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