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
repository of clinical code lists for
primary care database research
David A. Springate, University of Manchester
Centres for Primary Care and Biostatistics
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
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4. Addressing concerns about the validity of
PCD-based studies. . .
Active areas of research:
• Data quality
• Data completeness
• Confounding
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. 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. 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• The vast majority of PCD studies do not publish their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
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 …
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. 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. 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. Have to build new code lists for known
conditions from scratch
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. ClinicalCodes.org
Codes can be hosted for
• Diagnoses
• Drug exposures
• Tests
• Procedures
• Outcomes
Different coding systems
• Read
• ICD9/10
• SNOMED
• ICPC
18. ClinicalCodes.org users
1. PCD clinical 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 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!
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. 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...