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The Virtual Patient Metaphor:Lessons Learned And Roads To Go
Martin HofmannHead of the Department of BioinformaticsFraunhofer Institute for Algorithms and Scientific Computing (SCAI)and Professor for Applied Life Science InformaticsBonn-Aachen International Center for Information Technology (BFriedrich-Wilhelms-University of Bonn
Infinity Initiative #2; BioApril 2 – 3; Sophia Antipolis, France
The Virtual Patient Metaphor:Lessons Learned And Roads To Go
Martin Hofmann -ApitiusHead of the Department of BioinformaticsFraunhofer Institute for Algorithms and Scientific Computing (SCAI)
Professor for Applied Life Science InformaticsAachen International Center for Information Technology (B-IT)
University of Bonn
Infinity Initiative #2; Bio-ICT: The Heart in the Computer, 3; Sophia Antipolis, France
What is the “Virtual Patient Metaphor” ?
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What is the “Virtual Patient Metaphor” ?
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What is the “Virtual Patient Metaphor” ?
The “virtual patient metaphor” (VPM) is a concept for the representation of all
relevant clinical data required for personalized modelling and simulation of health
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relevant clinical data required for personalized modelling and simulation of health
conditions.
The VPM therefore provides the basis for
individualized clinical decision support
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What is the “Virtual Patient Metaphor” ?
The “virtual patient metaphor” (VPM) is a concept for the representation of all
relevant clinical data required for personalized modelling and simulation of health relevant clinical data required for personalized modelling and simulation of health
The VPM therefore provides the basis for case-based reasoning and subsequently
Seite 3
Other Names for the VPM
VPM concepts have been developed in several projects and communities. The HL
7 community has recently started a HL-7 project on the vMR, the “virtual medical
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7 community has recently started a HL-7 project on the vMR, the “virtual medical
record”. However, the vMR idea as such goes even back to the end of the 1990s.
At the conceptual level, VPM and vMR are almost identical approaches, however,
they differ with respect to the granularity of the underlying information models.
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Other Names for the VPM
VPM concepts have been developed in several projects and communities. The HL-
7 project on the vMR, the “virtual medical 7 project on the vMR, the “virtual medical
record”. However, the vMR idea as such goes even back to the end of the 1990s.
At the conceptual level, VPM and vMR are almost identical approaches, however,
they differ with respect to the granularity of the underlying information models.
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What Prompted us to Develop the VPM Concept?
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What Prompted us to Develop the VPM Concept?
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The @neurIST ProjectIn EU Integrated Project @neurIST we aim at developing
an IT system that
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•captures all patient data relevant for disease modelling
•provides all input needed for personalized risk
assessment
•supports clinical decision making
•ultimately integrates in a disease model all relevant
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scales, from the molecule level (individual risk based on
allelic variation) via the tissue and organ level
(individualized hemodynamic simulation) to the population
level (epidemiology)
In EU Integrated Project @neurIST we aim at developing
aptures all patient data relevant for disease modelling
rovides all input needed for personalized risk
ltimately integrates in a disease model all relevant
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scales, from the molecule level (individual risk based on
(individualized hemodynamic simulation) to the population
Can we achieve appropriate input conditions for all patients?
Vascular
example: haemodynamical simulation
Input boundary conditions
X
Image acquisition
Vascular model
Input boundary conditions Blood flow and pressure waveforms,
haematocrit, etc…
IA Patient
Can we achieve appropriate input conditions for all
Vascular
Flowpatters
Wall ShearStress
Input boundary conditions
Vascular model Haemodynamic
characterization
7
StressInput boundary conditions
Blood flow and pressure waveforms, haematocrit, etc…
?
Preliminary sensitivity analysisimpact of image modality and inflow rate conditions
CTA image
Flow waveform Patient 1
Model 1
IA Patient 2(no flow waveform)
3DRA image
Flow waveform Patient 3
Model 2
Preliminary sensitivity analysisimpact of image modality and inflow rate conditions
Is the observed range of
WSS2
WSS1
Is the observed range of variability realistic?
Image
8
WSS3
WSS2
Inflow
The Virtual Patient Metaphor (VPM) Concept
A virtual patient is a logical entity that can be queried for any and all information about a human being
The Virtual Patient Metaphor (VPM) Concept
A virtual patient is a logical entity that can be queried for any and all information about a human being
9
The Virtual Patient Metaphor
E
A
Y
B
Z
C D
@neurIST database
Virtual Patient
LiteratureComputed data
The Virtual Patient Metaphor
X
Average & deviationsinput conditions
Input requirements
+ Age, sex,
phenotype, genotype, etc…
10
Virtual Patient IA Patient(Flow waveforms,
pressure, haematocrit, etc… )
Representation of the VPM
• The VPM could be organised as a multi
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comprising all major data categories
• Two major challenges:
• Data model for the VPM
• Populating the VPM with data
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VPM
he VPM could be organised as a multi-dimensional “data cube”
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A Possible Implementation Template for the VPM
• In the course of EU project „Health-e-Child“, a flexible, expandable and scaling
implementation data model for patient data has been developed
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implementation data model for patient data has been developed
• Due to its design it is well suited to serve as an implementation model for the
VPM, but of course other approaches (e.g. the openEHR model) could also be
adapted to the task of representing the VPM
• The following slides give an idea about the overall design of the HeC patient
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data implementation model
A Possible Implementation Template for the VPM
Child“, a flexible, expandable and scaling
implementation data model for patient data has been developedimplementation data model for patient data has been developed
Due to its design it is well suited to serve as an implementation model for the
VPM, but of course other approaches (e.g. the openEHR model) could also be
adapted to the task of representing the VPM
The following slides give an idea about the overall design of the HeC patient
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HeC Integrated Data Model
• Data• ensures that all information all information • ensures that all information all information
storedstored and reused• Metadata
• ensures the abstractionabstraction required to integrate pieces of data into a coherent whole
• defines sufficient description of data description of data properly interpreted and compared
• primary means for data creation and access means for data creation and access can be stored and queried can be stored and queried
• Semantics• ensures that a formal semantics formal semantics
capturedcaptured• facilitates the semantic coherence semantic coherence • links to related concepts related concepts in a globally unambiguous way
HeC Integrated Data Model
all information all information recorded can be can be all information all information recorded can be can be
required to integrate pieces of data into a
description of data description of data elements so that they can be properly interpreted and compared
means for data creation and access means for data creation and access (describes how data can be stored and queried can be stored and queried
formal semantics formal semantics associated with data is properly
semantic coherence semantic coherence of the integrated datain a globally unambiguous way
HeC IDM: High- Level OverviewLevel Overview
HeC IDM: main entities
Measurement
Visit
Patient
Medical Event
Clinical Variable
DICOMImage
DICOMSeries
Classification
ExternalResource
Annotation
Measurement
Medical ConceptRelated CV
HeC IDM: main entities
Medical Event TypeMeasurement
Metadata
Clinical Variable Type
Medical Event Type
DICOMImage
DICOMSeries
Classification
ExternalResource
Annotation
Measurement
ClassificationDesc
ResourceDesc
Unit
Data Semantics
Medical Concept
Medical Concept
...
Data: Patient Hierarchy• Patient
• Gender, Demographics• Relatives, Family history
• Visit• Visit• Grouping / Context• Versioning
• Medical Event• Single examination, diagnosing,
treatment• Defined by metadata.
• Clinical Variable• Single typed atom of data• Defined by metadata
• Measurement• Pair (Number, Unit)• Pair (Number, Unit)
• Heart rate, blood pressure• Annotation
• Text• Comments, free text
• External Resource• Identified by URI
• Files on Grid (LFN), web links (URL)
Data: Patient Hierarchy
• Classification• Enumerations
• Tumour grades, severity scales, Yes/No/NA
• MedicalConceptInstance• Semantic concept
• Diagnosis, Drug treatments, • Diagnosis, Drug treatments, Symptoms & signs
• DICOMImage• extracted DICOM metadata
• DICOMSeries• group of DICOM images
• DICOM series, DICOM temporal series
• Others (e.g. genetics)
The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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The VPM as a Bayesian Model
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Types of Data for Populating the VPM
E
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E
A
@neurIST database
= clinical data
Computed Data
= derived data
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= clinical data= derived data
Types of Data for Populating the VPM
Y ZY
B
Z
C D
@neurIST database
= clinical data
Literature
= processed data
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= clinical data = processed data
Availability of Data for Populating the VPM
• Need for clinical data access, either via a central clinical data repository
(hosted by a European Medical Informatics Institute ?) or through
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(hosted by a European Medical Informatics Institute ?) or through
intelligent ways to access pseudonymized clinical data hosted locally
• Derived data (e.g. shape indices; flow field simulations) should also be
made available in an ordered way
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• Can literature – based knowledge be used to populate the VPM ?
Availability of Data for Populating the VPM
eed for clinical data access, either via a central clinical data repository
(hosted by a European Medical Informatics Institute ?) or through (hosted by a European Medical Informatics Institute ?) or through
intelligent ways to access pseudonymized clinical data hosted locally
erived data (e.g. shape indices; flow field simulations) should also be
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based knowledge be used to populate the VPM ?
Live Demo of @neuLink (if possible)
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Live Demo of @neuLink (if possible)
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Knowledge Extraction from Literature
• The following slides illustrate the capability of text mining technology
currently available for retrieval and extraction of knowledge associated
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currently available for retrieval and extraction of knowledge associated
e.g. with diseases from text
• Some of the technology shown here has been developed in the course
of EU project @neurIST
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Knowledge Extraction from Literature
The following slides illustrate the capability of text mining technology
currently available for retrieval and extraction of knowledge associated currently available for retrieval and extraction of knowledge associated
of the technology shown here has been developed in the course
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Retrieval of Literature Dealing with Simulation in
the Context of “Heart” Biology
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Retrieval of Literature Dealing with Simulation in
the Context of “Heart” Biology
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Semantic Search of Literature Dealing with
Hemodynamic Simulation Context
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Semantic Search of Literature Dealing with
Hemodynamic Simulation Context
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Knowledge Extraction of Drugs Used in the
Context of “Coronary Heart Disease”
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Knowledge Extraction of Drugs Used in the
Context of “Coronary Heart Disease”
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Knowledge Extraction of Odd Ratios Mentioned
in the Literature in th e Context of “Stroke”
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Knowledge Extraction of Odd Ratios Mentioned
e Context of “Stroke”
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Summary & Conclusion• The VPM is a concept that – if implemented
for “case-based reasoning“ and “individualized risk assessment”
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• The VPM will require substantial effort in modelling a “data cube”
representing all data relevant for personalized medicine
• The VPM will face the challenge of populating the data model with
relevant information.
• Automated information extraction from both, literature and clinical
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n • Automated information extraction from both, literature and clinical
records (which are essentially unstructured information) will be key
if implemented - will provide an ideal basis
based reasoning“ and “individualized risk assessment”
The VPM will require substantial effort in modelling a “data cube”
representing all data relevant for personalized medicine
The VPM will face the challenge of populating the data model with
Automated information extraction from both, literature and clinical
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Automated information extraction from both, literature and clinical
records (which are essentially unstructured information) will be key
Acknowledgement
The entire @neurIST consortium
• Alex Frangi (UPF)
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• Alex Frangi (UPF)• Alessandro Radaelli (UPF)• Rod Hose (Sheffield)• Christoph Friedrich (SCAI)• Robert Dunlop (InferMed)• Baldo Oliva (IMIM)
@neurISTContract number
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n Contract numberIST-2004-027703
From the Health-e-Child consortium
• Jörg Freund (Siemens)• Jörg Freund (Siemens)• Martin Huber (Siemens)• David Manset (Maat G)• Tamas Hauer (CERN; UWE)
Health-e-ChildContract number
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Contract number IST –027749”
