project_name project_id num_samples task_id task_name attributes description sample_type study_design_notes area data_type taskfn otufn_refseq otufn_gg taxafn_refseq taxafn_gg control_vars Montassier 2016 bacteremia 28 bacteremia_nobacteremia bacteremia vs no bacteremia "Treatment: bact, NObact" Patients prior to chemotherapy who did or did not develop bacteremia human stool Bacteremia binary ./datasets/bacteremia/task.txt ./datasets/bacteremia/refseq/otutable.txt ./datasets/bacteremia/gg/otutable.txt ./datasets/bacteremia/refseq/taxatable.txt ./datasets/bacteremia/gg/taxatable.txt N Wu 2011 bushman_cafe 10 bushman_diet high fat vs low fat diet "DIET: HighFat, LowFat" Individuals after completing a high fat or low fat diet intervention human stool "Two groups on highfat and lowfat diets respectively, followed longitudinally. We provide only the last sample day of the intervention." Diet binary ./datasets/bushman_cafe/task.txt ./datasets/bushman_cafe/refseq/otutable.txt ./datasets/bushman_cafe/gg/otutable.txt ./datasets/bushman_cafe/refseq/taxatable.txt ./datasets/bushman_cafe/gg/taxatable.txt N Cho 2012 cho 47 cho_control_ct_cecal "chlortetracycline vs control, cecal" "Abx: Control, Chlortetracycline" Five groups of mice treated with four different antibiotics or no antibiotics mouse cecal contents Antibiotics binary ./datasets/cho/task-control-ct-cecal.txt ./datasets/cho/refseq/otutable.txt ./datasets/cho/gg/otutable.txt ./datasets/cho/refseq/taxatable.txt ./datasets/cho/gg/taxatable.txt N Cho 2012 cho 45 cho_control_ct_fecal "chlortetracycline vs control, fecal" "Abx: Control, Chlortetracycline" Five groups of mice treated with four different antibiotics or no antibiotics mouse pellets Antibiotics binary ./datasets/cho/task-control-ct-fecal.txt ./datasets/cho/refseq/otutable.txt ./datasets/cho/gg/otutable.txt ./datasets/cho/refseq/taxatable.txt ./datasets/cho/gg/taxatable.txt N Cho 2012 cho 47 cho_pen_vanc_cecal "penicillin vs vancomycin, cecal" "Abx: Penicillin, Vancomycin" Five groups of mice treated with four different antibiotics or no antibiotics mouse cecal contents Antibiotics binary ./datasets/cho/task-penicillin-vancomycin-cecal.txt ./datasets/cho/refseq/otutable.txt ./datasets/cho/gg/otutable.txt ./datasets/cho/refseq/taxatable.txt ./datasets/cho/gg/taxatable.txt N Cho 2012 cho 45 cho_pen_vanc_fecal "penicillin vs vancomycin, fecal" "Abx: Penicillin, Vancomycin" Five groups of mice treated with four different antibiotics or no antibiotics mouse pellets Antibiotics binary ./datasets/cho/task-penicillin-vancomycin-fecal.txt ./datasets/cho/refseq/otutable.txt ./datasets/cho/gg/otutable.txt ./datasets/cho/refseq/taxatable.txt ./datasets/cho/gg/taxatable.txt N Claesson 2012 claesson 167 claesson_elderly elderly vs young "AGE: Elderly, Young" Elderly or young adults human stool "Elderly adults confounded by residence type, data not shown" Age binary ./datasets/claesson/task.txt ./datasets/claesson/refseq/otutable.txt ./datasets/claesson/gg/otutable.txt ./datasets/claesson/refseq/taxatable.txt ./datasets/claesson/gg/taxatable.txt N Gevers 2014 gevers 140 gevers_control_cd_ileum "control vs cd, ileum" "DIAGNOSIS: no, CD" Healthy controls and Crohn's Disease patients ileal biopsies "Samples represent those from the RISK collection only, and individuals without immunosuppression and not taking steroids; representative samples per site per person chosen arbitrarily" IBD binary ./datasets/gevers/task-ileum.txt ./datasets/gevers/refseq/otutable.txt ./datasets/gevers/gg/otutable.txt ./datasets/gevers/refseq/taxatable.txt ./datasets/gevers/gg/taxatable.txt N Gevers 2014 gevers 160 gevers_control_cd_rectum "control vs cd, rectum" "DIAGNOSIS: no, CD" Healthy controls and Crohn's Disease patients rectal biopsies "Samples represent those from the RISK collection only, and individuals without immunosuppression and not taking steroids; representative samples per site per person chosen arbitrarily" IBD binary ./datasets/gevers/task-rectum.txt ./datasets/gevers/refseq/otutable.txt ./datasets/gevers/gg/otutable.txt ./datasets/gevers/refseq/taxatable.txt ./datasets/gevers/gg/taxatable.txt N Gevers 2014 gevers 68 gevers_pcdai_ileum pcdai using baseline cd ileum PCDAI PCDAI scores of CD patients at 6 months post sampling ileal biopsies "Samples represent those from the RISK collection only, and individuals without immunosuppression and not taking steroids; representative samples per site per person chosen arbitrarily" IBD regression ./datasets/gevers/task-pcdai-ileum.txt ./datasets/gevers/refseq/otutable.txt ./datasets/gevers/gg/otutable.txt ./datasets/gevers/refseq/taxatable.txt ./datasets/gevers/gg/taxatable.txt N Gevers 2014 gevers 51 gevers_pcdai_rectum pcdai using baseline cd rectum PCDAI PCDAI scores of CD patients at 6 months post sampling rectal biopsies "Samples represent those from the RISK collection only, and individuals without immunosuppression and not taking steroids; representative samples per site per person chosen arbitrarily" IBD regression ./datasets/gevers/task-pcdai-rectum.txt ./datasets/gevers/refseq/otutable.txt ./datasets/gevers/gg/otutable.txt ./datasets/gevers/refseq/taxatable.txt ./datasets/gevers/gg/taxatable.txt N HMP 2012 hmp 180 hmp_male_female "male vs female, stool" "SEX: male, female" Healthy male and female adults human stool Only one representative sample per body site per person provided Gender binary ./datasets/hmp/task-sex.txt ./datasets/hmp/refseq/otutable.txt ./datasets/hmp/gg/otutable.txt ./datasets/hmp/refseq/taxatable.txt ./datasets/hmp/gg/taxatable.txt N Ravel 2011 ravel 200 ravel_white_black "white vs black, vaginal" "Ethnic_Group: White, Black" Vaginal microbiomes of white and black women vaginal swab Expected easy task Vaginal binary ./datasets/ravel/task-white-black.txt ./datasets/ravel/refseq/otutable.txt ./datasets/ravel/gg/otutable.txt ./datasets/ravel/refseq/taxatable.txt ./datasets/ravel/gg/taxatable.txt N Ravel 2011 ravel 199 ravel_black_hispanic "black vs hispanic, vaginal" "Ethnic_Group: Black, Hispanic" Vaginal microbiomes of black and hispanic women vaginal swab Expected difficult task Vaginal binary ./datasets/ravel/task-black-hispanic.txt ./datasets/ravel/refseq/otutable.txt ./datasets/ravel/gg/otutable.txt ./datasets/ravel/refseq/taxatable.txt ./datasets/ravel/gg/taxatable.txt N Ravel 2011 ravel 342 ravel_nugent_category low vs high nugent category "Nugent_score_category: low, high" "Predict nugent score category (low, high) from vaginal microbiome" vaginal swab "0-3 (Low), 7-10 (High) indication of BV" Vaginal binary ./datasets/ravel/task-nugent-category.txt ./datasets/ravel/refseq/otutable.txt ./datasets/ravel/gg/otutable.txt ./datasets/ravel/refseq/taxatable.txt ./datasets/ravel/gg/taxatable.txt N Ravel 2011 ravel 388 ravel_nugent_score nugent score Nugent_score Predict nugent score from vaginal microbiome vaginal swab "0-3 (Low), 4-6 (Intermediate), 7-10 (High) indication of BV" Vaginal regression ./datasets/ravel/task-nugent-score.txt ./datasets/ravel/refseq/otutable.txt ./datasets/ravel/gg/otutable.txt ./datasets/ravel/refseq/taxatable.txt ./datasets/ravel/gg/taxatable.txt N Ravel 2011 ravel 388 ravel_ph "ph, vaginal" pH Predict pH from vaginal microbiome vaginal swab Vaginal regression ./datasets/ravel/task-ph.txt ./datasets/ravel/refseq/otutable.txt ./datasets/ravel/gg/otutable.txt ./datasets/ravel/refseq/taxatable.txt ./datasets/ravel/gg/taxatable.txt N Morgan 2012 sokol 128 sokol_healthy_cd "healthy vs cd, stool" "ULCERATIVE_COLIT_OR_CROHNS_DIS: Crohn's disease, Healthy" "Healthy, Crohn's Disease, or Ulcerative Colitis patients" human stool IBD binary ./datasets/sokol/task-healthy-cd.txt ./datasets/sokol/refseq/otutable.txt ./datasets/sokol/gg/otutable.txt ./datasets/sokol/refseq/taxatable.txt ./datasets/sokol/gg/taxatable.txt N Morgan 2012 sokol 128 sokol_healthy_uc "healthy vs uc, stool" "ULCERATIVE_COLIT_OR_CROHNS_DIS: Ulcerative Colitis, Healthy" "Healthy, Crohn's Disease, or Ulcerative Colitis patients" human stool IBD binary ./datasets/sokol/task-healthy-uc.txt ./datasets/sokol/refseq/otutable.txt ./datasets/sokol/gg/otutable.txt ./datasets/sokol/refseq/taxatable.txt ./datasets/sokol/gg/taxatable.txt N Yatsunenko 2012 yatsunenko 49 yatsunenko_infantage infant age AGE Infants (up to Age 3) from the US human stool Individuals are aged 3 or younger and are all living in the US Age regression ./datasets/yatsunenko/task-baby-age.txt ./datasets/yatsunenko/refseq/otutable.txt http://metagenome.cs.umn.edu/public/MLRepo/yatsunenko2012.gg.otutable.txt ./datasets/yatsunenko/refseq/taxatable.txt ./datasets/yatsunenko/gg/taxatable.txt N Yatsunenko 2012 yatsunenko 54 yatsunenko_malawi_venezuela "malawi vs venezuela, adults only" "COUNTRY: GAZ:Venezuela, GAZ:Malawi" Individuals living in Malawi or Venezuela human stool "Individuals are older than age 18, and are all living in the Venezuela or Malawi" Geography binary ./datasets/yatsunenko/task-malawi-venezuela.txt ./datasets/yatsunenko/refseq/otutable.txt http://metagenome.cs.umn.edu/public/MLRepo/yatsunenko2012.gg.otutable.txt ./datasets/yatsunenko/refseq/taxatable.txt ./datasets/yatsunenko/gg/taxatable.txt N Yatsunenko 2012 yatsunenko 129 yatsunenko_male_female "male vs female, usa" "SEX: male, female" Males and females from the US human stool "Individuals are older than age 18, and are all living in the US" Gender binary ./datasets/yatsunenko/task-sex.txt ./datasets/yatsunenko/refseq/otutable.txt http://metagenome.cs.umn.edu/public/MLRepo/yatsunenko2012.gg.otutable.txt ./datasets/yatsunenko/refseq/taxatable.txt ./datasets/yatsunenko/gg/taxatable.txt N Yatsunenko 2012 yatsunenko 150 yatsunenko_us_malawi "us vs malawi, adults only" "COUNTRY: GAZ:United States of America, GAZ:Malawi" Individuals living in the US or Malawi human stool "Individuals are older than age 18, and are all living in the US or Malawi" Geography binary ./datasets/yatsunenko/task-usa-malawi.txt ./datasets/yatsunenko/refseq/otutable.txt http://metagenome.cs.umn.edu/public/MLRepo/yatsunenko2012.gg.otutable.txt ./datasets/yatsunenko/refseq/taxatable.txt ./datasets/yatsunenko/gg/taxatable.txt N David 2014 david 18 david_animal_plant "animal vs plant diet, last diet day" "Diet: Plant, Animal" Individuals on the last day of an animal or plant diet intervention human stool "Baseline on days -4-0, diet on days 0-4, washout on 4-10" Diet binary ./datasets/david/task.txt ./datasets/david/refseq/otutable.txt ./datasets/david/gg/otutable.txt ./datasets/david/refseq/taxatable.txt ./datasets/david/gg/taxatable.txt Y HMP 2012 hmp 2070 hmp_gastro_oral gastrointestinal vs oral "HMPBODYSUPERSITE: Oral, Gastrointestinal_tract, HOST_SUBJECT_ID" Gastrointestinal tract and oral cavity of healthy adults "human stool, oral" "Multiple samples provided per body site per individual, control for HOST_SUBJECT_ID" Body Habitat binary ./datasets/hmp/task-gastro-oral.txt ./datasets/hmp/refseq/otutable.txt ./datasets/hmp/gg/otutable.txt ./datasets/hmp/refseq/taxatable.txt ./datasets/hmp/gg/taxatable.txt Y HMP 2012 hmp 404 hmp_stool_tongue stool vs tongue "HMPBODYSUBSITE: Stool, Tongue_dorsum; HOST_SUBJECT_ID" Stool and tongue of healthy adults "human stool, oral" Samples collected from paired locations by HOST_SUBJECT_ID Body Habitat binary ./datasets/hmp/task-stool-tongue-paired.txt ./datasets/hmp/refseq/otutable.txt ./datasets/hmp/gg/otutable.txt ./datasets/hmp/refseq/taxatable.txt ./datasets/hmp/gg/taxatable.txt Y HMP 2012 hmp 408 hmp_sub_supra subgingival vs supragingival plaque "HMPBODYSUBSITE: Subgingival_plaque, Supragingival_plaque; HOST_SUBJECT_ID" Subgingival and supragingival plague of healthy adults oral Samples collected from paired locations by HOST_SUBJECT_ID Body Habitat binary ./datasets/hmp/task-sub-supragingivalplaque-paired.txt ./datasets/hmp/refseq/otutable.txt ./datasets/hmp/gg/otutable.txt ./datasets/hmp/refseq/taxatable.txt ./datasets/hmp/gg/taxatable.txt Y Kostic 2012 kostic 172 kostic_healthy_tumor "healthy vs tumor biopsy, paired" "DIAGNOSIS: Healthy, Tumor; HOST_SUBJECT_ID" Colorectal carcinoma tumors and adjacent nonaffected tissues colon biopsies Samples collected from paired locations by HOST_SUBJECT_ID Cancer binary ./datasets/kostic/task.txt ./datasets/kostic/refseq/otutable.txt ./datasets/kostic/gg/otutable.txt ./datasets/kostic/refseq/taxatable.txt ./datasets/kostic/gg/taxatable.txt Y Turnbaugh 2009 turnbaugh_twins 142 turnbaugh_lean_obese_all "lean vs obese, mz/dz/mom" "OBESITYCAT: Lean, Obese; ZYGOSITY: MZ, DZ, Mom" Lean or Obese individuals (monozygotic or dyzygotic twins or their mothers) human stool Obesity binary ./datasets/turnbaugh/task-obese-lean-all.txt ./datasets/turnbaugh/refseq/otutable.txt ./datasets/turnbaugh/gg/otutable.txt ./datasets/turnbaugh/refseq/taxatable.txt ./datasets/turnbaugh/gg/taxatable.txt Y Karlsson 2013 karlsson 96 karlsson_normal_diabetes normal vs diabetes glucose tolerance "Classification: NGT, T2D" Normal or type 2 diabetes glucose tolerance categories human stool Diabetes binary ./datasets/karlsson/task-normal-diabetes.txt ./datasets/karlsson/otutable.txt NA ./datasets/karlsson/taxatable.txt NA N Karlsson 2013 karlsson 101 karlsson_impaired_diabetes impaired vs diabetes glucose tolerance "Classification: IGT, T2D" Impaired or type 2 diabetes glucose tolerance categories human stool Diabetes binary ./datasets/karlsson/task-impaired-diabetes.txt ./datasets/karlsson/otutable.txt NA ./datasets/karlsson/taxatable.txt NA N Qin 2012 qin2012 124 qin_healthy_diabetes healthy vs type 2 diabetes "Diabetic: Y, N" Healthy or type 2 diabetes patients human stool Chinese patients Diabetes binary ./datasets/qin2012/task-healthy-diabetes.txt ./datasets/qin2012/otutable.txt NA ./datasets/qin2012/taxatable.txt NA N Qin 2014 qin2014 130 qin_healthy_cirrhosis healthy vs cirrhosis "Cirrhotic: Cirrhosis, Healthy" Healthy or cirrhosis patients human stool Chinese patients Cirrhosis binary ./datasets/qin2014/task-healthy-cirrhosis.txt ./datasets/qin2014/otutable.txt NA ./datasets/qin2014/taxatable.txt NA N