Transcript OntoDiagram - School of Computing and Engineering

OntoDiagram
Ontology Based Diagram
Generation
Congenital Heart Defects in Pediatric Cardiology
Kartik Vishwanath, Venkatesh Viswanath,
Yugyung Lee, Ph.D
School of Computing and Engineering
University of Missouri—Kansas City
William Drake, MD
Children's’ Mercy Hospital—Kansas City
OntoDiagram
Application for pediatric cardiology that
generates Mullin’s like diagram based on domain
descriptions, clinical observations and
measurements
– Mullin’s Atlas—A collection of widely used
diagrammatic representation of anatomy of heart
structure (Mullins Diagram)
– Mullin’s Diagrams are useful in hospital reporting
tools as they efficiently represent the defects
– Given a description of heart by domain experts, the
system should automatically generate the Mullin’s
diagram representing the conditions as described
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Sample Mullin’s Diagrams
Pulmonary
Atresia
Tricuspid
Atresia
Complex
TOF
TAPVR
LSVC
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Why Generate Diagrams?
Comprehending textual
descriptions is time consuming!
Situs and Relations:
There is levocardia with visceral and atrial situs solitus, atrioventricular concordance (D-looped ventricles) and
normally related great arteries {S,D,S} noteVenous Connections:
There are normal systemic and pulmonary venous connections, with the superior and inferior vana cavae returning
normally to the right atrium, and all four pulmonary identified returning normally to the left atrium. noteAtria:
The left and right atria have normal chamber size, structure, and relations. noteAtrioventricular Valves:
The mitral and tricuspid valves have normal structure, size, placement and function. There is no mitral insufficiency
and only physiologic tricuspid insufficiency. noteVentricles:
There is normal left ventricular chamber size and normal subjective left ventricular funtion with flattened
interventricular septal motion. note There is normal right ventricular chamber size. note The right ventricle wall
thickness is moderately increased. note There is normal global left ventricular function. note There is flattened
interventricular septal motion. noteOutflow Tracts:
The left ventricular outflow tract has normal size and geometry, without stenosis or narrowing. note The right
ventricular outflow tract has moderate hypoplasia. note There is no subaortic conus. note There is marked right
ventricular outflow tract turbulence (stenosis). note The peak right ventricular outflow tract velocity is 4.1
meters/second. note The peak right ventricular outflow tract gradient is 67 mmHg. noteSemilunar Valves:
The aortic valve is normal, with three normal leaflets, normal mobility and no prolapse. note There is non-turbulent
flow and a normal flow velocity across the aortic valve with no evidence of stenosis. note There is marked
hypoplasia of the pulmonary valve annulus. note The pulmonary valve annulus measures 2.1 mm in the long axis
outflow view. note The peak velocity across the aortic valve is 1.3 meters/second. note The pulmonary valve leaflets
are moderately thickened. noteAortic Root Ascending Aorta:
The aortic root, including the sinuses of valsalva, sinotubular ridge, and proximal ascending aorta are normal without
stenosis, narrowing, or dilation. notePulmonary and Thoracic Arteries:
There was supravalvular pulmonary stenosis present. note There was hypoplasia of the main pulmonary artery. note
The left pulmonary artery appeared hypoplastic. note The right pulmonary artery appeared hypoplastic. note There
was a right-sided aortic arch present. note There was a patent ductus arteriosus visualized. note There was a rightsided patent ductus arteriosus present. note There was left-to-right shunting demonstrated across the patent
ductus arteriosus. note There was a right aortic arch with a retroesophageal segment and left descending aorta
forming a vascular ring. noteSeptal Defects:
There is a malalignment type ventricular septal defect present. note The ventricular septal defect measures 12 mm from
the apical four-chamber view. note There is a moderate degree of aortic override. Fibro-annular continuity of the
aortic and mitral valves is present. note The aorta has about 50 per cent override. note
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Diagram is easier to understand!
Complex
TOF
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Motivation
• Visual representation is intuitively easier to
understand than text information.
• Pediatric Cardiology faces new or variations of
heart defects
• Mullin’s atlas are comprehensive but not
complete
– Difficult to search and retrieve similar
diagrams
• Domain experts manually draw diagrams by
hand or modify existing ones in Mullin's atlas
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Patent Foramen Ovale
Right-left shunt
Coarctation
anterior
Domain World
Pulmonary Artery
True PA
Bifurcation of PA
Aortic stenosis
Normal Bicuspid valve
Parachute
Mitral Valve
PDA
Domain Experts’ Perspective
Overriding Aorta
Tricuspid
insufficiency
hypoplasia
Ontological Framework
Mitral valve cleft
Heterogeneity
of
Perspectives
above
below
transposition
Hidden behind
translation
translation
Diagram Perspective
Component sheared
Scaled along long axis
Diagram World
connections
missing
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Challenges
• Heart Structure—”simple & complex”
• Mapping domain knowledge onto diagram specifications
– Perspective and representational gap between medical
domain and diagram domain
• Domain Modeling
–
–
–
–
Modeling congenital defect information
Modeling anatomical structure
Implicit domain knowledge
Anatomical consequence of defects
• Diagram Modeling
– Individual component modeling
– Spatial orientation between components
– Transformations on components to reflect changes
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Heart Structure
“Simple & Complex”
Simple
• An anatomically simple structure
• Intuitively hierarchical “part-of” relationships (left
heart, right heart, etc.)
• Heart components are less in count
• Anatomically new additions are very less and
predictable
Complex
• Variations of each component are large
• Variations of heart as a whole are diverse
• Complex relationship between various anomalous
conditions
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Simple
Complex
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OntoDiagram: Focus
• Translation from domain description to diagram
OntoDiagram
Physician’s description
Diagram
• Key issues
– Domain modeling (Ontology approach)
– Diagram modeling (Component based approach)
– Mapping domain onto diagram (Domain rules)
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OntoDiagram Architecture
Congenital
Heart Defect
Ontology
Heart
Anatomy
Ontology
Measurement
Ontology
Domain Ontologies
Diagram
Ontology
Diagram Ontology
Mapping System
OntoDiagram
Query
Interface
Domain Rules
Diagram
repository
Databases
Medical
Medical
Database
Database
Diagram
Composer
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Walk through the System
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Ontologies
• An ontology is an explicit formal specification of the
terms in the domain and relations among them (Gruber
1993).
• To share common understanding of the domain
knowledge on congenital heart defects among
cardiologists, nurse, database engineer or software
agents
• To make domain assumptions explicit so that defect
associations patterns could be extracted
• To separate domain knowledge from operational
knowledge
• To map different perspectives of domain and diagram
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Domain Modeling
• Modularizing domain knowledge
– Congenital Heart Defect Ontology [UMLS]
• Classification of defects, anomalous conditions
• Definition for domain terms like stenosis, atresia, etc.
• Anatomical consequences of defects
• Association between defects
– Anatomy ontology [FMA]
• Multi-perspective classification of heart anatomy
• Possible anatomical changes in each heart component
• Orientation between components
– Measurement and Diagram Ontology [LOINC]
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Diagram Modeling
• Diagram Models
• Component Association Model (Spatial Orientation
between components)
• Structure Model (Component hierarchy)
• Conversion Model (Transformations)
• Annotation Model (Relevant annotations)
• Diagram perspective of changes
•
•
•
•
•
Abnormal growth
Missing parts
Transposition
Transformation
Combination
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Component Association Model
Spatial relations with components and their neighboring
components
•
Six-tuple {Ct, Cn, D, A, O, P} where
– Ct and Cn components, D—spatial orientation of Ct with respect to Cn,
A—interface presence, O—orientation, P—presence of component
e.g. {Descending Aorta, Aortic Arch, bottom, attached, below, present}
right
right
top
top
top
right
top
bottom
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Structure Model
• The heart is considered to be made of
two layers
• The first layer consisting of the
chambers of the heart (wall of atria
and ventricles)
• The second layer consists of the
other components of heart
(Pulmonary artery and Pulmonary
valves, Aorta and Aorta valves, etc.)
• The relationships between the first and
the second layer components
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Interface Points & Gate Points
Component—Component
Layer—Layer
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Conversion Model
• Transformation of components
• Geometric transformation (e.g., Scale, Rotate, Translate)
• Polynomial transformation (e.g., Shear)
• Domain specific transformation (e.g, dilation, coarctation)
• Transformation model defined as {CT,T, P}
• CT—component being transformed
• T—name of the transformation
• P—transformation parameters
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Hierarchical Composition
• Hierarchical
model— closer to
domain
perspective
• Faster diagram
generation—few
components
change
• Optimal selection
of components
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Hierarchical Composition Steps
Step 1: Configuration
1.
2.
3.
Identify an appropriate set of components and their
abstraction level to be composed [Congenital Defects and
Association models]
Determine the components to be transformed [Conversion
Model]
Determine the relationships between components (below,
above) [Component Structure Model]
Step 2: Composition
Starting from the most specific level to the root
1.
2.
3.
4.
Transform component images using the transformation
operations if necessary (scale, rotation, etc)
Rank the components [Image Model - Color Schema]
Compose the components using interface points [Structure
Model]
Forward the interface points to the upper level
Step 3: Annotation
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OntoDiagram
System
Ontological Framework
Congenital
Heart Defect
Ontology
Anatom
y
Ontolog
y
Domain
ontologies
Measurement
Ontology
Diagram Instruction Files
Mapping System
Domain
Description
Diagram
Ontology
Diagram
Composer
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OntoDiagram Prototype
• Constructed domain ontologies using the
protégé in OWL.
• Implemented the query interface in Java
using the Jena.
• Implemented the image composition
module using the Java Advanced Imaging
package.
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Sample Output
(Patent Ductus Arteriosus)
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Conclusion
• The domain descriptions of the congenital heart
defects are mapped to generate a diagrammatic
representation of defects.
– Ontology based domain modeling
– Component based diagram modeling
– Rule based mapping between domain and diagram
– Hierarchical composition of components
• A prototype system is currently under testing at
the Children’s Mercy Hospitals and Clinics
– facilitate existing treatments for managing patients
with severe heart disorders.
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