The financial support of the European Commission is gratefully acknowledged. Material in this...
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The financial support of the European Commission is gratefully acknowledged. Material in this presentation reflects only the author’s views and the Commission is not liable for any use that may be made of the information Siegfried Benkner Institute of Scientific Computing University of Vienna, Austria for the Aneurist Consortium www.aneurist.org October 5, 2007
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Transcript of The financial support of the European Commission is gratefully acknowledged. Material in this...
The financial support of the European Commission is gratefully acknowledged. Material in this presentation reflects only the author’s views and the Commission is not liable for any use that may be made of the information contained herein.
Siegfried BenknerInstitute of Scientific Computing
University of Vienna, Austria
for the Aneurist Consortium
www.aneurist.org
October 5, 2007
@neurIST Copyright © 2007
2
EU Project @neurIST (2006-2009) IST-2004-027703
Development of a generic IT infrastructure for the management and processing of heterogeneous data associated with the diagnosis and treatment of cerebral aneurysms and subarachnoid haemorrhage.
Integrated Application Suites@neuRisk - personalised risk assessment
@neuEndo – virtual endovascular treatment planning & stent design
@neuLink - linking genetics to disease
@neuFuse - modeling, simulation & visualization of multimodal data
@neurIST service-oriented Grid infrastructure on-demand simulation and analysis services (semantic) data-integration services
handling multi-scale, multi-modal information at distributed sites.
http://www.aneurist.org
@neurIST Copyright © 2007
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Integrative Application Suites
Gen data
Personal data
Imaging data
@neuLink
@neuRisk
@neuFuse Genetic riskdatabases
@neuEndo
Epidemiologyknowledge
Patient
Pharma treatment
Modelling, simulationand analysis services
Modelling, simulationand analysis services
@neurIST Copyright © 2007
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@neurIST Grid Infrastructure
Storage Resources
BioISFilesDatabase
s
Compute Resources
AnalysisSimulatio
nModeling
Basic @neurIST Grid Layer (GEMSS2 / InnerGrid)
OGSA-DAIGDMSData TransferJob Execution
@neuInfo Services@neuCompute Services
@neurIST Client API
@neuFuseMultimodal
data processing&fusi
on
@neuEndoVirtual
endovascular treatment planning
@neuLinkLinking
genetics to disease
@neuRiskIntegrative rupture risk assesment
@neurIST Controller
Application Layer
Resource Layer
Middleware
Layer
Grid Middleware: GEMSS2, InnerGrid; Standard Web Services (WS-I) Data Integration: OGSA-DAI – WS-DAI; DQP; SQL Semantics: OWL, SPARQL
@neurIST Copyright © 2007
5
Data Integration
ApproachSemantic Data MediationFederation of ServicesCRIM, OntologySecurity, Pseudonymization, …
Hospital information systems Sheffield, Geneva, Rotterdam,… EHR, PACS, …
Public databases Genetic: EBI,NCBI Literature: Medline, etc.
Product design databases COTS stents, coils, etc.
ApplicationsUsers
PACS
PUBMED
PACS
Data Service
OGSA/DAI
GDMS
Data Service
OGSA/DAI
GDMS
Data Service
OGSA/DAI
GDMSPDD
EHR
EHR
EHR
@neurIST Copyright © 2007
6
Clinical Reference Information Model (CRIM) Defines all information to be captured for a patient
clinical information (imaging, diagnostic and treatment data, …)
administrative information
research results produced (indicators)
Biomedical data infostructure Two different architectures (see next slide)
Research ContextTreatment context
Federated
Biomedical
Info
Structure
Data CapturingImaging dataPatient record
Application SuitesProcessing &
Analysis
Distributedqueries
Knowledgediscovery
DenormalizationRe-identification
NormalizationDe-identification
Information
aquisition &
structuring
Information
access, analysis
& enrichment
@neurIST Copyright © 2007
7Geneva(OTF)
Sheffield(ANO) anoDB
XML/DICOM filesFiles
WS with SQL query
XML
WS with SQL queryXML
Hospital Intranet
Data formsEHR
PACS
IDDB
PACS EHR
Acquisition tool
IDDB
Private @neuInfoService
Public @neuInfoService
FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL
FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL FIREWAL
FIREWALL FIREWALL FIREWALL FIREWALL FIREWALL
Push mechanism
University network/DMZ
Public @neuInfoService
Inte
rnet
Data AcquisitionData StorageData Access
Hospital IntranetHospital DMZ
Logging
Filtering
Logging
Filtering
DICOM
DICOM
HL7SQL
DVDFTP
HTTP/XML
HTTP/XML
HTTP/XML
HTTP/XML
@neurIST Copyright © 2007
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@neurIST Ontology
Global conceptual schema of the disease
Conceptual spaceClinical Medicine
Molecular Biology
Epidemiology
Simulation
Disease
Risk factor
Incorporating “approved” existing ontologiesFMA - Foundational Model of Anatomy
GO - Gene Ontology
DOLCE as Upper Ontology
Concepts are mapped to Unified Medical Language System (UMLS)
OWL-DL
Lead partner: University of Freiburg
Classes
Relationship Types
Definitions UMLS Map
2139 85 1096 1183
@neurIST Copyright © 2007
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GDMS
DASDASDAS
Semantic Data Integration
SchemaSchema Schema
VirtualSchema
Mapping
Data
Access
Services
Data
Mediation
Services
Ontology
OGSA-DAI
annotation
@neurIST Copyright © 2007
10
Pseudonymisation Service
End-to-end security
Attribute-based access control (ABAC)
Certificate and Registration Authorities; Federated VO model
Security Token Service
Logging, Filtering Services
Auditing
Provenance
built on top of Web services security standards
@neurIST Security Architecture
@neurIST Copyright © 2007
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Contact
Project co-ordinator:Universitat Pompeu Fabra
Contact person:Dr.Alejandro FrangiTel: +34 93 542 14 51Fax: +34 93 542 25 17Email: [email protected]
WWW: http://www.aneurist.org
