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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There is global interest in UK PCDresearch

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• The vast majority of PCD studies do not publish theircodes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...

Thank you!

Any questions?

david.springate@manchester.ac.uk@medcodes

www.ClinicalCodes.org