importBugSigDB mixing Experiments?

[lwaldron]

Something weird happening with one experiment from one study. For Study 86, see how "Experiment 7" is shown twice, instead of "Experiment 8" which exists at https://bugsigdb.org/Study_86 and in the bulk export experiments.csv (edited to show only the Study 86 rows). Actually, many of the Experiment 7 attributes are shown twice instead of those from Experiment 8 (such as group names and definitions).

> dat <- bugsigdbr::importBugSigDB(version = "devel", cache = FALSE)
> dat[dat$Study=="Study 86", "Experiment"]
[1] "Experiment 1" "Experiment 2" "Experiment 2" "Experiment 3" "Experiment 4" "Experiment 5" "Experiment 6" "Experiment 7" "Experiment 7"
> dat[dat$Study=="Study 86", ]
       Study                             Study design     PMID                      DOI  URL
313 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
314 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
315 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
316 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
317 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
318 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
319 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
320 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
321 Study 86 time series / longitudinal observational 28512451 10.3389/fmicb.2017.00738 <NA>
                                                                                                                                   Authors
313 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
314 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
315 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
316 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
317 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
318 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
319 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
320 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
321 Wampach L,Heintz-Buschart A,Hogan A,Muller EEL,Narayanasamy S,Laczny CC,Hugerth LW,Bindl L,Bottu J,Andersson AF,de Beaufort C,Wilmes P
                                                                                                                                  Title                   Journal Year
313 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
314 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
315 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
316 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
317 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
318 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
319 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
320 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
321 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life Frontiers in microbiology 2017
      Experiment Location of subjects Host species Body site      UBERON ID        Condition      EFO ID                          Group 0 name
313 Experiment 1           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636             vaginal delivery at day 3
314 Experiment 2           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636             vaginal delivery at day 5
315 Experiment 2           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636             vaginal delivery at day 5
316 Experiment 3           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636            vaginal delivery at day 28
317 Experiment 4           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636           vaginal delivery at day 150
318 Experiment 5           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636           vaginal delivery at day 365
319 Experiment 6           Luxembourg Homo sapiens     feces UBERON:0001988  Premature birth EFO:0003917 full-term delivery >39 weeks at day 3
320 Experiment 7           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636                      vaginal delivery
321 Experiment 7           Luxembourg Homo sapiens     feces UBERON:0001988 Cesarean section EFO:0009636                      vaginal delivery
                                       Group 1 name                                      Group 1 definition Group 0 sample size Group 1 sample size
313                                       c-section meconium samples were collected at day 1 after delivery                   6                   3
314                                       c-section meconium samples were collected at day 1 after delivery                   7                   5
315                                       c-section meconium samples were collected at day 1 after delivery                   7                   5
316                                       c-section meconium samples were collected at day 1 after delivery                   7                   6
317                                       c-section meconium samples were collected at day 1 after delivery                   6                   4
318                                       c-section meconium samples were collected at day 1 after delivery                   5                   5
319                        late preterm 34-36 weeks meconium samples were collected at day 1 after delivery                   4                   5
320 overall time point infants samples of c-section meconium samples were collected at day 1 after delivery                   8                   7
321 overall time point infants samples of c-section meconium samples were collected at day 1 after delivery                   8                   7
                                                                       Antibiotics exclusion Sequencing type 16S variable region Sequencing platform        Statistical test
313 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
314 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
315 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
316 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
317 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
318 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
319 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina         Kruskall-Wallis
320 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
321 11 mothers (6 contols and 5 cases) used antibiotices 12 hours before and after delivery.             16S                   4            Illumina Mann-Whitney (Wilcoxon)
    Significance threshold MHT correction LDA Score above Matched on Confounders controlled for    Pielou   Shannon     Chao1 Simpson Inverse Simpson  Richness
313                   0.05           TRUE              NA       <NA>                       <NA> unchanged unchanged increased    <NA>            <NA> increased
314                   0.01           TRUE              NA       <NA>                       <NA> unchanged unchanged unchanged    <NA>            <NA> unchanged
315                   0.01           TRUE              NA       <NA>                       <NA> unchanged unchanged unchanged    <NA>            <NA> unchanged
316                   0.05           TRUE              NA       <NA>                       <NA> unchanged unchanged decreased    <NA>            <NA> unchanged
317                   0.05           TRUE              NA       <NA>                       <NA> unchanged unchanged unchanged    <NA>            <NA> unchanged
318                   0.05           TRUE              NA       <NA>                       <NA> unchanged unchanged unchanged    <NA>            <NA> unchanged
319                   0.01           TRUE              NA       <NA>                       <NA>      <NA>      <NA>      <NA>    <NA>            <NA>      <NA>
320                   0.05           TRUE              NA       <NA>                       <NA>      <NA>      <NA>      <NA>    <NA>            <NA>      <NA>
321                   0.05           TRUE              NA       <NA>                       <NA>      <NA>      <NA>      <NA>    <NA>            <NA>      <NA>
    Signature page name                  Source  Curated date           Curator     Revision editor
313         Signature 1    Figure 7 and Fig. S4 31 March 2019 Shaimaa Elsafoury        WikiWorks743
314         Signature 1               Figure 6S 31 March 2019 Shaimaa Elsafoury        WikiWorks743
315         Signature 2               Figure 6S 31 March 2019 Shaimaa Elsafoury        WikiWorks743
316         Signature 1   Figure 6S and Fig. S4 31 March 2019 Shaimaa Elsafoury        WikiWorks743
317         Signature 1               Figure 6S 31 March 2019 Shaimaa Elsafoury        WikiWorks743
318         Signature 1               Figure 6S 31 March 2019 Shaimaa Elsafoury        WikiWorks743
319         Signature 1 text pg11 and figure 7s 31 March 2019 Shaimaa Elsafoury        WikiWorks743
320         Signature 1     supplemantry file 9  1 April 2019 Shaimaa Elsafoury WikiWorks743,Fatima
321         Signature 2     supplemantry file 9  1 April 2019 Shaimaa Elsafoury        WikiWorks743
                                                                                       Description Abundance in Group 1
313 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            increased
314 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            increased
315 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            decreased
316 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            decreased
317 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            decreased
318 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            decreased
319 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            decreased
320 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            increased
321 qPCR validation of 16S rRNA gene sequencing data based differences according to delivery mode.            decreased
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         MetaPhlAn taxon names
313                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus, k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus
314                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  k__Bacteria|p__Firmicutes
315                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               k__Bacteria|p__Bacteroidetes
316                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                k__Bacteria|p__Bacteroidetes, k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides
317                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                k__Bacteria|p__Bacteroidetes, k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides
318                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               k__Bacteria|p__Bacteroidetes
319                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               k__Bacteria|p__Bacteroidetes
320 k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Akkermansiaceae|g__Akkermansia, k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae|g__Anaerostipes, k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae|g__Clostridium, k__Bacteria|p__Firmicutes|c__Negativicutes|o__Veillonellales|f__Veillonellaceae|g__Dialister, k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacterales|f__Enterobacteriaceae|g__Enterobacter, k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Enterococcaceae|g__Enterococcus, k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Oscillospiraceae|g__Flavonifractor, k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|g__Gemella, k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus, k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Lactobacillaceae|g__Lactobacillus, k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Propionibacteriales|f__Propionibacteriaceae|g__Propionibacterium, k__Bacteria|p__Actinobacteria|c__Actinomycetia|o__Micrococcales|f__Micrococcaceae|g__Rothia, k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Staphylococcaceae|g__Staphylococcus, k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus, k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae
321                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides, k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides, k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           NCBI Taxonomy IDs
313                                                                                                                                                                                                                                                                                                                                                                                                                             2|1239|91061|1385|90964|1279, 2|1239|91061|186826|33958|1578
314                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   2|1239
315                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    2|976
316                                                                                                                                                                                                                                                                                                                                                                                                                                                       2|976, 2|976|200643|171549|815|816
317                                                                                                                                                                                                                                                                                                                                                                                                                                                       2|976, 2|976|200643|171549|815|816
318                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    2|976
319                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    2|976
320 2|74201|203494|48461|1647988|239934, 2|1239|186801|186802|186803|207244, 2|1239|186801|186802|31979|1485, 2|1239|909932|1843489|31977|39948, 2|1224|1236|91347|543|547, 2|1239|91061|186826|81852|1350, 2|1239|186801|186802|216572|946234, 2|1239|91061|1385|1378, 2|1224|1236|135625|712|724, 2|1239|91061|186826|33958|1578, 2|201174|1760|85009|31957|1743, 2|201174|1760|85006|1268|32207, 2|1239|91061|1385|90964|1279, 2|1239|91061|186826|1300|1301, 2|1239|186801|186802|186803
321                                                                                                                                                                                                                                                                                                                                                                                       2|976|200643|171549|2005525|375288, 2|976|200643|171549|815|816, 2|976|200643|171549|171550|239759
       State          Reviewer
313 Complete Shaimaa Elsafoury
314 Complete Shaimaa Elsafoury
315 Complete Shaimaa Elsafoury
316 Complete Shaimaa Elsafoury
317 Complete Shaimaa Elsafoury
318 Complete Shaimaa Elsafoury
319 Complete Shaimaa Elsafoury
320 Complete            Fatima
321 Complete Shaimaa Elsafoury

[lwaldron]

I note also a joining issue that Experiments with no Signatures are dropped, such as https://bugsigdb.org/Study_89/Experiment_2 (this contrast is here to record that the contrast was made, and an Alpha diversity result is reported, even though no differentially abundant taxa were reported). I think the desired behavior for the full importBugSigDB data.frame would be for all the Signature-related columns (e.g. Abundance in Group 1, MetaPhlAn Taxon Names, ...) to be NA.

[lgeistlinger]

This is indeed by design that we are dropping experiments with no signatures. But I see the use case and we can change that: https://github.com/waldronlab/BugSigDBExports/issues/14

[lgeistlinger]

fixed in https://github.com/waldronlab/BugSigDBExports/issues/14 - should both clear up on Sunday's export.

[lgeistlinger]

As of today:

> df <- importBugSigDB(version = "devel", cache = FALSE)
> df[df$Study=="Study 86", ]
       Study                             Study design     PMID
313 Study 86 time series / longitudinal observational 28512451
314 Study 86 time series / longitudinal observational 28512451
315 Study 86 time series / longitudinal observational 28512451
316 Study 86 time series / longitudinal observational 28512451
317 Study 86 time series / longitudinal observational 28512451
318 Study 86 time series / longitudinal observational 28512451
319 Study 86 time series / longitudinal observational 28512451
320 Study 86 time series / longitudinal observational 28512451
321 Study 86 time series / longitudinal observational 28512451
322 Study 86 time series / longitudinal observational 28512451
                         DOI  URL
313 10.3389/fmicb.2017.00738 <NA>
314 10.3389/fmicb.2017.00738 <NA>
315 10.3389/fmicb.2017.00738 <NA>
316 10.3389/fmicb.2017.00738 <NA>
317 10.3389/fmicb.2017.00738 <NA>
318 10.3389/fmicb.2017.00738 <NA>
319 10.3389/fmicb.2017.00738 <NA>
320 10.3389/fmicb.2017.00738 <NA>
321 10.3389/fmicb.2017.00738 <NA>
322 10.3389/fmicb.2017.00738 <NA>
                                                                                                                                          Authors list
313 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
314 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
315 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
316 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
317 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
318 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
319 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
320 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
321 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
322 Wampach L, Heintz-Buschart A, Hogan A, Muller EEL, Narayanasamy S, Laczny CC, Hugerth LW, Bindl L, Bottu J, Andersson AF, de Beaufort C , Wilmes P
                                                                                                                                  Title
313 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
314 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
315 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
316 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
317 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
318 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
319 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
320 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
321 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
322 Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life
                      Journal Year   Experiment Location of subjects
313 Frontiers in microbiology 2017 Experiment 1           Luxembourg
314 Frontiers in microbiology 2017 Experiment 2           Luxembourg
315 Frontiers in microbiology 2017 Experiment 2           Luxembourg
316 Frontiers in microbiology 2017 Experiment 3           Luxembourg
317 Frontiers in microbiology 2017 Experiment 4           Luxembourg
318 Frontiers in microbiology 2017 Experiment 5           Luxembourg
319 Frontiers in microbiology 2017 Experiment 6           Luxembourg
320 Frontiers in microbiology 2017 Experiment 7           Luxembourg
321 Frontiers in microbiology 2017 Experiment 7           Luxembourg
322 Frontiers in microbiology 2017 Experiment 8           Luxembourg
    Host species Body site      UBERON ID        Condition      EFO ID
313 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
314 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
315 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
316 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
317 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
318 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
319 Homo sapiens     feces UBERON:0001988  Premature birth EFO:0003917
320 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
321 Homo sapiens     feces UBERON:0001988 cesarean section EFO:0009636
322 Homo sapiens  meconium UBERON:0007109 cesarean section EFO:0009636
                             Group 0 name
313             vaginal delivery at day 3
314             vaginal delivery at day 5
315             vaginal delivery at day 5
316            vaginal delivery at day 28
317           vaginal delivery at day 150
318           vaginal delivery at day 365
319 full-term delivery >39 weeks at day 3
320                      vaginal delivery
321                      vaginal delivery
322                      vaginal delivery
                                       Group 1 name
313                                       c-section
314                                       c-section
315                                       c-section
316                                       c-section
317                                       c-section
318                                       c-section
319                        late preterm 34-36 weeks
320 overall time point infants samples of c-section
321 overall time point infants samples of c-section
322                                       C-section
                                         Group 1 definition Group 0 sample size
313 meconium samples were collected at day 1 after delivery                   6
314 meconium samples were collected at day 1 after delivery                   7
315 meconium samples were collected at day 1 after delivery                   7
316 meconium samples were collected at day 1 after delivery                   7
317 meconium samples were collected at day 1 after delivery                   6
318 meconium samples were collected at day 1 after delivery                   5
319 meconium samples were collected at day 1 after delivery                   4
320 meconium samples were collected at day 1 after delivery                   8
321 meconium samples were collected at day 1 after delivery                   8
322                                                    <NA>                   4
    Group 1 sample size
313                   3
314                   5
315                   5
316                   6
317                   4
318                   5
319                   5
320                   7
321                   7
322                   6