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README.md

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+# 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.
+
+## Primary care
+
+Clinical event codes are provided using Read v2 and Clinical Terms Version 3 (CTV3) classifications.
+
+### Conditions ([csv](primary_care/conditions.csv)/[rds](primary_care/conditions.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](primary_care/biomarkers.csv)/[rds](primary_care/biomarkers.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](primary_care/other.csv)/[rds](primary_care/other.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](drugs/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](drugs/README.md).**
+
+:warning: UK Biobank [guidance](https://biobank.ndph.ox.ac.uk/showcase/ukb/docs/primary_care_data.pdf) highlights issues including incomplete and/or inconsistently formatted BNF codes, missing Read v2 codes and missing drug names. The [ukbb-ehr-data repository](https://github.com/philipdarke/ukbb-ehr-data/) 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](secondary_care/conditions.csv)/[rds](secondary_care/conditions.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](https://biobank.ndph.ox.ac.uk/showcase/ukb/docs/primary_care_data.pdf) 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](https://doi.org/10.1016/S2589-7500(19)30012-3) (2019) includes a map of 308 physical and mental health conditions. Read v2 codes are available at [CALIBER](https://caliberresearch.org/portal) 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/
+
+## Licence
+
+Made available under a [Creative Commons Attribution 4.0 International License](https://github.com/philipdarke/ehr-codesets/blob/master/LICENSE).

drugs/README.md

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+# Drug code sets for Electronic Health Record research
+
+:warning: UK Biobank [guidance](https://biobank.ndph.ox.ac.uk/showcase/ukb/docs/primary_care_data.pdf) highlights issues including incomplete and/or inconsistently formatted BNF codes, missing Read v2 codes and missing drug names. The [ukbb-ehr-data repository](https://github.com/philipdarke/ukbb-ehr-data/) includes example code to handle these issues and identify periods of prescriptions using the code sets below.
+
+## Drug coding
+
+[prescriptions.rds](drugs/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`
+
+For each drug category the following codes are provided:
+
+Name | Description
+--------- | -----------
+`read` | Read v2 codes for the drug category. Partial matching should be used e.g. `bxi` means select all Read v2 codes starting `bxi` (those matching the regular expression `^bxi`).
+`bnf` | BNF codes for the drug category. Partial matching should be used e.g. `0212000AA` means select all Read v2 codes starting `0212000AA` (those matching the regular expression `^0212000AA`).
+`search` | Search terms that can be used to identify drugs based on the `drug_name` field. E.g. `statin` means select any drug matching the regular expression `statin` (case insensitive).
+
+Search terms aim to cover all potential generic and brand names for drugs in each category. Results should be carefully reviewed when using these terms.
+
+## Anti-diabetes drugs
+
+Codes are provided for:
+
+Drug category | Name
+------------- | ---------
+Any anti-diabetes drug | `all`
+Insulin | `insulin`
+All anti-diabetic drugs excluding insulin | `non_insulin`
+Metformin | `metformin`
+
+For the avoidance of doubt, metformin codes are included under `non_insulin`.
+
+For example, the following returns BNF codes for anti-diabetes drugs:
+
+```R
+drug_codes <- readRDS("drugs/prescriptions.rds")
+drug_codes$diabetes$all$bnf  # codes for all anti-diabetes drugs
+drug_codes$diabetes$insulin$bnf  # codes for insulin only
+```
+
+## Anti-hypertensives
+
+Codes are provided for:
+
+Drug category | Name
+------------- | ---------
+Any anti-hypertensive | `all`
+Thiazides and related diuretics | `thiazides`
+Potassium-sparing diuretics and aldosterone antagonists | `potassium_aldosterone`
+Potassium sparing diuretics and compounds | `potassium_compounds`
+Beta adrenoceptor blocking drugs | `beta_blockers`
+Vasodilator antihypertensive drugs | `vasodilator`
+Centrally-acting antihypertensive drugs | `centrally_acting`
+Adrenergic neurone blocking drugs | `adrenergic_blockers`
+Alpha-adrenoceptor blocking drugs | `alpha_blockers`
+Renin-angiotensin system drugs | `renin_system`
+Calcium-channel blockers | `calcium_blockers`
+
+For example, the following returns Read v2 codes for anti-hypertensives:
+
+```R
+drug_codes <- readRDS("drugs/prescriptions.rds")
+drug_codes$hypertension$all$read  # codes for all anti-hypertensives
+drug_codes$hypertension$vasodilator$read  # codes for vasodilators only
+```
+
+
+## Atypical anti-psychotics
+
+The following returns the search terms for all atypical anti-psychotics including depot injections:
+
+```R
+drug_codes <- readRDS("drugs/prescriptions.rds")
+drug_codes$antipsychotic$all$search
+```
+
+## Steroids
+
+The following returns BNF codes for all steroids including depot injections:
+
+```R
+drug_codes <- readRDS("drugs/prescriptions.rds")
+drug_codes$steroids$all$bnf
+```
+
+## Statins
+
+The following returns Read v2 codes for all statins:
+
+```R
+drug_codes <- readRDS("drugs/prescriptions.rds")
+drug_codes$statins$all$read
+```