 candidate respiratory conditions288 terms selected for inclusion in the RefSet (83%)

57% terms were congenital 27% terms were general terms

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

RefSet for Respiratory Disorders

46% terms fully defined, 33% have synonyms

Long tail phenomenon

9% of these terms used at least once per month23% used at least once per six months60% used less than once per year

74% of the infrequently used terms were terms for therepresentation of congenital disorders of the respiratory system

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Emphasis upon function . . .

Abnormal

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

Functional perspective . . .

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

RDS: Structural perspective . . .

is_a disorder of the alveolus

is_a disorder of the lung

is_a disorder of the lower respiratory system

is_a disorder of the respiratory system

is_a disorder

is_a finding

Signs, Symptoms and Findings: Towards an Ontology for Clinical Phenotypes Milan, September 4-5, 2009

RDS: Functional perspective . . .

is_a disorder of surfactant function

is_a disorder of stability of the alveolus

is_a disorder of alveolar function

is_a disorder of pulmonary gas exchange

is_a disorder of the respiratory system

is_a disorder

is_a finding