Metadata for human samples

The following table contains an overview of the core and partially harmonised metadata attributes. For ease of use, the Metalog website shows more descriptive field names. The table contains both the name shown in the download files and the one shown here on the website. Click the icons in the table to see more information for each field.

For human samples, the following columns are harmonised by an automatic mapping: diet, intervention, sex, smoker, subject_disease_status, type_of_birth

Field name
Label shown on website
Count
Most common values
age_category
age category
84592
adult, baby, child
age_range
age range (years)
29101
adult, 50 to 64, 18 to 70
age_years
age (years)
55491
1, 0.25, 25
artificial
artificial or special treatment
749
cultivation, paleosample, enrichment
birth_year
3604
2018, 2014, 2010
bmi
body mass index
24664
23, 24, 20
diet
diet
7997
omnivore, breastfed, formula-fed
environment_feature
source material environment
93144
intestine environment [ENVO:2100002], mouth environment [ENVO:08000002], skin environment [ENVO:2100003]
environment_material
source material
93144
fecal material [ENVO:00002003], saliva material [ENVO:02000036], supragingival dental plaque [UBERON:0016485]
geographic_location
country/ocean region
93144
USA, China, United Kingdom
height_cm
height (cm)
12927
170, 160, 165
intervention
kind of intervention
18793
antibiotics, diet intervention, fecal microbiota transplant
latitude
93136
37.38, 31.99, 32.08
location
79518
USA, China, Canada
location_resolution
resolution of location info
93144
country, city, site
longitude
93136
-92.87, 113.26, 34.81
medication
medication
14818
ATC J01, Ciprofloxacin; Metronidazole, Ibuprofen
sample_alias
93144
Aggarwala_2020_FMT_RCDI.sample_1001095A, Aggarwala_2020_FMT_RCDI.sample_1001095F, Aggarwala_2020_FMT_RCDI.sample_1001095G
sex
sex
58206
female, male
smoker
smoking status
7171
non-smoker, smoker, ex-smoker
study_code
93144
Zhou_2022_MS, Dai_2023_child_allergy, Valles-Colomer_2023_transmission
subject_disease_status
disease status
82216
COHORT, CTR, multiple sclerosis
subject_id
93144
Poyet_2019_BIOML.am, Fukuyama_2017_bowelcleansing.AAB, Poyet_2019_BIOML.ao
timepoint
days since first sample
88153
0, 1, 28
timeseries_available
time series data available?
93144
no, yes
timeseries_count
time series: count of timepoints
93144
1, 2, 3
timeseries_duration
time series: length in days
88409
0, 28, 1
type_of_birth
type of birth
9223
Vaginal birth, Caesarean section
weight_kg
weight (kg)
13905
60, 65, 79.4

Field name
Label shown on website
Count
Most common values
Blood_group
98
A+, B+, O+
Comorbidities
30
Hypertension, renal impairment, hyperlipidemia, Diabetes mellitus, hypertension, hyperlipidemia, Hypertension, Chronic hepatitis B carrier
Drug_antibiotic_last3y
211
No, 2 months
age_days
6472
7, 21, 4
age_months
431
10, 11, 8
amy1cn
140
10.82439393, 12.7950299, 3.655166954
antibiotic
466
oral ciprofloxacin 500 mg bi-daily and oral metronidazole 500 mg tri-daily for a period of 7 days, Broad spectrum antibiotics, Narrow spectrum antibiotics
antibiotic_dosage
72
100 mg twice daily for 56 days, 20 mg twice daily for 56 days, 500mg three times daily for 14 days
birth_country
145
SWE, DEU, DNK
birth_gestational_age_weeks
3939
26, 25, 28
birth_mode
2711
Vaginal Delivery, Caesarean Section
birth_term_status
7212
preterm, extremely preterm, very preterm
birth_weight_kg
45
0.734, 2.847
bmi_range
1548
over 30, over 23, 20 to 25
bristol_stool_scale
1555
4, 3, 5
cause_of_death
11
Sudden cardiac death, multiple organ failure, enteric volvulus, hemorrhagic infarct
cohort
107
exercise cohort, sedentary cohort, validation cohort
common_timepoint
796
0, 7M, 5M
comorbidities
56
Liver steatosis, Acute respiratory disease, COPD
couple_id
1885
10009, 10049, 10007
couple_timepoint
1981
7, 21, 4
cultivation_condition
191
aerobic (with 5% CO2) culture in the presence of 32 μg/ml cefoxitin (FOX-CO2), maximum enrichment broth aerobic culture (air enriched with 5% CO2) (MEB-CO2), maximum enrichment broth anaerobic culture (MEB-ANA)
cultivation_duration
191
7 days
days_since_antibiotics
2089
0, 4, 16
days_since_fmt
117
-1, -2, 11
diet_full
2523
expressed breast milk, formula-fed, expressed breast milk and formula-fed
donor_d0
844
Smillie_2018_FMT_CDI.FMT2, PT-18-0008, PT-18-0002
donor_d28
18
SAMN03955540, SAMN03955542, SAMN03955544
ethnicity
10796
White, Caucasian/Hispanic, Caucasian
family
4508
MyMicrobes.FAM02, MyMicrobes.FAM01, MyMicrobes.FAM06
fmt_donor
117
D0097, D0044, D0485
full_description
1613
stool sample (during watchful waiting) of participant 802, stool sample (during watchful waiting) of participant 803, stool sample (during watchful waiting) of participant 804
gestational_age_weeks
292
33.85714286, 32.85714286, 34.42857143
gestational_state
292
pregnant
group
137
14, 7
hip_cm
116
103, 99, 100
host
39
Homo sapiens
intervention_full
1229
ABX, FMT, probiotic
lifestyle
330
rural agriculturalist, Peri-urban industralist, Hunter-gatherer
linked_to
1318
M0018_mother, M0038_mother, M0059_mother
medical_history_notduringstudy
26
AV block; ADHD, Afib, hyperlipidemia, At least two recurrences of CDI; obesity; RA
medical_operation
39
Roux-en-Y gastric bypass, vertical sleeve gastrectomy, metbaolic gastric bypass
medication_full
14366
antibiotic, antibiotics, ciprofloxacin; metronidazole
medicinal_plant
67
Tripterygium wilfordii
menopausal_status
215
Post-Menopausal, Pre-Menopausal, Going Through Menopause
note
6543
dataset contains multiple samples per subject, but these cannot be linked with the available metadata, additional metadata available upon request (see paper), The stated sample location differs between the paper and the uploaded metadata. Coordinates follow the paper.
original_timepoint
929
7, 8, 5
pregnancy_week
68
30, 37
pregnant
362
0, 1
probiotic
1413
Labinic, Supherb Bio-25 bi-daily, InfloranUK
range_days_since_antibiotics
2147
unclear data, 0-7, 0-90
recipient_donor
433
recipient, Recipient, donor
sample_description
40431
Keywords: GSC:MIxS;MIMS:5.0, Keywords: GSC:MIxS;MIMS:6.0, saliva_metagenome_from_USA
sample_title
72583
Metagenome or environmental sample from human gut metagenome, MIMS Environmental/Metagenome sample from human gut metagenome, Preterm stool metagenome
skin_site_type
1459
sebaceous, moist, rarely_intermittently_moist
stool_consistency
415
Normal, Hard, Mushy
study_accession
1590
PRJNA912122, PRJEB48269, PRJEB60773
subject_disease_status_full
5986
CTR, prediabetes, obesity
synbiotic
68
Bifidobacterium infantis, human milk oligosaccharides
time_period
57
1770-1855, 1200-1400 BP, 5300 BP
timepoint_note
152
second clinic visit 4 to 19 weeks (on average 60 days), precision of date: day, colostrum (milk at birth)
tissue_type
1613
Stool, Transverse colon mucosa, Descending colon mucosa
vaccine_name
382
BioNTech, SinoVac
vaginal_pH
192
4, 4.4, 4.7
village
871
FijiCOMP.village.1, FijiCOMP.village.3, FijiCOMP.village.2
waist_cm
680
80, 79, 82