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