science as a conversation across borders · 2011-11-05 · “data integration and modelling in...

“Data integration and modelling in health sciences”

Science as a conversation across bordersJuni PalmgrenKarolinska Institutet and FIMM, Helsinki University

Open data – key to the futureHelsinki 2011-11-01

Data explosion in health sciences

e-infrastructure for data

ELSI revisited

Nordic collaboration?

Focus

2 november 20113

Complex human disease

Cured

Dead

Chronic/currentdisease

time

DiagnosisHealthy

Population based

Focus on early detection, prevention

and cure

Population based registries

4

L I F E

Birth

Congenital Malformations

EARLY LIFE

Cause of Death

LATE LIFE

Twin Migration

Multiple GenerationPopulation

GENETICALLY INFORMATIVE

Clinical Quality Registries

Specific DiseaseRegistries

Hospital DischargeCancer

LIFE SPAN REGISTRIES

Register of prescribed drug sales

Genomes(Sanger, EBI +

NCBI)

Nucleotide sequenceEMBL-Bank+Genbank+DDBj

Gene expressionArrayExpress, GEO

Protein sequenceUniProt(EBI/SIB/PIR)

Protein families, motifs and domains

InterPro(12 collaborators)

Protein structurewwPDB(RCSB,EBI,PDBj)

Protein interactionsIntAct with Imex,

PRIDE

Chemical entitiesChEBI; PubChem

PathwaysKegg;

Reactome

SystemsBioModels

Integration with HTP ‘omics’ data

From Janet Thornton, EBI

N=2 000 n=20 000

Individual data

Molecular data

Size matters!

Leena Peltonen & Mark McCarthy

NORWAY

SWEDEN

FINLAND

DENMARK

POLANDGERMANY

HOLLAND

UNITEDKINGDOM

IRELAND

NORTH. IRELAND

BELGIUM

FRANCE

LUXEM-BOURG

CZECH. REP.

AUSTRIA

SLOVAK REP.

SWITZERLANDSLOVENIA

CROATIA

BOSNIA -HERCEGOVINA

ITALYJUGOSLAVIA

HUNGARY

MACEDONIAALBANIA

ROMANIA

BULGARIA

GREECETURKEY

UKRAINE

MOLDAVIA

GEORGIAAZERBAIJAN

KAZAKHSTANBELORUSSIA

RUSSIA RUSSIALITHUANIA

LATVIA

ESTONIA

SPAIN

PORTUGAL

ICELAND

ARMENIA

ENGAGE

Total n = 22 562

4909

954

169

10336

1643

709

1086

1558

715

424Australia

The Breast Cancer Association Consortium BCAC 45 groups around the world start 2005

35000 cases from 34 studies

Biomedinfra.fi is a joint approach to develop biomedical research infrastructure

Tutkimuksen infrastruktuurit Euroopassa ja Suomessa

02.06.2010 10

“Tutkimusta, tietoa ja terveyttä suomalaisille”

FIMM

CSC

THL

Biomedinfra.fi

BiobanksClinical & lifestyle dataMolecular profiling results

IT-solutionsBioinformaticsKnowledge mining

Risk models & estimatesDiagnostics developmentPersonalised medicine

Competitiveness of Finland & Europe

National researchinfrastructure

Data explosion in health sciences

e-infrastructure for data

ELSI revisited

Nordic collaboration?

Focus

J Palmgren 12

13

232 Biobanks28 EU countries

Construction of new infrastructures -preparatory phase

FP7-INFRASTRUCTURES-2007-1

14

Federated database

Virtual database (HUB)Sweden(Oracle)

Netherlands(Oracle)

Norway(SQL Server) UK

(SQL Server)Italy(MySQL)

Sensitive data!Secure connections!

Data explosion in health sciences

e-infrastructure for data

ELSI revisited

Nordic collaboration?

Focus

EU Data Protection Directive 95/46/EC

Article 81. Member States shall prohibit the processing of personal data …. concerning health

..2. Paragraph 1 shall not apply where:

(a) the data subject has given his explicit consent 3. Paragraph 1 shall not apply where processing of the data is required for the

purposes of preventive medicine, medical diagnosis, the provision of care or treatment or the management of health-care services, and where those data are processed by a health professional subject under national law or rules established by national competent bodies to the obligation of professional secrecy or by another person also subject to an equivalent obligation of secrecy.

4. Subject to the provision of suitable safeguards, Member States may, for reasons of substantial public interest, lay down exemptions in addition to those laid down in paragraph 2 either by national law or by decision of the supervisory authority.

Sweden’s interpretaion: Under Article 8.4 a system for using person data in research is possible

EU Data Directive currently under revision!

The national legislation in Sweden

Is based on the Data Protection Directive and the Freedom of Information Legislation (Tryckfrihetsförordningen 1766):Public access to information and secrecyPersonal dataEthical reviewBiobank law Archiving, Official statistics, Health data etc.

Revision of legislation need careful balance between security for the individual and possibility to do research based on populations.

Summary for health sciences

DataData explosion in molecular and health sciences. Unprecedented opportunitiesLarge numbers – international collaboratione-infrastructureNeed systems for data preservation, curation, harmonisation, authentication, authorisation, access –in a global perspectiveNew tech solutions for secure transferELSIELSI solutions that balances research opportunities and the protection of individual integrity

Data explosion in health sciences

e-infrastructure for data

ELSI revisited

Nordic collaboration?

Focus

Nordic collaboration onpreservation and access to data.

Complex data projects of joint Nordic interestBBMRI.FI, BBMRI.SE, BBMRI.DK, BBMRI.NOMany more….

e-Infrastructures NORDUnetNDGF/NeIC for data storage and computationNordForsk eScience Globalisation initiative

Harmonisation of laws, directives, interpretation and practicesOn high political level nationally; Joint input to EU

Much more can be done!

21

Beware!Ownership of data

Mine!

The politics of data ownership and the lack of confidence In complex synchronization can stall

projects before they have even started.