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Database harmonisation and IT infrastructure Jan-Eric Litton, Karolinska Institutet, Stockholm, Sweden 16 September 2009 P...
Connecting Biobanks -  leading design principals
We are using a HUB and spoke structure with federated databases.  <ul><li>HUB  - In general, a hub is the central part of ...
Hub and Spoke for European  Biobank Network <ul><li>No need to connect all with all on “network” level </li></ul><ul><ul><...
GenomEUtwin and TwinNET
bbmri.no bbmri.se id=1 id=1 bbmri.au id=1 bbmri.nl id=1 bbmri.fi id=1
Common Schema for all national HUBS
A simple example
A simple example
WP5 -  objectives Task 1  – consensus on the requirements for a general information management system for biobanks in Euro...
WP5 -  lexicon Swedish version English version Spanish version Italian version Estonia version database federato un tipo d...
WP5 -  crew Andrea Calabria, CNR-ITB (IT) Mario Caccamo, EMBL-EBI (UK) Claus Dabringer, UNI-KLU (AT) Johann Eder, UNI-KLU ...
WP5 <ul><li>Meetings arranged: </li></ul><ul><ul><li>1st WP5 team meeting, March 26-27, 2008, Stockholm, Sweden </li></ul>...
Challenges…. <ul><li>Data definitions change over time </li></ul><ul><li>How to connect to medical ontologies </li></ul><u...
<ul><li>Jan-Eric Litton, Prof </li></ul><ul><li>Department of Medical Epidemiology and Biostatistics </li></ul><ul><li>Kar...
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Fabrizia Bignami

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Fabrizia Bignami

  1. 1. Database harmonisation and IT infrastructure Jan-Eric Litton, Karolinska Institutet, Stockholm, Sweden 16 September 2009 Preparatory Phase Grant Agreement 212111
  2. 2. Connecting Biobanks - leading design principals
  3. 3. We are using a HUB and spoke structure with federated databases. <ul><li>HUB - In general, a hub is the central part of a wheel where the spokes come together. The term is familiar to frequent fliers who travel through airport &quot;hubs&quot; to make connecting flights from one point to another. In data communications, a hub is a place of convergence where data arrives from one or more directions and is forwarded out in one or more other directions. </li></ul>
  4. 4. Hub and Spoke for European Biobank Network <ul><li>No need to connect all with all on “network” level </li></ul><ul><ul><li>Database federation system does the routing of traffic (queries) </li></ul></ul><ul><ul><li>Hubs provide the database services </li></ul></ul><ul><ul><ul><li>Single access point (simpler to manage) </li></ul></ul></ul><ul><ul><li>Hubs can be federated as well </li></ul></ul><ul><ul><li>We can have many Hubs in different geographical places, genotype Hub, phenotype Hub, Sample Hub, Meta Data Hub, National Hub </li></ul></ul>
  5. 5. GenomEUtwin and TwinNET
  6. 6. bbmri.no bbmri.se id=1 id=1 bbmri.au id=1 bbmri.nl id=1 bbmri.fi id=1
  7. 7. Common Schema for all national HUBS
  8. 8. A simple example
  9. 9. A simple example
  10. 10. WP5 - objectives Task 1 – consensus on the requirements for a general information management system for biobanks in Europe Task 2 – how to maintain unique and secure identities (object models) for specimens, subjects and biobanks Task 3 – strategy for communication between biobanks including a common nomenclature, compatible software techniques and appropriate information transmission policies
  11. 11. WP5 - lexicon Swedish version English version Spanish version Italian version Estonia version database federato un tipo di sistema di gestione di basi di dati che integra, in maniera trasparente …..
  12. 12. WP5 - crew Andrea Calabria, CNR-ITB (IT) Mario Caccamo, EMBL-EBI (UK) Claus Dabringer, UNI-KLU (AT) Johann Eder, UNI-KLU (AT) Paul Flicek, EMBL-EBI (UK) Ruslan Fomkin, KI (SE) Martin Fransson, KI (SE) Hákon Gudbjartsson, deCODE (IS) Andy Harris, UK Biobank (UK) Hans Hillege, UMCG (NL) Maria Krestyaninova, EMBL-EBI (UK) Klaus Kuhn, TUM (DE) Erkki Leego, UTARTU (EE) Jan-Eric Litton, KI (SE) Fernando López, VITRO, SA (ES) Ioannis Michalopoulos, BRFAA (GR) Luciano Milanesi, CNR-ITB (IT) Juha Muilu, NPHI (FI) Louis Rechaussat, INSERM (FR) Blandine Rimbault, INSERM (FR) Tore Risch, UU (SE) Pedro Roiz, VITRO, SA (ES) Paolo Romano, IST (IT) Morris Swertz, UMCG (NL)
  13. 13. WP5 <ul><li>Meetings arranged: </li></ul><ul><ul><li>1st WP5 team meeting, March 26-27, 2008, Stockholm, Sweden </li></ul></ul><ul><ul><li>2nd WP5 team meeting, September 28-29, 2008, Reykjavik, Iceland </li></ul></ul><ul><ul><li>3rd WP5 team meeting, March 23-34, 2009, Brussels, Belgium </li></ul></ul><ul><li>Upcoming meetings </li></ul><ul><ul><li>4th WP5 team meeting, October 14-15, Milan, Italy </li></ul></ul>
  14. 14. Challenges…. <ul><li>Data definitions change over time </li></ul><ul><li>How to connect to medical ontologies </li></ul><ul><li>Integration of phenotype and genotype data </li></ul><ul><li>The natural language issue </li></ul><ul><li>And of course ELSI </li></ul>
  15. 15. <ul><li>Jan-Eric Litton, Prof </li></ul><ul><li>Department of Medical Epidemiology and Biostatistics </li></ul><ul><li>Karolinska Institutet </li></ul><ul><li>Box 281 </li></ul><ul><li>SE-17177 Stockholm </li></ul><ul><li>Sweden </li></ul><ul><li>Tel: +46 8 52487759 </li></ul><ul><li>E-mail: jan-eric.litton@ki.se </li></ul><ul><li>www. bbmri . eu </li></ul>Further information

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