faustin laurentiu roman, daniel abler, vassiliki kanellopoulos cern ific, univ. of oxford, univ. of...

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]

1

mailto:[email protected]

Content

• Introduction• Reporting side effects• Conditions

• HISP Proposal• Architecture

• Prototype implementation• Technology• Outlook


2

PARTNER

Marie Curie Initial Training Network

• funded by EC • 25 researchers • 12 European institutions


3

Particle Training Network for European Radiotherapy

Multidisciplinary training to create the next generation of hadron therapy experts

Hadron Therapy


4

• 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


5

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


6

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


7

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


8

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


9

Architecture

DB 1

Hospital 1

Hospital 1 data sourcesHIS, PACS, TPS …

Patient DB

PortalVirtual DBUSER

DB 2

Hospital 2 data sourcesHIS, PACS, TPS …

Medical requirement

Hospital 2

Schema/Semantic Mapping

HISP


10

Data model

SIDE EFFECTS

TREATMENT

TUMOR

PATIENT INFO


11

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


12

Portal structure (roles)

Patient DB

Hospital DB1

Doctor in H1

Patient


13

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


14

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


15

http://www.liferay.com/

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


16

http://openxava.org/web/guest/credits

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


17

http://vinetoolkit.org/

https://voms.ific.uv.es:8443/voms/vo.partner.eu/

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


18

http://www.jboss.org/teiid/

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


19

Acknowledgements

Clinical input

http://partner.web.cern.ch

K. KirkbyN. KirkbyR. Jena

M. DosanjhJ. ShiersM. CirilliA. Di GirolamoA. Valassi

J. Salt CairolsG. AmorosA. FernándezV. Méndez

K. PeachJ. DaviesS. HarrisC. Crichton

Dr. Rajesh Jena, Cambridge Univ. H.NHS Foundation trust

Prof. Ramona MayerEBG MedAustron

Prof. Bleddyn Jones Gray Inst., PTCRi

Valencia & Oxford hospitals


20

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)

http://partner.web.cern.ch/

http://partner.web.cern.ch/

Portal screenshot

EGI User Forum, Vilnius, 11.04.2011, [email protected] 21

Follow-up form in Portal

EGI User Forum, Vilnius, 11.04.2011, [email protected] 22

faustin laurentiu roman, daniel abler, vassiliki kanellopoulos cern ific, univ. of oxford, univ. of...

Documents