Metadata field: note

Studies:

Scope: all

Type: string

Description: Any issues encountered during annotation.

Examples:

  • Timepoints are not exact (4-6 months)
  • Intervention not explicitly stated, but inferred from group size
  • Dataset contains multiple samples per subject, but these cannot be linked with the available metadata.
  • The stated sample location differs between the paper and the uploaded metadata. Coordinates follow the paper.
Value Count
dataset contains multiple samples per subject, but these cannot be linked with the available metadata 2934
additional metadata available upon request (see paper) 924
Sample dietary class information was not provided. 724
MC samples include both microscopic colitis and chronic diarrhea (≥ 3 bowel movements/day and BSS > 5) patients; information on microscopic colitis activity (active: ≥3 bowel movements/day and BSS > 5, remission: <3 bowel movements/day and BSS ≤ 5) is not available, median time between active to remission samples was ≥8 weeks, median 159 days (IQR 89-238). 428
The stated sample location differs between the paper and the uploaded metadata. Coordinates follow the paper. 400
no antibiotic treatment 2 months before sampling 368
exact timepoint unknown 305
up to three stool samples were collected from each participant and mixed 298
gestational age and age in days do not always match 293
due to incomplete metadata, is is not possible to identify subjects, timepoints, BMI and intervention 152
age range: 10th to 90th percentile 149
allogeneic haematopoietic stem-cell transplant recipient 136
subject identifiers are unknown 128
Disease status and timepoints inferred from sample alias, no explicit information 100
related paper: https://doi.org/10.1371/journal.pntd.0008783 96
Donor samples are mixtures of stool from two donors 93
Sample dietary class information was not provided. Age is the midpoint of the reported 1-2 weeks range. 84
Collection date were not given, approximate timepoints calculated based on figure 1 in the publication, where time between baseline 2 and the first cycle is 4 weeks and between cycle 1 and cycle 2 is 8 weeks 71
bowel preparation using macrogol at timepoint -1 (one day before FMT); FMT via nasoduodenal tube 63
ENA coordinates were inconsistent with the paper and were corrected based on the paper. Sample-level timepoints and other supplement details were not provided. 54
no antibiotics 60d prior to FMT; no probiotics 30d prior; steroids tapered for at least 14d prior to FMT 49
500 mg twice daily for five days 43
FMT donor 41
mapping between deposited sequences and metadata needed to be manually inferred by Sebastian Schmidt 41
recent HIV infection 35
each subject provided duplicate fecal samples 30
subject took no medication and had no allergies 30
Small adenoma, but used as control 28
most patients received antibiotics 26
treatment metadata is unclear 25
inconsistent metadata on sex and birth weight given 22
FMT donor 2 sample 18
FMT donor sample 16
pre thoracic aortic dissection operation 14
FMT donor 1 sample 11
SAMEA104393740 is mislabelled: it clusters with the donor samples instead of the recipients; experiment has been removed from the db 11
second antibiotic taken Cotrimoxazole 9
post thoracic aortic dissection operation 8
It is unclear whether the disease abbreviation ""CB"" refers to chronic bronchitis or cerebral bleeding. 7
Sample taken after overnight fasting and ingestion of 10^8 colonoy-forming units of Escherichia coli 7
Subject also on vancomycin 7
Subjects Langdon_2021_RCDI.subject_A24.1 and Langdon_2021_RCDI.subject_A24.2 are the same person, but relative timing is unclear 7
Subjects Langdon_2021_RCDI.subject_A7.1 and Langdon_2021_RCDI.subject_A7.2 are the same person, but relative timing is unclear 7
FMT donor was unrelated 6
Subject also on vancomycin, fidaxomycin 6
Subjects Langdon_2021_RCDI.subject_A10.1 and Langdon_2021_RCDI.subject_A10.2 are the same person, but relative timing is unclear 6
Subjects Langdon_2021_RCDI.subject_A17.1 and Langdon_2021_RCDI.subject_A17.2 are the same person, but relative timing is unclear 6
antibiotics administered peri-partum 6
Manually incremented by 1 to avoid same timepoint as T7 5
Subjects Langdon_2021_RCDI.subject_A14.1 and Langdon_2021_RCDI.subject_A14.2 are the same person, but relative timing is unclear 5
Subjects Langdon_2021_RCDI.subject_A18.1 and Langdon_2021_RCDI.subject_A18.2 are the same person, but relative timing is unclear 5
Subjects Langdon_2021_RCDI.subject_A20.1 and Langdon_2021_RCDI.subject_A20.2 are the same person, but relative timing is unclear 5
Subjects Langdon_2021_RCDI.subject_A4.1 and Langdon_2021_RCDI.subject_A4.2 are the same person, but relative timing is unclear 5
Subjects Langdon_2021_RCDI.subject_A8.1 and Langdon_2021_RCDI.subject_A8.2 are the same person, but relative timing is unclear 5
age uncertain 5
Metadata unclear 4
Subjects Langdon_2021_RCDI.subject_A13.1 and Langdon_2021_RCDI.subject_A13.2 are the same person, but relative timing is unclear 4
Subjects Langdon_2021_RCDI.subject_A23.1 and Langdon_2021_RCDI.subject_A23.2 are the same person, but relative timing is unclear 4
Subjects Langdon_2021_RCDI.subject_A28.1 and Langdon_2021_RCDI.subject_A28.2 are the same person, but relative timing is unclear 4
Subjects Langdon_2021_RCDI.subject_A29.1 and Langdon_2021_RCDI.subject_A29.2 are the same person, but relative timing is unclear 4
Subjects Langdon_2021_RCDI.subject_A3.1 and Langdon_2021_RCDI.subject_A3.2 are the same person, but relative timing is unclear 4
Subjects Langdon_2021_RCDI.subject_A5.1 and Langdon_2021_RCDI.subject_A5.2 are the same person, but relative timing is unclear 4
Subjects Langdon_2021_RCDI.subject_A6.1 and Langdon_2021_RCDI.subject_A6.2 are the same person, but relative timing is unclear 4
antibiotics administered prepartum 4
FMT donor was spouse 3
NB: correct donor, but unclear whether sample was used in FMT 3
Subjects Langdon_2021_RCDI.subject_A11.1 and Langdon_2021_RCDI.subject_A11.2 are the same person, but relative timing is unclear 3
Subjects Langdon_2021_RCDI.subject_A2.1 and Langdon_2021_RCDI.subject_A2.2 are the same person, but relative timing is unclear 3
Subjects Langdon_2021_RCDI.subject_A27.1 and Langdon_2021_RCDI.subject_A27.2 are the same person, but relative timing is unclear 3
cefprozil 10.23-11.05, probiotic resumed after antibiotic; It is unclear whether the disease abbreviation ""CB"" refers to chronic bronchitis or cerebral bleeding. 3
Subjects Langdon_2021_RCDI.subject_A26.1 and Langdon_2021_RCDI.subject_A26.2 are the same person, but relative timing is unclear 2
Subjects Langdon_2021_RCDI.subject_A33.1 and Langdon_2021_RCDI.subject_A33.2 are the same person, but relative timing is unclear 2
ceftazidime 10.26-11.5, 12.19-12.31; probiotic resumed after antibiotic 2
former melanoma patient who has recovered >1 year ago 2
no records on antibiotic treatment 2
A sample Ch36-1 was sequenced, but not used in the original publication 1
A sample Ch41-1 was sequenced, but not used in the original publication 1
BMI according to paper: 0.002156454491374 1
BMI according to paper: 72 1
BMI according to paper: 78.5 1
Male player 1 at home 1
Male player 1 baseline 1
Male player 1 post Australia 1
Male player 1 post India 1
Male player 1 post UAE 1
Male player 1 post Zambia/Namibia 1
Male player 11 at home 1
Male player 11 baseline 1
Male player 11 post Australia 1
Male player 11 post India 1
Male player 11 post UAE 1
Male player 11 post Zambia/Namibia 1
Male player 2 at home 1
Male player 2 baseline 1
Male player 2 post Australia 1
Male player 2 post India 1
Male player 2 post UAE 1
Male player 2 post Zambia/Namibia 1
Male player 3 at home 1
Male player 3 baseline 1
Male player 3 post Australia 1
Male player 3 post India 1
Male player 3 post UAE 1
Male player 3 post Zambia/Namibia 1
Subject also on metronidazole, vancomycin 1
Subject also on metronidazole, vancomycin, probiotic (Cuturelle) 1
Subject also on vancomycin, probiotics 1
The subject ID differs slightly in the ENA metadata, but is inferred to originate from the same host. The subject ID was retained, while other host-related information was harmonized with the records from the same host. 1
antibiotic treatment in the month before sampling 1
antibiotic treatment in the week before sampling 1
treated with Cotrimoxazole two times 1