Data
Location
Sandbox
/finngen/library-red/finngen_R12/kanta_lab_1.0/data/finngen_R12_kanta_lab_1.0.txt.gzin textual TSV-gzipped format (for use withawk,grep, UNIX piping)/finngen/library-red/finngen_R12/kanta_lab_1.0/data/finngen_R12_kanta_lab_1.0.parquetin binary Parquet format (for use with Python pandas, R data.frame)
BigQuery
Available in this table:
finngen-production-library.sandbox_tools_r12.kanta_r12_v1
Data columns
Overview
FINNGENID
Study ID (Pseudonymised ID given to the FinnGen participant)
✓
✓
SEX
Sex of the individual, female or male
✓
EVENT_AGE
Age (in years) at time of event, e.g. 12.012
✓
✓
APPROX_EVENT_DATETIME
✓
✓
TEST_NAME
Short name of the lab test, e.g. p-alat, s-tsh
✓
✓
TEST_ID
Code of the lab test (national or local lab test ID)
✓
✓
TEST_ID_IS_NATIONAL
Whether or not the TEST_ID is using the national lab test code system
✓
OMOP_CONCEPT_ID
OMOP Concept ID mapped from the TEST_ID and MEASUREMENT_UNIT
✓
✓
MEASUREMENT_VALUE
Value of the test measurement
✓
✓
MEASUREMENT_UNIT
Corresponding unit for the test measurement
✓
✓
MEASUREMENT_VALUE_HARMONIZED
Value of the test measurement, after harmonization across the OMOP Concept ID
✓
✓
MEASUREMENT_UNIT_HARMONIZED
Corresponding unit for the harmonized measurement value
✓
✓
TEST_OUTCOME
✓
✓
TEST_OUTCOME_IMPUTED
✓
MEASUREMENT_STATUS
✓
✓
REFERENCE_RANGE_GROUP
Reference range for this event, as text
✓
REFERENCE_RANGE_LOW_VALUE
Value for the low bound of the reference range
✓
✓
REFERENCE_RANGE_LOW_UNIT
Corresponding unit for the low bound of the reference range
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REFERENCE_RANGE_HIGH_VALUE
Value for the high bound of the reference range
✓
✓
REFERENCE_RANGE_HIGH_UNIT
Corresponding unit for the high bound of the reference range
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CODING_SYSTEM_ORG
Derived from CODING_SYSTEM_OID
✓
CODING_SYSTEM_OID
Original name: tutkimuskoodistonjarjestelmaid
✓
✓
TEST_ID_SOURCE
Code of the lab test, as it appeared before preprocessing of the data
✓
TEST_NAME_SOURCE
Short name of the lab test, as it appeared before preprocessing of the data
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MEASUREMENT_VALUE_SOURCE
Value of the test measurement, as it appeared before data cleaning
✓
MEASUREMENT_UNIT_SOURCE
Unit of the test measurement, as it appeared before data cleaning
✓
TEST_OUTCOME
TEST_OUTCOMEThis column provides a label comparing the measured value against a reference range.
N
Normal
A
Abnormal
AA
Very abnormal
L
Low
LL
Very low
H
High
HH
Very high
TEST_OUTCOME_IMPUTED
TEST_OUTCOME_IMPUTEDSome rows are missing the TEST_OUTCOME, so an imputed one is provided. The TEST_OUTCOME_IMPUTED is derived by looking at the data from the same OMOP Concept ID for which there are MEASUREMENT_VALUE and TEST_OUTCOME.
N
Imputed Normal
L
Imputed Low
L*
Imputed Low. Less confidence in the imputation due to over-representation of L and H from TEST_OUTCOME
H
Imputed High
H*
Imputed High. Less confidence in the imputation due to over-representation of L and H from TEST_OUTCOME
MEASUREMENT_STATUS
MEASUREMENT_STATUSC
Corrected result
F
Final result
R
Unverified result
S
Partial result
Other reference tables
Test name abbreviations
Test name abbreviations come from different laboratory testing centers around Finland. Some are standardized nationally and some are used only locally in different hospitals and test centers.
We have put a lot of effort into standardizing these to international OHDSI OMOP Concept ID (primarily from LOINC) so we hope that you do not need to interpret them very often! However, in case you have reason to use them, we provide the meaning of most abbreviations here.
Prefixes for lab test name abbreviations
aB
Arterial blood
Af
Puncture fluid
aG
Alveolar gas
Am
Amniotic fluid
As
Ascitic fluid
B
Blood
Bf
Bronchus fluid
Bi
Bile
Bl
Bronchoalveolar lavation
Bm
Bone Marrow
Bo
Bone
Br
Breast
Bu
Bursa
Ca
Cannula/IV port
cB
Capillary blood
Cf
Cervix fluid
Cn
Central nervous system
cU
Collected urine
Cv
Choroid villus
Di
Dialysis fluid
Dj
Duodenal juice
dU
Diurnal urine
E
Erythrocyte
Ex
Sputum
F
Fecal
fB
Fasting blood
Fl
Vaginal fluor
fP
Fasting plasma
fS
Fasting serum
Gi
Gastrointestinal
Gj
Gastric juice
Hb
Hemoglobin
He
Heart
Ki
Kidney
L
Leukocytes
Lf
Lacrimal fluid
Li
Likvor/CSF
Ln
Lymph Node
Lr
Liver
Lu
Lung
Ly
Lymphocytes
M
Muscle
mB
Machine blood
Me
Meconium
Mf
Mammary fluid
Mm
Maternal milk
Mu
Mucosa
Ne
Nerve
Ns
Nasal secretion
nU
Nocturnal urine
P
plasma
Pd
Peritoneal dialysis
Pf
Pleura
Pi
Pituitary gland
Pl
Placenta
Pp
Periodontal pocket
Ps
Pharyngeal secretion
Pt
Patient
Pu
Pus
S
Serum
Sa
Saliva
Se
Secretion
Sk
Skin
Sp
Semen
Sw
Sweat
Sy
Syncytial fluid
T
Thrombocyte
Ts
Tissue
Tu
Tumor
U
Urine
uA
Umbilical arterial blood
Ug
Urogenital
uS
Umbilical serum
uV
Umbilical venous blood
vB
Venous blood
W
Water
Suffixes for lab test name abbreviations
-Ab
Antibody
-AbA
IgA antibody
-AbE
IgE antibody
-AbG
IgG antibody
-AbM
IgM antibody
-Ag
Antigen
-Akt
Activity
-Aktt
Activation products
-Cl
Clearance
-Ct
Control
-D
DNA
-Di
Dialysis
-EVi
Special culture
-EM
Electron Microscopic
-F
Fetal
-Fc
Flow cytometry
-Fr
Fraction
-Gr
Gestational
-IF
Immunofluorescence
-IH
Immunohistochemistry
-Ind
Index
-Ion
Ionized
-Is
Iso enzymes
-ISH
in situ -hybridisation
-Jtk
Follow-up study
-Jvi
Follow-up culture
(jatkoviljely)
-Kj
Conjugate
-Lm
Species specificity
-MS
Mass spectrometry
-Nh
Nucleic acid
-O
Qualitative
-Oc
Oligoclonal
-Pa
Long term
-Pse
Screening and categorization
-PT
Rapid test
-R
Exercise stress test
-S
Stimulation
-Sc
Sub classes
-Ty
Typing
-V
Free or unconjugated
-Vi
Microbiology culture (e.g. u-Baktvi = bacterial culture from urine, ps-stravi = Strep A culture in pharayngeal secretion, F-sienVi = fungal culture in stool)
-Vit
Vitamine
-Vr
Staining
-Vt
Point of care (vieritesti), often a rapid test
Reference range terms
Test reference ranges are a free text string that can have a lot of Finnish in them. For those who don’t speak Finnish, we provide here translations of some of the common words you will see in reference ranges:
General terms:
AIKUISET: Adults
ALLE: Under/Below
ALK: Abbreviation for "alkaen", meaning "starting from" or "beginning at"
ALTISTUMATTOMAT: Unexposed (individuals)
AAMUNÄYTE: Morning sample
EDELLEEN: Still, continuing
FERTIILI-IKÄ: Fertile age
HOITOALUE: Treatment range
JA: And
JÄÄNNÖSPIT: Residual concentration
KAIKKI: All, everyone
KATSO: See, look at
KK: Abbreviation for "kuukausi", meaning month
KS: Abbreviation for "katso", meaning "see" or "look at"
KTS: Another abbreviation for "katso"
KYMENLAAKSONLAB: Kymenlaakso Laboratory (a specific lab in Finland)
LAPSET: Children
LEUK: Leukocytes (white blood cells)
LIER: Likely referring to "lieriöt", meaning casts (in urine analysis)
MIEHET: Men
NAISET: Women
NEGAT: Negative
NORMAALI: Normal
OHJEKIRJA: Manual, guidebook
PAASTO: Fasting
POJAT: Boys
POSTMENOPAUSSI: Postmenopausal
PREMENOPAUSAALISET: Premenopausal
PUBERT: Puberty
RASKAUS: Pregnancy
SUOSITELTAVA: Recommended
TAVOITE: Target, goal
TAVOITEARVO: Target value
TERAP: Therapeutic
TOKSINEN: Toxic
TULKINTA: Interpretation
TUPAKOIMATTOMAT: Non-smokers
TYTÖT: Girls
V: Abbreviation for "vuosi", meaning year
VASTASYNT: Newborn
VIITEARVO: Reference value
VKO: Abbreviation for "viikko", meaning week
VRK: Abbreviation for "vuorokausi", meaning day (24-hour period)
YLI: Over, above
Age-related terms:
0-6PV: 0-6 days
1KK-1V: 1 month to 1 year
1V-: 1 year and older
2-4V: 2-4 years
5-10V: 5-10 years
11-15V: 11-15 years
16V-: 16 years and older
18V-: 18 years and older
Medical terms:
ERYT: Erythrocytes (red blood cells)
EPIT.SOLUT: Epithelial cells
FOLLIKK.VAIHE: Follicular phase (of menstrual cycle)
MAKUU: Lying down (usually referring to blood pressure measurement)
MENARKEA: Menarche (first menstrual period)
PYSTY: Standing (usually referring to blood pressure measurement)
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