clinical & genetic data integration

Clinical & Genetic Data Integration

Nirvana or Pandora’s Box ?

Glasgow

Edinburgh

Dundee

Aberdeen

Generation Scotland

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

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!!!!

Data Integration/Federation (Why?)

• Obtain Significant Populations

• Population Variation• Others ??

Data Federation

Data Issues (Illustration)

MSSQL DatabaseDeath code based on top 10 causes mapped to Snomed

Access DatabaseDeath code based on top 10 causes mapped to Snomed

MySQL DatabaseDeath code based on top 10 causes mapped to ICD9

Cause of Death obtained from Autopsy reportsBy clinical staff

Cause of Death obtained from Subject QuestionnaireCoded by clerk

Cause of Death obtained from Direct linkage to death register database

Issues of provenanceIssues of appropriate codingIssues of ontology mappingIssues of data reliability

Integration OKMapping Probably OKTechnically Sound

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 Genetics 4, 337-345 (2003)

PandoraOne 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!!