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Clinical & Genetic Data Integration

Clinical & Genetic Data Integration. Nirvana or Pandora’s Box ?. Generation Scotland. Aberdeen. Dundee. Edinburgh. Glasgow. Generation Scotland (Goals). 21CGH – Infrastructure research and development. ~2,500 subjects SFHS – initially 15,000 rising to 50,000 Subjects

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Clinical & Genetic Data Integration

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  1. Clinical & Genetic Data Integration Nirvana or Pandora’s Box ?

  2. Generation Scotland Aberdeen Dundee Edinburgh Glasgow

  3. Generation Scotland (Goals) • 21CGH – Infrastructure research and development. ~2,500 subjects • SFHS – initially 15,000 rising to 50,000 Subjects • Genotype and Phenotype Information • Base Resource for future research

  4. Data Integration/Federation (Technologies) • Link Integration Web publication of data and searching by investigators • View Integration databases linked to appear as single entity (Grid Based Technologies, Proprietary Systems, Websphere) • Data Warehousing Data amalgamated into a single large Datastore • Web Services Sort of amalgamation of Link and View Integration • It CAN be done Technically!!!!

  5. Data Integration/Federation (Why?) • Obtain Significant Populations • Population Variation • Others ??

  6. Data Federation

  7. MSSQL Database Death code based on top 10 causes mapped to Snomed Access Database Death code based on top 10 causes mapped to Snomed MySQL Database Death code based on top 10 causes mapped to ICD9 Cause of Death obtained from Subject Questionnaire Coded by clerk Cause of Death obtained from Autopsy reports By clinical staff Cause of Death obtained from Direct linkage to death register database Data Issues (Illustration) Issues of provenance Issues of appropriate coding Issues of ontology mapping Issues of data reliability Integration OK Mapping Probably OK Technically Sound

  8. Data Issues • As long as the data providers continue to produce online databases without regard for the way in which the information will be aggregated, integration will be a monumental task. However, in the absence of accepted standards for the representation and exchange of biological data, it is far from simple for data providers to achieve the goal of making their data available in a form that can be cleanly integrated and maintained. (Lincoln D. Stein  ) Nature Reviews Genetics4, 337-345 (2003)

  9. Pandora One day, Pandora's curiosity got the better of her and she opened it, releasing all the misfortunes of mankind (plague, sorrow, poverty, crime, etc.). Once opened, she shut it in time to keep one thing in the box: Hope. The world remained extremely bleak for an unspecified interval, until Pandora "chanced" to revisit the box again, at which point Hope fluttered out. Thus, mankind always has Hope in times of evil, but Hope has a great deal of catching up to do. Time to Catch up!!

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