Faustin Laurentiu Roman, Daniel Abler, Vassiliki KanellopoulosCERN
IFIC, Univ. of Oxford, Univ. of [email protected]
HISP: a data-driven portal for hadron therapy
EGI User Forum, Vilnius, 11.04.2011, [email protected]
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Content
• Introduction
• Reporting side effects
• Conditions
• HISP Proposal
• Architecture
• Prototype implementation
• Technology
• Outlook
EGI User Forum, Vilnius, 11.04.2011, [email protected]
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PARTNER
Marie Curie Initial Training Network
• funded by EC
• 25 researchers
• 12 European institutions
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Particle Training Network for European Radiotherapy
Multidisciplinary training to create the next generation of hadron therapy experts
Hadron Therapy
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• A highly advanced technique of cancer radiotherapy
• Uses beams of protons of ions, instead of conventional X-rays
DIAGNOSTIC
RESEARCH
FOLLOW-UP
TREATMENT
REFERRAL
INITIAL TREATMENT
DISCOVER
TRAINING
Hospital1
Hospital2
(HT centre)
Hospital1
Research centre
Hospital2
Patient at home
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Scenario
Domain challenges
Hospital Information Systems (HIS)• unusual to be linked (except if parts of a single entity)• undesirable to central storage/local copy• few systems offer opportunity for the patient to input data
Standard interfaces to access clinical data• no standard method for aggregating clinical information for patients treated in multiple institutions
Access rights to clinical data is strongly controlled• varying local policies for user authentication and audit trails• research data: vary between countries/institutions.
Data ownership model different in different countries• legal and ethical policies
• property of a central state healthcare system• property of the hospital
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Project challenges
Get real data and access to systems!!!• difficult since facilities just started• similar data proved difficult to extract from cancer registries
Decision• confine platform to side effects scenario• generate data based on published clinical studies from EU and US• emulate hospital systems in traditional RDBMS• concentrate on patient and tumor characteristics rather than images
Focus• test key functionalities• be useful for research
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Reporting side effects
Why• part of treatment quality assurance• effects of specific therapies in clinical trials• Research strategies for prevention
How• Scoring systems• differ in in type, modality, grades…
• recording in multiple locations• over many years
What• Doctors and patient report side effects• Doctors can view a record of the patient’s side effects across institutions.• Researchers can request access to statistical information
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Proposal
GOAL: unified patient record over heterogeneous resources and distributed treatment centers
• Data remains in each hospital
• Data federation is used to link information
• Meaning described using a semantic framework
• Secure access for all actors (MD, researcher, patient)
• Intuitive forms record follow-up information
STORAGE
DATA
INFO
KNOWLEDGE
USERS
Hadron therapy Information Sharing Prototype (HISP):A data-driven portal for hadron therapy
EGI User Forum, Vilnius, 11.04.2011, [email protected]
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Architecture
DB 1
Hospital 1
Hospital 1 data sources
HIS, PACS, TPS …
Patient DB
Portal
Virtual DBUSER
DB 2
Hospital 2 data sources
HIS, PACS, TPS …
Medical
requirement
Hospital 2
Schema/Semantic Mapping
HISP
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Data model
SIDE EFFECTS
TREATMENT
TUMOR
PATIENT INFO
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Data Reporting
Data recording forms for • Doctors -> based on typical scoring systems• Patients -> based on “Patient reported outcome measures” (PROM)
Functionalities:
• “Data-aware”: reusing data elements
• Input validation
• Choice of reporting standard left to medical doctor.
• Support for data entry by generating form that only presents the most likely reporting options for a specific patient
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Portal structure (roles)
Patient DB
Hospital DB1
Doctor
in H1
Patient
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Hospital 2
DB2MySQL
HIS, TPS
Implementation
Hospital 1
Liferay
VDB ViewTeiid
USER HISP
What Liferay OpenXava Teiid MySQL Vine toolkit VOMS
Why Open Source Standard Free Enterpriseready or compatible
DB1MySQL
HIS, TPS
Federation and Semantic Mapping
Patient DBMySQL
AuthN&Z
Patient workspace
Doctor workspace
Researcher workspace
VOMS
Vine TK
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Alternatives: Gridsphere, Genius Portal, amgaNavigator, etc…
(grid specific)
Liferay www.liferay.com
• enterprise web platform, free and open source
• user management, content management, lucene-based search
• standards: AJAX, JSR-168, JSR-286 (Portlet 2.0), JSF-314 (JSF 2.0)
Experience
• easy to install and maintain but heavy on resources (Tomcat…)
• good documentation
• far too many features by default (is not a –)
• works with Vine Toolkit (see dedicated slide)
Portal
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Java MVC, Spring, Hibernate works but slow for non-experts…
OpenXava http://openxava.org/web/guest/credits
• RIA framework to develop JavaEE/J2EE applications
• Liferay compatible
• Eclipse, ant based
• CRUD interface
• Fast development
• Fast customization
• Good docs and tutorials
UI
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Vine Toolkit vinetoolkit.org
• software framework to create Grid-aware web applications
– web application based on Flex technologies
– add Grid context to the web components
– abstract different middlewares implementation
• Link Liferay portal to VOMS: https://voms.ific.uv.es:8443/voms/vo.partner.eu/
• Use VOMS for authentication and authorization
Experience
• still buggy but good support (thanks to Piotr Dziubecki!)
• more documentation and tutorials needed
• General GSI challenges
– Grid certificate generation
– Synchronization of portal/grid roles and privileges
Grid and Security
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Database federation
Database federation = access to heterogeneous repositories while leaving data where it was created and not copying it centrally (data warehousing)
Jboss Teiid http://www.jboss.org/teiid/
• Open source, free
• Connectors to RDBMS, files, WS
• JDBC driver
• Teiid designer
Experience
• Good docs and tutorial
• Easy installation
• Designer slow on large models
• Issues on data types casting
• Data sources have to be up and synchronized to VDB otherwise DB inactive
EGI User Forum, Vilnius, 11.04.2011, [email protected]
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Overview
Present status:first steps towards a prototype data-driven collaborative portal
Next steps:• Data integration between resources and portal• Domain specific data recording forms• Data annotation and semantic integration• Analysis tools for research part
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Acknowledgements
Clinical input
http://partner.web.cern.ch
K. Kirkby
N. Kirkby
R. Jena
M. Dosanjh
J. Shiers
M. Cirilli
A. Di Girolamo
A. Valassi
J. Salt Cairols
G. Amoros
A. Fernández
V. Méndez
K. Peach
J. Davies
S. Harris
C. Crichton
Dr. Rajesh Jena, Cambridge Univ. H.NHS Foundation trust
Prof. Ramona MayerEBG MedAustron
Prof. Bleddyn Jones Gray Inst., PTCRi
Valencia & Oxford hospitals
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This research project has been supported by a Marie Curie Early Initial Training Network Fellowship of the European Community’s Seventh Framework Programme under contract number (PITN-GA-2008-215840-PARTNER)