ClinicalCodes.org: An online
repository of clinical code lists for
primary care database research
David A. Springate, Univ...
Outline
1. The Clinical code problem
2. www.ClinicalCodes.org
3. Motivations
Primary Care Database study popularity
Number of UK PCD
publications is rapidly
increasing
1990 1995 2000 2005 2010
050100...
Addressing concerns about the validity of
PCD-based studies. . .
Active areas of research:
• Data quality
• Data completen...
Addressing concerns about the validity of
PCD-based studies. . .
Active areas of research:
• Data quality
• Data completen...
Deciding on a code list. . .
Nicholson A, Ford E, Davies KA, Smith HE, Rait G, et al. (2013)
Optimising Use of Electronic ...
Code list? What Code list?
• The vast majority of PCD studies do not publish their
codes
• Currently no obligation to publ...
In 45 UK PCD
case-control studies
on diabetes:
In 45 UK PCD
case-control studies
on diabetes:
• Only 5 reported
ANY clinical codes
at all
• Only 2 of these
published cod...
Code lists are not available. . . So
what?
Codes not subject to scrutiny or peer review
• No way of knowing if a
condition diagnosis is valid
• Clinical decisions ba...
No way to replicate
research
“Non-reproducible single
occurrences are of no
significance to science.”
—– Karl Popper (1959)...
Difficulties in comparing studies
• Definitions change over time
• GPs may change coding
practice in response to
regulations/...
Have to build new code lists for known
conditions from scratch
www.ClinicalCodes.org
ClinicalCodes.org
... an online repository for primary
care database researchers to upload
and download clinical code
defin...
ClinicalCodes.org
Codes can be hosted for
• Diagnoses
• Drug exposures
• Tests
• Procedures
• Outcomes
Different coding sys...
ClinicalCodes.org users
1. PCD clinical researchers
• Validaton of PCD studies
• Building on previous code lists
• Matchin...
ClinicalCodes.org users
2. Informaticians / ‘meta-analysts’
• Study replications across databases
• Tracking changes in di...
ClinicalCodes.org users
2. Informaticians / ‘meta-analysts’
• Study replications across databases
• Tracking changes in di...
Why would I want to upload my codes?
I’ve spent months
building these code lists
– I don’t want to give all
my good ideas ...
Motivations
Motivations
• Upload is simple and
painless
• Faster and more
consistent development
of new code lists
• Exposure and pote...
Motivations
• Uploading should be
required by
– Journals
– Funding bodies
– Databases (ISAC)
• Movement towards open
data ...
Thank you!
Any questions?
david.springate@manchester.ac.uk
@medcodes
www.ClinicalCodes.org
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ClinicalCodes.org: An online repository of clinical code lists for primary care database research

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ClinicalCodes.org: An online repository of clinical code lists for primary care database research

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ClinicalCodes.org: An online repository of clinical code lists for primary care database research

  1. 1. ClinicalCodes.org: An online repository of clinical code lists for primary care database research David A. Springate, University of Manchester Centres for Primary Care and Biostatistics
  2. 2. Outline 1. The Clinical code problem 2. www.ClinicalCodes.org 3. Motivations
  3. 3. Primary Care Database study popularity Number of UK PCD publications is rapidly increasing 1990 1995 2000 2005 2010 050100150 PCD articles in pubmed year Numberofarticles There is global interest in UK PCD research Institutions affiliated with UK PCD publications xx x x x xxxxxx x x x x xx x x x xx x xx x xxx xx xxx x xx xxxxxx xx xx x xx x x x xx x x x xx x x xxxxxx x x x x x x xx x xxx x xxxxx xxx xxx x x x x xx xxx xx x xx x x xxx xx x x x x x x x x x x xx xx x xxx x x x x x x x x xx xx x xx xxxx x x x x xx x xx x xxx x xx xx xx x x xx x xxxxxx x x x xx x xxx x x xxx x x x x xxxxx x xx x xx xxxxxx xx xx x x x x xx x xxx x x xx xx x xxxxx x xxxxx x xx xxx x x x xx xx xxx x x x x xx x xx xx x x x x xx xx xxxxxx x x x xx x x x x x x x xx x x x x x xx x x x xxx x xxxxx x x x xxxx x x xxxxx xx xx x x xxxxxxxx xxx x xxxxx x x xx xxx x x xx xxxx x x xxx xx x xx xxxxx x xx x x xx x x x xx x x x xxx x xx x xxxx xx xxx xx x xx x xx x xxxx xxx x x xxx x x xxxx x x x x x x x x x x x x x x xxxxxx xxxx xx x xxx x x x x x x x x xx x x x x x xxx x x x xx x xxx x x x x x x x xx x x x x x x xx xx xxxx x x x x xxx x x xx xxx x x xxx x x x xx xxxxxxxxx xx xx x xxxx xx x xxxx x x xx x x x x xx x xxx x xx xxxxxx xx x xx x x x xxx x x x xxxxx xx xx x x x x x x x x x x x xxxxx x xx xxx x xxx x x x x x x x xx x x x x x xxx xx x xxxxx x x xx xx x x x xxxxxxx xx x x xxxx xx xx x x x x xxxx xx xx xxx xxx x xx xx x xxx x x x x x xxx x x x x xxxx x x x x xxxx xxx xxxxxxxx x xx xx xx x xxxx x x x xxxx x x x xx xxxx xx x xx xxx xxx x x x xxx xxxx xxxx x xx x x x x xx x x x x xx xxx x x x x x x x x xxxxxxxx x xxx xx x xxx x xx xxxx xx x xxxxxxxx xxxxx x xx xx x xxxxxxx x x xx xxx x x xx x xx xx x x xx x x x xxx x x x xxx x x xx xx xx xxx x x x xx x x xxx x x x x xx x x xxx x xx xxxxxxxx x x x x x x xx x xxxxxx x x xxxx xxx x xxx x x x x xx x x xx x x x x x x x x x x x x x x xx x xx xx x x x xx x x x xxx x xxx x xx xx x x x x x xx xx xx x x xx x xxxxxxx x xxxxxxxxxxx xxxxxxxxxxx xxx x x x xxxx x xxxx xxxxxxxxxxxxxxxxxx xxxxx
  4. 4. Addressing concerns about the validity of PCD-based studies. . . Active areas of research: • Data quality • Data completeness • Confounding
  5. 5. Addressing concerns about the validity of PCD-based studies. . . Active areas of research: • Data quality • Data completeness • Confounding But addressing these assumes that the underlying definitions of clinical entities are valid!
  6. 6. Deciding on a code list. . . Nicholson A, Ford E, Davies KA, Smith HE, Rait G, et al. (2013) Optimising Use of Electronic Health Records to Describe the Presentation of Rheumatoid Arthritis in Primary Care: A Strategy for Developing Code Lists. PLoS ONE 8(2): e54878. doi:10.1371/journal.pone.0054878
  7. 7. Code list? What Code list? • The vast majority of PCD studies do not publish their codes • Currently no obligation to publish code lists by funding bodies, journals or databases • No centralised repository for clinical codes
  8. 8. In 45 UK PCD case-control studies on diabetes:
  9. 9. In 45 UK PCD case-control studies on diabetes: • Only 5 reported ANY clinical codes at all • Only 2 of these published codes in appendix • Only 1 provided full set of code lists Potential cases of diabetes were identified using predefined diabetes codes and prescriptions of oral anti-diabetics and insulin Cases with DM were included in the analyses if they had a first-time DM code recorded plus at least one prescription for an anti-diabetic drug Using medical READ codes, we identified all subjects in the GPRD who had a first- time diagnosis of …
  10. 10. Code lists are not available. . . So what?
  11. 11. Codes not subject to scrutiny or peer review • No way of knowing if a condition diagnosis is valid • Clinical decisions based on invalid condition definitions (Even though the analysis is rigorous)?
  12. 12. No way to replicate research “Non-reproducible single occurrences are of no significance to science.” —– Karl Popper (1959) ”an experiment is reproducable until another laboratory tries to repeat it.” — Alexander Kohn http://xkcd.com/242
  13. 13. Difficulties in comparing studies • Definitions change over time • GPs may change coding practice in response to regulations/incentives (e.g. QOF) • Different studies may use different markers (test scores, drugs, symptoms etc.)
  14. 14. Have to build new code lists for known conditions from scratch
  15. 15. www.ClinicalCodes.org
  16. 16. ClinicalCodes.org ... an online repository for primary care database researchers to upload and download clinical code definitions • Deposit code lists upon publication • Download historical code lists • Archive for all QOF business rules from 2004 • Metadata • Unique URI
  17. 17. ClinicalCodes.org Codes can be hosted for • Diagnoses • Drug exposures • Tests • Procedures • Outcomes Different coding systems • Read • ICD9/10 • SNOMED • ICPC
  18. 18. ClinicalCodes.org users 1. PCD clinical researchers • Validaton of PCD studies • Building on previous code lists • Matching appropriate disease definitions in time
  19. 19. ClinicalCodes.org users 2. Informaticians / ‘meta-analysts’ • Study replications across databases • Tracking changes in disease definitions and doctors’ coding practice though time
  20. 20. ClinicalCodes.org users 2. Informaticians / ‘meta-analysts’ • Study replications across databases • Tracking changes in disease definitions and doctors’ coding practice though time • Research objects Bechhofer S, Buchan I, De Roure D, Missier P, Ainsworth J, Bhagat J, Couch P, Cruickshank D, Delderfield M, Dunlop I, Gamble M, Michaelides D, Owen S, Newman D, Sufi S, Goble C. (2013) Why linked data is not enough for scientists Future Generation Computer Systems 29(2): 599-611. http://dx.doi.org/10.1016/j.future.2011.08.004
  21. 21. Why would I want to upload my codes? I’ve spent months building these code lists – I don’t want to give all my good ideas away to other groups for nothing! I am very busy and I don’t have time to upload my codes! I will not download codes so what’s the benefit to me? Publishing codes will expose the flaws in my coding strategy!
  22. 22. Motivations
  23. 23. Motivations • Upload is simple and painless • Faster and more consistent development of new code lists • Exposure and potential citations • Improvements in research quality • A way of finding out who is working in the same area
  24. 24. Motivations • Uploading should be required by – Journals – Funding bodies – Databases (ISAC) • Movement towards open data and greater transparency in publishing protocols • Research without accessible codelists is of questionable validity...
  25. 25. Thank you! Any questions? david.springate@manchester.ac.uk @medcodes www.ClinicalCodes.org

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