Code sets for Electronic Health Record research

Primary and secondary care code sets for Electronic Health Record research. The code sets were developed primarily for use with UK Biobank data.

:student: Please cite this work if you use it!

Primary care

Clinical event codes are provided using Read v2 and Clinical Terms Version 3 (CTV3) classifications.

Conditions (csv/rds)

Variable | Value | Level | Description -------- | ----- | ----- | ----------- angina | diagnosis | stable | Stable angina angina | diagnosis | unstable | Unstable angina bipolar | diagnosis | - | Bipolar disorder diabetes | diagnosis | - | Diabetes (type unknown) diabetes | diagnosis | type1 | Type 1 diabetes diabetes | diagnosis | type2 | Type 2 diabetes diabetes | diagnosis | gestational | Gestational diabetes diabetes | diagnosis | secondary | Secondary diabetes diabetes | diagnosis | remission | Diabetes remission diabetes | diagnosis | resolved | Diabetes resolution diabetes | family_history | - | Family history of diabetes hypertension | diagnosis | - | Hypertension learning_disabilities | diagnosis | - | Learning disabilities mi | diagnosis | - | Myocardial infarction/heart attack pcos | diagnosis | - | Polycystic ovarian syndrome schizophrenia | diagnosis | - | Schizophrenia stroke | diagnosis | haemorrhagic | Haemorrhagic stroke stroke | diagnosis | ischaemic | Ischaemic stroke tia | diagnosis | - | Transient ischaemic attack

Biomarkers (csv/rds)

Variable | Value | Level | Description -------- | ----- | ----- | ----------- blood_glucose | fpg | - | Fasting plasma glucose blood_glucose | hba1c | - | Glycated hemoglobin blood_glucose | ogtt | 2hour | 2 hour oral glucose tolerance test blood_glucose | random | - | Random blood sugar blood_glucose | unknown | - | Glucose test (unknown type) anthropometric | bmi | - | Body mass index anthropometric | height | - | Height anthropometric | weight | - | Weight anthropometric | waist | - | Waist circumference

Demographic/other (csv/rds)

Variable | Value | Level | Description -------- | ----- | ----- | ----------- smoking | current | trivial | Current trivial smoker smoking | current | light | Current light smoker smoking | current | moderate | Current moderate smoker smoking | current | heavy | Current heavy smoker smoking | current | very_heavy | Current very heavy smoker smoking | current | - | Current smoker (level unknown) smoking | former | trivial | Former trivial smoker smoking | former | light | Former light smoker smoking | former | moderate | Former moderate smoker smoking | former | heavy | Former heavy smoker smoking | former | very_heavy | Former very heavy smoker smoking | former | - | Former smoker (level unknown) smoking | never | - | Never smoked smoking | non | - | Non-smoker (assumed current) smoking | passive | - | Passive smoker (assumed current) smoking | consumption | - | Cigarette consumption

Drug prescriptions

Around 76% of UK Biobank prescription records have a BNF code. 99.7% of records have a BNF and/or Read v2 code. Prescription codes are therefore provided using British National Formulary (BNF) and Read v2 classifications.

prescriptions.rds is a named "list of lists" for the following drug categories:

Drug category | Name ------------- | --------- Anti-diabetes drugs | diabetes Anti-hypertensives | hypertension Atypical anti-psychotics | antipsychotic Steroids | steroids Statins | statins

Further details are provided here.

:warning: UK Biobank guidance highlights issues including incomplete and/or inconsistently formatted BNF codes, missing Read v2 codes and missing drug names. The ukbb-ehr-data repository includes example code to handle these issues and extract drugs using these code sets.

Secondary care

Secondary care diagnoses are provided using ICD-9 and ICD-10 coding classifications. Procedures are provided using OPCS-3 and OPCS-4 classifications.

Conditions (csv/rds)

Variable | Value | Level | Description -------- | ----- | ----- | ----------- diabetes | diagnosis | - | Diabetes (type unknown) diabetes | diagnosis | type1 | Type 1 diabetes diabetes | diagnosis | type2 | Type 2 diabetes diabetes | diagnosis | gestational | Gestational diabetes diabetes | diagnosis | secondary | Secondary diabetes

Other resources

Open repositories

The majority of diagnosis records in the interim EHR data release use the CTV3 coding classification. The code set repositories below typically only cover Read v2 diagnostic codes and limited prescription coding.

• https://phenotypes.healthdatagateway.org/
• https://www.opencodelists.org/
• https://clinicalcodes.rss.mhs.man.ac.uk/
• https://caliberresearch.org/portal is no longer updated

Kuan et al (2019) includes a map of 308 physical and mental health conditions. Read v2 codes are available at CALIBER and https://github.com/spiros/chronological-map-phenotypes.

Prescription coding

• https://openprescribing.net/bnf/ includes a browsable BNF with high-level prescribing trends
• https://www.thedatalab.org/blog/161/prescribing-data-bnf-codes/ summarises the BNF coding structure

Code mapping

• https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=592
• https://isd.digital.nhs.uk/

Citing this work

If you use this work, please cite it as below:

@article{10.1093/jamia/ocab260, author = {Darke, Philip and Cassidy, Sophie and Catt, Michael and Taylor, Roy and Missier, Paolo and Bacardit, Jaume}, title = "{Curating a longitudinal research resource using linked primary care EHR data - a UK Biobank case study}", journal = {Journal of the American Medical Informatics Association}, volume = {29}, number = {3}, pages = {546-552}, year = {2021}, month = {12}, issn = {1527-974X}, doi = {10.1093/jamia/ocab260}, url = {https://doi.org/10.1093/jamia/ocab260}, eprint = {https://academic.oup.com/jamia/article-pdf/29/3/546/42333190/ocab260.pdf}, }

Licence

Made available under a Creative Commons Attribution 4.0 International License.