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ClinicalCodes.org: An online repository of clinical code lists for primary care database research
This document discusses ClinicalCodes.org, an online repository for clinical code lists used in primary care database research. It outlines issues with a lack of published code lists, such as inability to validate or replicate studies and difficulty comparing studies over time as condition definitions change. ClinicalCodes.org aims to address these issues by providing a central location for researchers to upload, download, and archive code lists. This would improve research quality and allow other researchers to build upon previous work in a standardized way. Motivations for researchers to upload their code lists include validation of their work, increased citations, and a requirement by journals and funders for transparent and accessible code lists.
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ClinicalCodes.org: An online repository of clinical code lists for primary care database research
- 1. ClinicalCodes.org: An online repositoryof clinical code lists for primary care database research David A. Springate, University of Manchester Centres for Primary Care and Biostatistics
- 2. Outline 1. The Clinicalcode problem 2. www.ClinicalCodes.org 3. Motivations
- 3. Primary Care Databasestudy 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. Addressing concerns aboutthe validity of PCD-based studies. . . Active areas of research: • Data quality • Data completeness • Confounding
- 5. Addressing concerns aboutthe 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. Deciding on acode 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. Code list? WhatCode 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. In 45 UKPCD case-control studies on diabetes:
- 9. In 45 UKPCD 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. Code lists arenot available. . . So what?
- 11. Codes not subjectto 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. No way toreplicate 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. Difficulties in comparingstudies • 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. Have to buildnew code lists for known conditions from scratch
- 15.
- 16. ClinicalCodes.org ... an onlinerepository 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. ClinicalCodes.org Codes can behosted for • Diagnoses • Drug exposures • Tests • Procedures • Outcomes Different coding systems • Read • ICD9/10 • SNOMED • ICPC
- 18. ClinicalCodes.org users 1. PCDclinical researchers • Validaton of PCD studies • Building on previous code lists • Matching appropriate disease definitions in time
- 19. ClinicalCodes.org users 2. Informaticians/ ‘meta-analysts’ • Study replications across databases • Tracking changes in disease definitions and doctors’ coding practice though time
- 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. Why would Iwant 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.
- 23. Motivations • Upload issimple 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. Motivations • Uploading shouldbe 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.