https://github.com/philipdarke/ehr-codesets

Code sets for Electronic Health Record research
https://github.com/philipdarke/ehr-codesets

clinical-terminologies codeset ehr electronic-health-records healthcare uk-biobank

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Code sets for Electronic Health Record research

Host: GitHub
URL: https://github.com/philipdarke/ehr-codesets
Owner: philipdarke
License: cc-by-sa-4.0
Created: 2021-11-05T13:41:13.000Z (over 3 years ago)
Default Branch: main
Last Pushed: 2024-11-25T15:56:58.000Z (6 months ago)
Last Synced: 2025-02-03T12:52:53.867Z (4 months ago)
Topics: clinical-terminologies, codeset, ehr, electronic-health-records, healthcare, uk-biobank
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Stars: 5
Watchers: 2
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md
- Citation: CITATION.cff

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README

        # 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](#citing-this-work) 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](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/

## 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](https://github.com/philipdarke/ehr-codesets/blob/master/LICENSE).

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