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