ClinicalCodes.org: An online repository of clinical code lists for primary care database research
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Transcript of ClinicalCodes.org: An online repository of clinical code lists for primary care database research
ClinicalCodes.org: An onlinerepository of clinical code lists forprimary care database research
David A. Springate, University of ManchesterCentres for Primary Care and Biostatistics
Outline
1. The Clinical code problem
2. www.ClinicalCodes.org
3. Motivations
Primary Care Database study popularity
Number of UK PCDpublications is rapidlyincreasing
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Institutions affiliated with UK PCD publications
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Addressing concerns about the validity ofPCD-based studies. . .
Active areas of research:
• Data quality
• Data completeness
• Confounding
But addressing these assumes that the underlyingdefinitions of clinical entities are valid!
Addressing concerns about the validity ofPCD-based studies. . .
Active areas of research:
• Data quality
• Data completeness
• Confounding
But addressing these assumes that the underlyingdefinitions of clinical entities are valid!
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 inPrimary Care: A Strategy for Developing Code Lists.PLoS ONE 8(2): e54878. doi:10.1371/journal.pone.0054878
Code list? What Code list?
• The vast majority of PCD studies do not publish theircodes
• Currently no obligation to publish code lists byfunding bodies, journals or databases
• No centralised repository for clinical codes
In 45 UK PCDcase-control studieson diabetes:
• Only 5 reportedANY clinical codesat all
• Only 2 of thesepublished codes inappendix
• Only 1 providedfull set of codelists
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 …
In 45 UK PCDcase-control studieson diabetes:
• Only 5 reportedANY clinical codesat all
• Only 2 of thesepublished codes inappendix
• Only 1 providedfull set of codelists
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 …
Code lists are not available. . . Sowhat?
Codes not subject to scrutiny or peer review
• No way of knowing if acondition diagnosis is valid
• Clinical decisions based oninvalid condition definitions(Even though the analysis isrigorous)?
No way to replicateresearch
“Non-reproducible singleoccurrences are of nosignificance to science.”
—– Karl Popper (1959)
”an experiment isreproducable untilanother laboratory triesto repeat it.”
— Alexander Kohn
http://xkcd.com/242
Difficulties in comparing studies
• Definitions change over time
• GPs may change codingpractice in response toregulations/incentives (e.g.QOF)
• Different studies may usedifferent markers (test scores,drugs, symptoms etc.)
Have to build new code lists for knownconditions from scratch
www.ClinicalCodes.org
ClinicalCodes.org
... an online repository for primarycare database researchers to uploadand download clinical codedefinitions
• Deposit code lists uponpublication
• Download historical code lists
• Archive for all QOF businessrules from 2004
• Metadata
• Unique URI
ClinicalCodes.org
Codes can be hosted for
• Diagnoses
• Drug exposures
• Tests
• Procedures
• Outcomes
Different coding systems
• Read
• ICD9/10
• SNOMED
• ICPC
ClinicalCodes.org users
1. PCD clinical researchers
• Validaton of PCD studies
• Building on previous code lists
• Matching appropriate disease definitions in time
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 scientistsFuture Generation Computer Systems 29(2): 599-611.http://dx.doi.org/10.1016/j.future.2011.08.004
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 scientistsFuture Generation Computer Systems 29(2): 599-611.http://dx.doi.org/10.1016/j.future.2011.08.004
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!
Motivations
Motivations
• Upload is simple andpainless
• Faster and moreconsistent developmentof new code lists
• Exposure and potentialcitations
• Improvements inresearch quality
• A way of finding outwho is working in thesame area
Motivations
• Uploading should berequired by
– Journals– Funding bodies– Databases (ISAC)
• Movement towards opendata and greatertransparency inpublishing protocols
• Research withoutaccessible codelists is ofquestionable validity...