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Metadata

Phenotyping algorithms for common biomarkers in primary care EHR for UK Biobank

A semi-supervised approach for rapidly creating clinical biomarker phenotypes in the UK Biobank, across different primary care EHR and clinical terminology systems.

The UK Biobank is making primary care electronic health records available for the entire cohort for COVID-19 research. This repository provides machine-readable versions (CSV files) of electronic health record phenotyping algorithms for 31 commonly-measured biomakers, many of which are associated with COVID-19 comorbidities such as body mass index, cardiovascular disease and respiratory disease.

Details on how these algorithms were bootstrapped and validated can be found in the publication:

Spiros Denaxas, Anoop D Shah, Bilal A Mateen, Valerie Kuan, Jennifer K Quint, Natalie Fitzpatrick, Ana Torralbo, Ghazaleh Fatemifar, 
Harry Hemingway, A semi-supervised approach for rapidly creating clinical biomarker phenotypes in the UK Biobank using 
different primary care EHR and clinical terminology systems, JAMIA Open, Volume 3, Issue 4, December 2020, Pages 545–556, 
https://doi.org/10.1093/jamiaopen/ooaa047

Phenotypes

Phenotype Category Units Definition Download
Glucose Blood biochemistry mmol/L Blood-based glucose level derived from plasma. Excludes fasting measurements. Glucose.csv
Triglycerides Blood biochemistry mmol/L Serum triglycerides measurements. Algorithm excludes plasma-derived measurements. Includes fasting/non-fasting/random values. Triglycerides.csv
HDL Blood biochemistry mmol/L Serum fasting/non-fasting/random HDL cholesterol level. HDL.csv
HbA1c Blood biochemistry mmol/mol HbA1c level recorded using International Federation of Clinical Chemistry and Laboratory Medicine or Diabetes Control and Complications Trial (DCCT). HbA1c.csv
Creatinine Blood biochemistry umol/L Creatinine levels including corrected levels. Algorithm includes serum, plasma, and unspecified source measurements. Creatinine.csv
Cholesterol Blood biochemistry mmol/L Serum cholesterol measurent including total cholesterol measurements but excluding plasma-derived measurements. The phenotype includes fasting and non-fasting measurements. Cholesterol.csv
Calcium Blood biochemistry mmol/L Serum calcium measurement. Excludes ionized calcium level measurements. The phenotype does not include corrected/adjusted levels. Calcium.csv
CRP Blood biochemistry mg/L Serum C reactive protein level excluding plasma-derived measurements. CRP.csv
ALT Blood biochemistry U/L Serum alanine aminotransferase level ALT.csv
ALP Blood biochemistry U/L Serum alkaline phosphatase measurement excluding liver isoenzyme level. ALP.csv
Total bilirubin Blood biochemistry umol/L Serum bilirubin level. Excludes conjugated bilirubin levels. Totalbilirubin.csv
Urea Blood biochemistry mmol/L Serum / plasma urea level Urea.csv
Albumin Blood biochemistry g/L Serum albumin levels. Albumin.csv
Haemoglobin conc Blood count g/dL Haemoglobin estimation Haemoglobinconc.csv
MCV Blood count fL Mean corpuscular volume (MCV) MCV.csv
WBC Blood count 10^9/L Total white cell count. Excludes polymorphonuclear leukocyte count. WBC.csv
MCHb conc Blood count g/dL Mean corpusc. Hb. conc. (MCHC) MCHbconc.csv
Haematocrit perc Blood count % Haematocrit / packed cell volume Haematocritperc.csv
Basophills Blood count 10^9/L Basophil count Basophills.csv
RBC Blood count 10^12/L Red blood cell (RBC) count excluding nucleated RBC values. RBC.csv
Platelets Blood count 10^9/L Platelet count. Excludes platelet distribution width measurements. Platelets.csv
Neutrophills Blood count 10^9/L Neutrophil count Neutrophills.csv
Monocytes Blood count 10^9/L Monocyte count Monocytes.csv
Lymphocytes Blood count 10^9/L Leucocyte count Lymphocytes.csv
Eosinophills Blood count 10^9/L Eosinophil count Eosinophills.csv
Height Physical measures cm Height Height.csv
FVC Physical measures L Forced vital capacity measurement. Excludes predictd values and measurements post-bronchodialation. FVC.csv
SBP Physical measures mmHg Systolic blood pressure. SBP.csv
DBP Physical measures mmHg Diastolic blood pressure. DBP.csv
Weight Physical measures Kg Weight Weight.csv
FEV1 Physical measures L Forced expired volume in 1 second. Excludes predicted values and measurements post-bronchodialation. FEV1.csv

ALP

Metadata
Name ALP
Category Blood biochemistry
Type Biomarker
UK Biobank field 30610
Units U/L (UO_0000179)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 11
Definition Serum alkaline phosphatase measurement excluding liver isoenzyme level.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        ALP = value1

    ELSE IF data_provider = Scotland (2)
        ALP = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        ALP = value1
Terminology Read code Read term
read2 44F..00 Serum alkaline phosphatase
read2 44F3.00 Total alkaline phosphatase
read2 44FZ.00 Serum alkaline phosphatase NOS
read2 44F1.00 Serum alk. phos. normal
read2 44F2.00 Serum alk. phos. raised
ctv3 XE2px Serum alkaline phosphatase
ctv3 XE2px Serum alkaline phosphatase level
ctv3 44F3. Alkaline phosphatase level
ctv3 44FZ. Serum alkaline phosphatase NOS
ctv3 44F1. Serum alk. phos. normal
ctv3 44F2. Serum alk. phos. raised

ALT

Metadata
Name ALT
Category Blood biochemistry
Type Biomarker
UK Biobank field 30620
Units U/L (UO_0000179)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 11
Definition Serum alanine aminotransferase level
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        ALT = value1

    ELSE IF data_provider = Scotland (2)
        ALT = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        ALT = value1
Terminology Read code Read term
read2 44G3.00 ALT/SGPT serum level
read2 44GB.00 Serum alanine aminotransferase level
read2 44G..11 ALT - blood level
read2 44G3000 ALT/SGPT level normal
read2 44G3100 ALT/SGPT level abnormal
ctv3 44G3. ALT/SGPT serum level
ctv3 XaLJx Serum alanine aminotransferase level
ctv3 X771f ALT - blood level
ctv3 X771e SGPT - blood level
ctv3 44G30 ALT.SGPT level normal
ctv3 44G31 ALT.SGPT level abnormal

Albumin

Metadata
Name Albumin
Category Blood biochemistry
Type Biomarker
UK Biobank field 30600
Units g/L (UO_0000175)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 7
Definition Serum albumin levels.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Albumin = value1

    ELSE IF data_provider = Scotland (2)
        Albumin = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Albumin = value1
Terminology Read code Read term
read2 44M4.00 Serum albumin
read2 44M4000 Serum albumin normal
read2 44M4100 Serum albumin low
ctv3 XE2eA Serum albumin
ctv3 XE2eA Serum albumin level
ctv3 44M40 Serum albumin normal
ctv3 44M41 Serum albumin low

Basophills

Metadata
Name Basophills
Category Blood count
Type Biomarker
UK Biobank field 30160
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 8
Definition Basophil count
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Basophills = value1

    ELSE IF data_provider = Scotland (2)
        Basophills = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Basophills = value1
Terminology Read code Read term
read2 42L..00 Basophil count
read2 42LZ.00 Basophil count NOS
read2 42L1.00 Basophil count normal
ctv3 42L.. Basophil count
ctv3 42LZ. Basophil count NOS
ctv3 42L1. Basophil count normal
read2 42L3.00 Basophil count abnormal
read2 42L2.00 Basophilia

CRP

Metadata
Name CRP
Category Blood biochemistry
Type Biomarker
UK Biobank field 30710
Units mg/L (UO_0000273)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 6
Definition Serum C reactive protein level excluding plasma-derived measurements.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        CRP = value1

    ELSE IF data_provider = Scotland (2)
        CRP = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        CRP = value1
Terminology Read code Read term
read2 44CS.00 Serum C reactive protein level
read2 44CC000 C reactive protein normal
read2 44CC100 C reactive protein abnormal
ctv3 XaINL Serum C reactive protein level
ctv3 44CC0 C-reactive protein normal
ctv3 44CC1 C-reactive protein abnormal

Calcium

Metadata
Name Calcium
Category Blood biochemistry
Type Biomarker
UK Biobank field 30680
Units mmol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 7
Definition Serum calcium measurement. Excludes ionized calcium level measurements. The phenotype does not include corrected/adjusted levels.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Calcium = value1

    ELSE IF data_provider = Scotland (2)
        Calcium = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Calcium = value1
Terminology Read code Read term
read2 44I8.00 Serum calcium
read2 44I8000 Normal serum calcium level
ctv3 XE2q3 Serum calcium
ctv3 XE2q3 Serum calcium level
ctv3 44I80 Normal serum calcium level
ctv3 Xabpk Serum adjusted calcium concentration
read2 44h4.00 Blood calcium level

Cholesterol

Metadata
Name Cholesterol
Category Blood biochemistry
Type Biomarker
UK Biobank field 30690
Units mmol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 21
Definition Serum cholesterol measurent including total cholesterol measurements but excluding plasma-derived measurements. The phenotype includes fasting and non-fasting measurements.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Cholesterol = value1

    ELSE IF data_provider = Scotland (2)
        Cholesterol = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Cholesterol = value1
Terminology Read code Read term
read2 44P..00 Serum cholesterol
read2 44PJ.00 Serum total cholesterol level
read2 44PH.00 Total cholesterol measurement
read2 44P3.00 Serum cholesterol raised
read2 44P1.00 Serum cholesterol normal
read2 44PZ.00 Serum cholesterol NOS
read2 44P9.00 Serum cholesterol studies
read2 44P2.00 Serum cholesterol borderline
read2 44PK.00 Serum fasting total cholesterol
read2 44P4.00 Serum cholesterol very high
ctv3 XE2eD Serum cholesterol
ctv3 XE2eD Serum cholesterol level
ctv3 XaJe9 Serum total cholesterol level
ctv3 XSK14 Total cholesterol measurement
ctv3 44P3. Serum cholesterol raised
ctv3 44P1. Serum cholesterol normal
ctv3 44PZ. Serum cholesterol NOS
ctv3 44P9. Serum cholesterol studies
ctv3 44P2. Serum cholesterol borderline
ctv3 XaLux Serum fasting total cholesterol
ctv3 44P4. Serum cholesterol very high

Creatinine

Metadata
Name Creatinine
Category Blood biochemistry
Type Biomarker
UK Biobank field 30700
Units umol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 17
Definition Creatinine levels including corrected levels. Algorithm includes serum, plasma, and unspecified source measurements.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Creatinine = value1

    ELSE IF data_provider = Scotland (2)
        Creatinine = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Creatinine = value1
Terminology Read code Read term
read2 44J3.00 Serum creatinine
read2 44J3200 Serum creatinine normal
read2 44J3z00 Serum creatinine NOS
read2 44J3300 Serum creatinine raised
read2 44JD.00 Corrected serum creatinine level
read2 44JC.00 Corrected plasma creatinine level
read2 44J3100 Serum creatinine low
read2 44J3000 Serum creatinine abnormal
ctv3 XE2q5 Serum creatinine
ctv3 XE2q5 Serum creatinine level
ctv3 44J32 Serum creatinine normal
ctv3 44J3z Serum creatinine NOS
ctv3 44J33 Serum creatinine raised
ctv3 XaERc Corrected serum creatinine level
ctv3 XaERX Corrected plasma creatinine level
ctv3 44J31 Serum creatinine low
ctv3 44J30 Serum creatinine abnormal

DBP

Metadata
Name DBP
Category Physical measures
Type Biomarker
UK Biobank field 94
Units mmHg (UO_0000272)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 0
Definition Diastolic blood pressure.
Version alpha

Implementation

IF data_provider = England Vision (1)
    IF read_2 = “246..00 O/E - blood pressure reading”' 
        SBP = value1
        DBP = value2

ELSE IF data_provider = Scotland (2)
    IF read_2 = “246..00 O/E - blood pressure reading”
        DBP = value1
        SBP = value2
    ELSE IF read_2 = “2469.00 O/E - Systolic BP reading”
        SBP = value1
    ELSE IF read_2 = “246A.00 O/E - Diastolic BP reading”
        DBP = value1

IF data_provider = England TPP (3)
    IF read_3 = “2469.00 O/E - Systolic BP reading” 
        SBP = value1
    ELSE IF read_3 = “246A.00 O/E - Diastolic BP reading” 
        DBP = value1

IF data_provider = Wales (4)
    IF read_2 = “246..00 O/E - blood pressure reading”
        SBP = value1
        DBP = value2
    ELSE IF read_2 = “2469.00 O/E - Systolic BP reading”
        SBP = value1
    ELSE IF read_2 = “246A.00 O/E - Diastolic BP reading”
        DBP = value1

Eosinophills

Metadata
Name Eosinophills
Category Blood count
Type Biomarker
UK Biobank field 30150
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 9
Definition Eosinophil count
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Eosinophills = value1

    ELSE IF data_provider = Scotland (2)
        Eosinophills = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Eosinophills = value1
Terminology Read code Read term
read2 42K..00 Eosinophil count
read2 42KZ.00 Eosinophil count NOS
read2 42K1.00 Eosinophil count normal
read2 42K3.00 Eosinophil count raised
ctv3 42K.. Eosinophil count
ctv3 42KZ. Eosinophil count NOS
ctv3 42K1. Eosinophil count normal
ctv3 42K3. Eosinophil count raised
read2 42K2.00 Eosinopenia

FEV1

Metadata
Name FEV1
Category Physical measures
Type Biomarker
UK Biobank field 3063
Units L (UO_0000099)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 7
Definition Forced expired volume in 1 second. Excludes predicted values and measurements post-bronchodialation.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        FEV1 = value1

    ELSE IF data_provider = Scotland (2)
        FEV1 = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        FEV1 = value1
Terminology Read code Read term
read2 339O.00 Forced expired volume in 1 second
read2 3397.00 Forced expiratory volume - FEV
read2 339a.00 FEV1 before bronchodilation
read2 3397000 FEV normal
ctv3 X77Qu Forced expired volume in 1 second
ctv3 XaIxQ FEV1 before bronchodilation
ctv3 33970 FEV normal

FVC

Metadata
Name FVC
Category Physical measures
Type Biomarker
UK Biobank field 3062
Units L (UO_0000099)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 7
Definition Forced vital capacity measurement. Excludes predictd values and measurements post-bronchodialation.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        FVC = value1

    ELSE IF data_provider = Scotland (2)
        FVC = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        FVC = value1
Terminology Read code Read term
read2 3396.00 Forced vital capacity - FVC
read2 3396000 FVC - forced vital capacity normal
read2 3396100 FVC - forced vital capacity abnormal
ctv3 3396. Forced vital capacity
ctv3 33960 FVC - forced vital capacity normal
ctv3 33961 FVC - forced vital capacity abnormal
read2 339s.00 Forced vital capacity before bronchodilation

Glucose

Metadata
Name Glucose
Category Blood biochemistry
Type Biomarker
UK Biobank field 30740
Units mmol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 16
Definition Blood-based glucose level derived from plasma. Excludes fasting measurements.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Glucose = value1

    ELSE IF data_provider = Scotland (2)
        Glucose = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Glucose = value1
Terminology Read code Read term
read2 44g..00 Plasma glucose level
read2 44g0.00 Plasma random glucose level
ctv3 XM0ly Plasma glucose level
ctv3 44g0. Plasma random glucose level
read2 44U..00 Blood glucose result
read2 44TJ.00 Blood glucose level
read2 44U..11 Blood sugar result
read2 44TA.00 Plasma glucose
read2 44U4.00 Blood glucose 5-6.9 mmol/L
read2 44T1000 Random blood sugar normal
read2 44U3.00 Blood glucose 2.5-4.9 mmol/L
read2 44U8.00 Blood glucose normal
read2 44U5.00 Blood glucose 7-9.9 mmol/L
read2 44U..12 Plasma glucose level
read2 44U6.00 Blood glucose 10-13.9 mmol/L
read2 44T5.00 Laboratory blood sugar

HDL

Metadata
Name HDL
Category Blood biochemistry
Type Biomarker
UK Biobank field 30760
Units mmol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 6
Definition Serum fasting/non-fasting/random HDL cholesterol level.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        HDL = value1

    ELSE IF data_provider = Scotland (2)
        HDL = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        HDL = value1
Terminology Read code Read term
read2 44P5.00 Serum HDL cholesterol level
read2 44PB.00 Serum fasting HDL cholesterol level
read2 44PC.00 Serum random HDL cholesterol level
ctv3 44P5. Serum HDL cholesterol level
ctv3 44PB. Serum fasting HDL cholesterol level
ctv3 44PC. Serum random HDL cholesterol level

Haematocrit perc

Metadata
Name Haematocrit perc
Category Blood count
Type Biomarker
UK Biobank field 30030
Units % (UO_0000187)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 18
Definition Haematocrit / packed cell volume
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Haematocrit perc = value1

    ELSE IF data_provider = Scotland (2)
        Haematocrit perc = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Haematocrit perc = value1
Terminology Read code Read term
read2 4258.00 Haematocrit
read2 4257.00 Packed cell volume
read2 425..00 Haematocrit - PCV
read2 425..11 Packed cell volume - PCV
read2 425Z.00 Haematocrit - PCV - NOS
read2 4254.00 Haematocrit - PCV - low
read2 4251.00 Haematocrit - PCV - normal
ctv3 X76tb Haematocrit
ctv3 X76tc Packed cell volume
ctv3 XE2Zq Haematocrit - PCV
ctv3 XE2Zq Haematocrit - PCV level
ctv3 425Z. Haematocrit - PCV - NOS
ctv3 4254. Haematocrit - PCV - low
ctv3 4251. Haematocrit - PCV - normal
read2 4255.00 Haematocrit - borderline low
read2 4253.00 Haematocrit - PCV - high
read2 4256.00 Haematocrit - PCV - abnormal
read2 4252.00 Haematocrit - borderline high

Haemoglobin conc

Metadata
Name Haemoglobin conc
Category Blood count
Type Biomarker
UK Biobank field 30020
Units g/dL (UO_0000208)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 22
Definition Haemoglobin estimation
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Haemoglobin conc = value1

    ELSE IF data_provider = Scotland (2)
        Haemoglobin conc = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Haemoglobin conc = value1
Terminology Read code Read term
read2 423..00 Haemoglobin estimation
read2 423..11 Hb estimation
read2 4237.00 Haemoglobin normal
read2 4235.00 Haemoglobin low
read2 423Z.00 Haemoglobin estimation NOS
read2 4239.00 Haemoglobin high
read2 4236.00 Haemoglobin borderline low
read2 4234.00 Haemoglobin very low
read2 423B.00 Haemoglobin abnormal
ctv3 Xa96v Haemoglobin concentration
ctv3 XE2m6 Haemoglobin estimation
ctv3 XM1Vu Hb estimation
ctv3 4237. Haemoglobin normal
ctv3 4235. Haemoglobin low
ctv3 423Z. Haemoglobin estimation NOS
ctv3 4239. Haemoglobin high
ctv3 4236. Haemoglobin borderline low
ctv3 X76ti Haemoglobin H inclusion
ctv3 4234. Haemoglobin very low
ctv3 423B. Haemoglobin abnormal
read2 4238.00 Haemoglobin borderline high
read2 423A.00 Haemoglobin very high

HbA1c

Metadata
Name HbA1c
Category Blood biochemistry
Type Biomarker
UK Biobank field 30750
Units mmol/mol (nan)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 25
Definition HbA1c level recorded using International Federation of Clinical Chemistry and Laboratory Medicine or Diabetes Control and Complications Trial (DCCT).
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        HbA1c = value1

    ELSE IF data_provider = Scotland (2)
        HbA1c = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        HbA1c = value1
Terminology Read code Read term
read2 42W5.00 Haemoglobin A1c level - IFCC standardised
read2 42W4.00 HbA1c level (DCCT aligned)
read2 42W..00 Hb. A1C - diabetic control
read2 42W..11 Glycosylated Hb
read2 42W..12 Glycated haemoglobin
read2 42W2.00 Hb. A1C 7-10% - borderline
read2 42W1.00 Hb. A1C < 7% - good control
read2 42WZ.00 Hb. A1C - diabetic control NOS
read2 42W3.00 Hb. A1C > 10% - bad control
ctv3 XaPbt Haemoglobin A1c level - International Federation of Clinical Chemistry and Laboratory Medicine standardised
ctv3 XaERp HbA1c level (DCCT aligned)
ctv3 XE24t Hb. A1C - diabetic control
ctv3 X80U3 Glycated haemoglobin
ctv3 X80U3 Glycosylated Hb
ctv3 42W2. Hb. A1C 7-10% - borderline
ctv3 42W1. Hb. A1C < 7% - good control
ctv3 42WZ. Hb. A1C - diabetic control NOS
ctv3 42W3. Hb. A1C > 10% - bad control
read2 44TB.00 Haemoglobin A1c level
read2 42c..00 HbA1 - diabetic control
read2 42c3.00 HbA1 level (DCCT aligned)
read2 42c1.00 HbA1 7 - 10% - borderline control
read2 42c0.00 HbA1 < 7% - good control
read2 44TC.00 Haemoglobin A1 level
read2 42c2.00 HbA1 > 10% - bad control

Height

Metadata
Name Height
Category Physical measures
Type Biomarker
UK Biobank field 50
Units cm (UO_0000015)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 6
Definition Height
Version alpha

Implementation

IF data_provider = England Vision (1) OR data_provider = Wales (4) IF read_2 in phenotype codes Height = value1

ELSE IF data_provider = Scotland (2) IF read_2 = “229.. O/E – height” Height = value1

ELSE IF data_provider = England TPP (3) IF CTV3 code = read_3 Height = value1

Terminology Read code Read term
read2 229..00 O/E - height
read2 229Z.00 O/E - height NOS
read2 2293.00 O/E -height within 10% average
ctv3 229.. O/E - height
ctv3 229Z. O/E - height NOS
ctv3 2293. O/E -height within 10% average

Lymphocytes

Metadata
Name Lymphocytes
Category Blood count
Type Biomarker
UK Biobank field 30120
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 7
Definition Leucocyte count
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Lymphocytes = value1

    ELSE IF data_provider = Scotland (2)
        Lymphocytes = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Lymphocytes = value1
Terminology Read code Read term
read2 42M..00 Lymphocyte count
read2 42MZ.00 Lymphocyte count NOS
read2 42M1.00 Lymphocyte count normal
read2 42M4.00 Abnormal lymphocytes
ctv3 42M.. Lymphocyte count
ctv3 42MZ. Lymphocyte count NOS
ctv3 42M1. Lymphocyte count normal

MCHb conc

Metadata
Name MCHb conc
Category Blood count
Type Biomarker
UK Biobank field 30060
Units g/dL (UO_0000208)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 10
Definition Mean corpusc. Hb. conc. (MCHC)
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        MCHb conc = value1

    ELSE IF data_provider = Scotland (2)
        MCHb conc = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        MCHb conc = value1
Terminology Read code Read term
read2 429..00 Mean corpusc. Hb. conc. (MCHC)
read2 429Z.00 MCHC - NOS
read2 4291.00 MCHC - normal
ctv3 429.. Mean cell haemoglobin concentration
ctv3 429Z. MCHC - NOS
ctv3 4291. MCHC - normal
read2 4294.00 MCHC - raised
read2 4293.00 MCHC - low
read2 4292.00 MCHC - borderline low
read2 4295.00 MCHC - borderline raised

MCV

Metadata
Name MCV
Category Blood count
Type Biomarker
UK Biobank field 30040
Units fL (UO_0000104)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 13
Definition Mean corpuscular volume (MCV)
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        MCV = value1

    ELSE IF data_provider = Scotland (2)
        MCV = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        MCV = value1
Terminology Read code Read term
read2 42A..00 Mean corpuscular volume (MCV)
read2 42A..11 Mean cell volume
read2 42AZ.00 MCV - NOS
read2 42A1.00 MCV - normal
read2 42A3.00 MCV - raised
read2 42A4.00 MCV - low
ctv3 42A.. Mean cell volume
ctv3 42AZ. MCV - NOS
ctv3 42A1. MCV - normal
ctv3 42A3. MCV - raised
ctv3 42A4. MCV - low
read2 42A2.00 MCV - borderline raised
read2 42A5.00 MCV - borderline low

Monocytes

Metadata
Name Monocytes
Category Blood count
Type Biomarker
UK Biobank field 30130
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 9
Definition Monocyte count
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Monocytes = value1

    ELSE IF data_provider = Scotland (2)
        Monocytes = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Monocytes = value1
Terminology Read code Read term
read2 42N..00 Monocyte count
read2 42NZ.00 Monocyte count NOS
read2 42N1.00 Monocyte count normal
read2 42N5.00 Monocyte count abnormal
ctv3 42N.. Monocyte count
ctv3 42NZ. Monocyte count NOS
ctv3 42N1. Monocyte count normal
ctv3 42N5. Monocyte count abnormal
read2 42N2.00 Monocyte count raised

Neutrophills

Metadata
Name Neutrophills
Category Blood count
Type Biomarker
UK Biobank field 30140
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 13
Definition Neutrophil count
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Neutrophills = value1

    ELSE IF data_provider = Scotland (2)
        Neutrophills = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Neutrophills = value1
Terminology Read code Read term
read2 42J..00 Neutrophil count
read2 42JZ.00 Neutrophil count NOS
read2 42J..11 Granulocyte count
read2 42J2.00 Neutropenia
read2 42J1.00 Neutrophil count normal
read2 42J3.00 Neutrophilia
read2 42J4.00 Neutrophil count abnormal
ctv3 42J.. Neutrophil count
ctv3 42JZ. Neutrophil count NOS
ctv3 42J2. Neutropenia
ctv3 42J1. Neutrophil count normal
ctv3 42J3. Neutrophilia
ctv3 42J4. Neutrophil count abnormal

Platelets

Metadata
Name Platelets
Category Blood count
Type Biomarker
UK Biobank field 30080
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 12
Definition Platelet count. Excludes platelet distribution width measurements.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Platelets = value1

    ELSE IF data_provider = Scotland (2)
        Platelets = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Platelets = value1
Terminology Read code Read term
read2 42P..00 Platelet count
read2 42P1.00 Platelet count normal
read2 42PZ.00 Platelet count NOS
read2 42P2.00 Thrombocytopenia
read2 42P3.00 Thrombocythaemia
read2 42P4.00 Platelet count abnormal
ctv3 42P.. Platelet count
ctv3 42P1. Platelet count normal
ctv3 42PZ. Platelet count NOS
ctv3 XE24o Thrombocytopenia
ctv3 42P3. Thrombocythaemia
ctv3 42P4. Platelet count abnormal

RBC

Metadata
Name RBC
Category Blood count
Type Biomarker
UK Biobank field 30010
Units 10^12/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 12
Definition Red blood cell (RBC) count excluding nucleated RBC values.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        RBC = value1

    ELSE IF data_provider = Scotland (2)
        RBC = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        RBC = value1
Terminology Read code Read term
read2 426..00 Red blood cell (RBC) count
read2 426Z.00 RBC count NOS
read2 4261.00 RBC count normal
read2 4263.00 RBC count low
ctv3 426.. Red blood cell count
ctv3 426Z. RBC count NOS
ctv3 4261. RBC count normal
ctv3 4263. RBC count low
read2 4262.00 RBC count borderline low
read2 4264.00 RBC count raised
read2 4267.00 RBC count abnormal
read2 4265.00 RBC count borderline raised

SBP

Metadata
Name SBP
Category Physical measures
Type Biomarker
UK Biobank field 93
Units mmHg (UO_0000272)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 0
Definition Systolic blood pressure.
Version alpha

Implementation

IF data_provider = England Vision (1)
    IF read_2 = “246..00 O/E - blood pressure reading”' 
        SBP = value1
        DBP = value2

ELSE IF data_provider = Scotland (2)
    IF read_2 = “246..00 O/E - blood pressure reading”
        DBP = value1
        SBP = value2
    ELSE IF read_2 = “2469.00 O/E - Systolic BP reading”
        SBP = value1
    ELSE IF read_2 = “246A.00 O/E - Diastolic BP reading”
        DBP = value1

IF data_provider = England TPP (3)
    IF read_3 = “2469.00 O/E - Systolic BP reading” 
        SBP = value1
    ELSE IF read_3 = “246A.00 O/E - Diastolic BP reading” 
        DBP = value1

IF data_provider = Wales (4)
    IF read_2 = “246..00 O/E - blood pressure reading”
        SBP = value1
        DBP = value2
    ELSE IF read_2 = “2469.00 O/E - Systolic BP reading”
        SBP = value1
    ELSE IF read_2 = “246A.00 O/E - Diastolic BP reading”
        DBP = value1

Total bilirubin

Metadata
Name Total bilirubin
Category Blood biochemistry
Type Biomarker
UK Biobank field 30840
Units umol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 15
Definition Serum bilirubin level. Excludes conjugated bilirubin levels.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Total bilirubin = value1

    ELSE IF data_provider = Scotland (2)
        Total bilirubin = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Total bilirubin = value1
Terminology Read code Read term
read2 44EC.00 Serum total bilirubin level
read2 44E..00 Serum bilirubin level
read2 44E3.00 Total bilirubin
read2 44E1.00 Serum bilirubin normal
read2 44EZ.00 Serum bilirubin NOS
read2 44E2.00 Serum bilirubin raised
read2 44E6.00 Serum bilirubin borderline
ctv3 XaERu Serum total bilirubin level
ctv3 44E.. Serum bilirubin level
ctv3 XE2qu Total bilirubin level
ctv3 XE2qu Total bilirubin
ctv3 44E1. Serum bilirubin normal
ctv3 44EZ. Serum bilirubin NOS
ctv3 44E2. Serum bilirubin raised
ctv3 44E6. Serum bilirubin borderline

Triglycerides

Metadata
Name Triglycerides
Category Blood biochemistry
Type Biomarker
UK Biobank field 30870
Units mmol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 15
Definition Serum triglycerides measurements. Algorithm excludes plasma-derived measurements. Includes fasting/non-fasting/random values.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Triglycerides = value1

    ELSE IF data_provider = Scotland (2)
        Triglycerides = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Triglycerides = value1
Terminology Read code Read term
read2 44Q..00 Serum triglycerides
read2 44Q4.00 Serum fasting triglyceride level
read2 44Q5.00 Serum random triglyceride level
read2 44QZ.00 Serum triglycerides NOS
read2 44Q1.00 Serum triglycerides normal
read2 44Q3.00 Serum triglycerides raised
read2 44Q2.00 Serum triglycerides borderline
ctv3 XE2q9 Serum triglycerides
ctv3 XE2q9 Serum triglyceride levels
ctv3 44Q4. Serum fasting triglyceride level
ctv3 44Q5. Serum random triglyceride level
ctv3 44QZ. Serum triglycerides NOS
ctv3 44Q1. Serum triglycerides normal
ctv3 44Q3. Serum triglycerides raised
ctv3 44Q2. Serum triglycerides borderline

Urea

Metadata
Name Urea
Category Blood biochemistry
Type Biomarker
UK Biobank field 30670
Units mmol/L (UO_0010003)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 17
Definition Serum / plasma urea level
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        Urea = value1

    ELSE IF data_provider = Scotland (2)
        Urea = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        Urea = value1
Terminology Read code Read term
read2 44J9.00 Serum urea level
read2 44J8.00 Blood urea
read2 44J..11 Urea - blood
read2 44JA.00 Plasma urea level
read2 44J..00 Blood urea/renal function
read2 44J1.00 Blood urea normal
read2 44J2.00 Blood urea abnormal
read2 44J..13 Serum urea level
read2 44JZ.00 Blood urea/renal function NOS
read2 44J8.11 Urea - blood
ctv3 XM0lt Serum urea level
ctv3 X771P Blood urea
ctv3 X771P Urea - blood
ctv3 XaDvl Plasma urea level
ctv3 44J1. Blood urea normal
ctv3 44J2. Blood urea abnormal
ctv3 44JZ. Blood urea/renal function NOS

WBC

Metadata
Name WBC
Category Blood count
Type Biomarker
UK Biobank field 30000
Units 10^9/L (UO_0000317)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 19
Definition Total white cell count. Excludes polymorphonuclear leukocyte count.
Version alpha

Implementation

IF Read v2 code = read_2
    IF data_provider = England Vision (1) OR data provider = Wales (4)
        WBC = value1

    ELSE IF data_provider = Scotland (2)
        WBC = value2
        units = value3

ELSE IF CTV3 code = read_3 
    IF data_provider = England TPP (3)
        WBC = value1
Terminology Read code Read term
read2 42H..00 Total white cell count
read2 42H..11 White blood count
read2 42H..12 White cell count
read2 42H7.00 Total white blood count
read2 42H1.00 White cell count normal
read2 42HZ.00 Total white cell count NOS
read2 42H3.00 Leucocytosis -high white count
read2 42H8.00 Total WBC (IMM)
read2 42H2.00 Leucopenia - low white count
read2 42H5.00 White cell count abnormal
ctv3 XaIdY Total white blood count
ctv3 42H.. White blood cell count
ctv3 42H.. White blood cell count - observation
ctv3 42H1. White cell count normal
ctv3 42H3. Leucocytosis
ctv3 42HZ. Total white cell count NOS
ctv3 XaIdZ Total WBC (IMM)
ctv3 42H2. Leucopenia
ctv3 42H5. White cell count abnormal

Weight

Metadata
Name Weight
Category Physical measures
Type Biomarker
UK Biobank field 21002
Units Kg (UO_0000009)
Data source UK Biobank
Sex Male/female
Controlled clinical terminologies Read v2, Clinical Terms Version 3
Total terms 18
Definition Weight
Version alpha

Implementation

IF read_2 in phenotype codes IF data_provider = England Vision (1) OR data_provider = Wales (4) Weight = value1

ELSE IF data_provider = Scotland (2)
    IF read_2 = '22A.. O/E - weight' 
        Weight = value2

ELSE IF read_3 in phenotype codes IF data_provider = England TPP (3) Weight = value1

Terminology Read code Read term
read2 22A..00 O/E - weight
read2 22AZ.00 O/E - weight NOS
read2 22A4.00 O/E - weight 10-20% over ideal
read2 22A3.00 O/E - weight within 10% ideal
read2 22A5.00 O/E - weight > 20% over ideal
read2 22A4.11 O/E - overweight
read2 22A5.11 O/E - obese
read2 22A6.00 O/E - Underweight
ctv3 22A.. O/E - weight
ctv3 22AZ. O/E - weight NOS
ctv3 XE1h3 O/E - weight 10-20% over ideal
ctv3 XM1YD O/E - overweight
ctv3 22A3. O/E - weight within 10% ideal
ctv3 222A. O/E - obese
ctv3 22A6. O/E - Underweight
read2 1622.00 Weight increasing
read2 22A2.00 O/E -weight 10-20% below ideal
read2 22A1.00 O/E - weight > 20% below ideal

Units

Raw value Cleaned
MEA000
MEA001 %
MEA016 /hour
MEA021 /mL
MEA026 1
MEA031 10*12/L
MEA035 10*6/L
MEA037 10*9/L
MEA038 10*9/mL
MEA047 fL
MEA056 g/dL
MEA057 g/L
MEA058 h
MEA061 IU/L
MEA062 IU/mL
MEA071 L/min
MEA080 mg
MEA082 mg/dL
MEA083 mg/L
MEA086 mg/mmol
MEA090 mL/min
MEA093 mm(Hg)
MEA095 mmol/d
MEA096 mmol/L
MEA097 mmol/mol
MEA099 mol/L
MEA104 ng
MEA106 ng/mL
MEA110 nmol/L
MEA114 pg
MEA116 pg/dL
MEA124 s
MEA127 U/L
MEA142 umol/L
MEA151 ratio
MEA153 10*9
MEA154 L
MEA156 mmol
MEA161 1/1
MEA169 mIU/L
MEA178 ug/mL
MEA183 10*-2
MEA184 10*-3
MEA185 L/L
MEA187 nmol/g
MEA194 titre
MEA205 nmol/gHb/h
MEA210 #G ( )/L
MEA215 %Hb
MEA252 mmol/g(dry wt)
x10^9/l 10^9/L
10^9/L 10^9/L
x10^9/L 10^9/L
10^9/l 10^9/L
10 ^9/L 10^9/L
x10^9 /L 10^9/L
x10-9/l 10^9/L
10*9/L 10^9/L
x10 ^9/L 10^9/L
x10 9/L 10^9/L
X10 9/L 10^9/L
*10^9/l 10^9/L
10 ^9/l 10^9/L
10*9/l 10^9/L
x10^12/l 10^12/L
10^12/L 10^12/L
x10^12/L 10^12/L
10 ^12/L 10^12/L
10^12/l 10^12/L
x10-12/l 10^12/L
10*12/L 10^12/L
fl fL
g/l g/L
mmHG mmHg
mm/Hg mmHg
mm Hg mmHg
mg/l mg/L
g/dl g/dL
l L
litre L
litres L
Litres L
mmol/l mmol/L
mmol/L mmol/L
mmol/mol Hb mmol/mol
MMOL/L mmol/L
umol/L umol/L
umol/l umol/L
Mmol/mol mmol/L
nmol/l nmol/L
%Hb %
per cent %
Ratio ratio
% total Hb %
%total Hb %
µmol/L umol/L
u/l U/L
IU/L U/L
iu/l U/L
No UOM assigned
Unknown

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Metadata

Phenotyping algorithms for common biomarkers in primary care EHR for UK Biobank

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