From 8ab88129d9647ad00a902685ed6fef9693c093dc Mon Sep 17 00:00:00 2001 From: Gavin Rhys Lloyd Date: Fri, 22 Sep 2023 11:50:06 +0100 Subject: [PATCH] use httptest when building vignette to avoid bioc build errors if workbench query times out during build --- DESCRIPTION | 3 +- ...Introduction_to_metabolomicsWorkbenchR.Rmd | 4 +- vignettes/example_using_structToolbox.Rmd | 2 + .../rest/compound/regno/11/all.json | 11 + .../rest/gene/gene_name/acetyl-CoA/all.json | 99 + .../analysis_id/AN000023/untarg_factors.json | 74 + .../rest/study/study_id/ST000001/data.json | 3572 ++ .../rest/study/study_id/ST000001/factors.json | 146 + .../rest/study/study_id/ST000001/summary.json | 14 + .../rest/study/study_id/ST000009/data.json | 50252 ++++++++++++++++ .../rest/study/study_id/ST000009/factors.json | 686 + .../rest/study/study_id/ST000009/summary.json | 14 + .../study_id/ignored/untarg_studies.json | 10170 ++++ .../study/study_title/Diabetes/summary.json | 366 + .../analysis_id/AN000025/untarg_factors.json | 41 + .../rest/study/study_id/ST000010/summary.json | 14 + .../study_id/ignored/untarg_studies.json | 10170 ++++ 17 files changed, 75636 insertions(+), 2 deletions(-) create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/compound/regno/11/all.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA/all.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_factors.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/data.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/factors.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/summary.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json create mode 100644 vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_title/Diabetes/summary.json create mode 100644 vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000025/untarg_factors.json create mode 100644 vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000010/summary.json create mode 100644 vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json diff --git a/DESCRIPTION b/DESCRIPTION index d529070..256e9d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: metabolomicsWorkbenchR Type: Package Title: Metabolomics Workbench in R -Version: 1.7.0 +Version: 1.7.1 Authors@R: c( person( c("Gavin","Rhys"), @@ -43,6 +43,7 @@ Suggests: covr, knitr, HDF5Array, + httptest, rmarkdown, structToolbox, testthat, diff --git a/vignettes/Introduction_to_metabolomicsWorkbenchR.Rmd b/vignettes/Introduction_to_metabolomicsWorkbenchR.Rmd index 3c3615f..09a06f3 100644 --- a/vignettes/Introduction_to_metabolomicsWorkbenchR.Rmd +++ b/vignettes/Introduction_to_metabolomicsWorkbenchR.Rmd @@ -21,8 +21,10 @@ vignette: > --- ```{r echo = FALSE,include=FALSE} +suppressPackageStartupMessages(library(grid)) +suppressPackageStartupMessages(library(httptest)) suppressPackageStartupMessages(library(metabolomicsWorkbenchR)) -library(grid) +httptest::start_vignette('introduction') ``` diff --git a/vignettes/example_using_structToolbox.Rmd b/vignettes/example_using_structToolbox.Rmd index 762deee..d48b984 100644 --- a/vignettes/example_using_structToolbox.Rmd +++ b/vignettes/example_using_structToolbox.Rmd @@ -23,6 +23,8 @@ vignette: > ```{r echo = FALSE,include=FALSE} suppressPackageStartupMessages(library(metabolomicsWorkbenchR)) library(structToolbox) +library(httptest) +httptest::start_vignette('structToolbox_example') ``` diff --git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/compound/regno/11/all.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/compound/regno/11/all.json new file mode 100644 index 0000000..cd66cc8 --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/compound/regno/11/all.json @@ -0,0 +1,11 @@ +{ + "regno": "11", + "formula": "C47H75N5O8", + "exactmass": "837.561565", + "inchi_key": "JLBSVDZUWJLOCF-ZLKQSCCRSA-N", + "name": "Dideoxymycobactin", + "sys_name": "[(2R)-4-oxo-4-[[(3S)-2-oxoazepan-3-yl]amino]butan-2-yl] (2S)-2-[[(4S)-2-(2-hydroxyphenyl)-4-methyl-5H-1,3-oxazole-4-carbonyl]amino]-6-[[(Z)-icos-2-enoyl]amino]hexanoate", + "lm_id": "LMFA00000015", + "pubchem_cid": "136029221", + "smiles": "CCCCCCCCCCCCCCCCC/C=C\\C(=O)NCCCC[C@H](NC(=O)[C@]1(C)COC(c2ccccc2O)=N1)C(=O)O[C@H](C)CC(=O)N[C@H]1CCCCNC1=O" +} diff --git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA/all.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA/all.json new file mode 100644 index 0000000..59b6cb3 --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/gene/gene_name/acetyl-CoA/all.json @@ -0,0 +1,99 @@ +{ + "Row1": { + "gene_name": "acetyl-CoA acyltransferase 1", + "mgp_id": "MGP000015", + "gene_id": "30", + "gene_symbol": "ACAA1", + "gene_synonyms": "ACAA; THIO; PTHIO;", + "alt_names": "3-ketoacyl-CoA thiolase, peroxisomal; acetyl-Coenzyme A acyltransferase 1; beta-ketothiolase; peroxisomal 3-oxoacyl-CoA thiolase; peroxisomal 3-oxoacyl-Coenzyme A thiolase;", + "chromosome": "3", + "map_location": "3p22.2", + "summary": "This gene encodes an enzyme operative in the beta-oxidation system of the peroxisomes. Deficiency of this enzyme leads to pseudo-Zellweger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + }, + "Row2": { + "gene_name": "acetyl-CoA carboxylase alpha", + "mgp_id": "MGP000016", + "gene_id": "31", + "gene_symbol": "ACACA", + "gene_synonyms": "ACC; ACAC; ACC1; ACCA; ACACAD;", + "alt_names": "acetyl-CoA carboxylase 1; ACC-alpha; acetyl-Coenzyme A carboxylase alpha;", + "chromosome": "17", + "map_location": "17q21", + "summary": "Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. There are two ACC forms, alpha and beta, encoded by two different genes. ACC-alpha is highly enriched in lipogenic tissues. The enzyme is under long term control at the transcriptional and translational levels and under short term regulation by the phosphorylation/dephosphorylation of targeted serine residues and by allosteric transformation by citrate or palmitoyl-CoA. Multiple alternatively spliced transcript variants divergent in the 5' sequence and encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + }, + "Row3": { + "gene_name": "acetyl-CoA carboxylase beta", + "mgp_id": "MGP000017", + "gene_id": "32", + "gene_symbol": "ACACB", + "gene_synonyms": "ACC2; ACCB; HACC275;", + "alt_names": "acetyl-CoA carboxylase 2; ACC-beta; acetyl-Coenzyme A carboxylase beta;", + "chromosome": "12", + "map_location": "12q24.11", + "summary": " Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin-containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate-limiting step in fatty acid synthesis. ACC-beta is thought to control fatty acid oxidation by means of the ability of malonyl-CoA to inhibit carnitine-palmitoyl-CoA transferase I, the rate-limiting step in fatty acid uptake and oxidation by mitochondria. ACC-beta may be involved in the regulation of fatty acid oxidation, rather than fatty acid biosynthesis. There is evidence for the presence of two ACC-beta isoforms. [provided by RefSeq, Jul 2008]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + }, + "Row4": { + "gene_name": "acetyl-CoA acetyltransferase 1", + "mgp_id": "MGP000023", + "gene_id": "38", + "gene_symbol": "ACAT1", + "gene_synonyms": "T2; MAT; ACAT; THIL;", + "alt_names": "acetyl-CoA acetyltransferase, mitochondrial; acetoacetyl Coenzyme A thiolase; acetoacetyl-CoA thiolase; acetyl-Coenzyme A acetyltransferase 1; mitochondrial acetoacetyl-CoA thiolase;", + "chromosome": "11", + "map_location": "11q22.3", + "summary": "This gene encodes a mitochondrially localized enzyme that catalyzes the reversible formation of acetoacetyl-CoA from two molecules of acetyl-CoA. Defects in this gene are associated with 3-ketothiolase deficiency, an inborn error of isoleucine catabolism characterized by urinary excretion of 2-methyl-3-hydroxybutyric acid, 2-methylacetoacetic acid, tiglylglycine, and butanone. [provided by RefSeq, Feb 2009]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + }, + "Row5": { + "gene_name": "acetyl-CoA acetyltransferase 2", + "mgp_id": "MGP000024", + "gene_id": "39", + "gene_symbol": "ACAT2", + "alt_names": "acetyl-CoA acetyltransferase, cytosolic; acetoacetyl Coenzyme A thiolase; acetyl-CoA transferase-like protein; cytosolic acetoacetyl-CoA thiolase;", + "chromosome": "6", + "map_location": "6q25.3", + "summary": "The product of this gene is an enzyme involved in lipid metabolism, and it encodes cytosolic acetoacetyl-CoA thiolase. This gene shows complementary overlapping with the 3-prime region of the TCP1 gene in both mouse and human. These genes are encoded on opposite strands of DNA, as well as in opposite transcriptional orientation. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2014]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + }, + "Row6": { + "gene_name": "solute carrier family 33 (acetyl-CoA transporter), member 1", + "mgp_id": "MGP003828", + "gene_id": "9197", + "gene_symbol": "SLC33A1", + "gene_synonyms": "AT1; AT-1; ACATN; SPG42; CCHLND;", + "alt_names": "acetyl-coenzyme A transporter 1;", + "chromosome": "3", + "map_location": "3q25.31", + "summary": "The protein encoded by this gene is required for the formation of O-acetylated (Ac) gangliosides. The encoded protein is predicted to contain 6 to 10 transmembrane domains, and a leucine zipper motif in transmembrane domain III. Defects in this gene have been reported to cause spastic paraplegia autosomal dominant type 42 (SPG42) in one Chinese family, but not in similar patients of European descent. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2010]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + }, + "Row7": { + "gene_name": "acetyl-CoA acyltransferase 2", + "mgp_id": "MGP004244", + "gene_id": "10449", + "gene_symbol": "ACAA2", + "gene_synonyms": "DSAEC;", + "alt_names": "3-ketoacyl-CoA thiolase, mitochondrial; T1; acetyl-Coenzyme A acyltransferase 2; beta ketothiolase; beta-ketothiolase; mitochondrial 3-oxoacyl-CoA thiolase; mitochondrial 3-oxoacyl-Coenzyme A thiolase;", + "chromosome": "18", + "map_location": "18q21.1", + "summary": "The encoded protein catalyzes the last step of the mitochondrial fatty acid beta-oxidation spiral. Unlike most mitochondrial matrix proteins, it contains a non-cleavable amino-terminal targeting signal. [provided by RefSeq, Jul 2008]", + "taxid": "9606", + "species": "Human", + "species_long": "Homo sapiens" + } +} diff --git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_factors.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_factors.json new file mode 100644 index 0000000..31e70da --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000023/untarg_factors.json @@ -0,0 +1,74 @@ +{ + "1": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "3" + }, + "2": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:12MO | ROUX_EN_Y": "1" + }, + "3": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:6MO | GASTRIC_BAND": "4" + }, + "4": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "11" + }, + "5": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "7" + }, + "6": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "7" + }, + "7": { + "AFTER_MEAL_TIME:30_MIN | female | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "12" + }, + "8": { + "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "2" + }, + "9": { + "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "2" + }, + "10": { + "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "4" + }, + "11": { + "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "2" + }, + "12": { + "AFTER_MEAL_TIME:30_MIN | male | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "2" + }, + "13": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "3" + }, + "14": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:12MO | ROUX_EN_Y": "1" + }, + "15": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:6MO | GASTRIC_BAND": "4" + }, + "16": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "11" + }, + "17": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "7" + }, + "18": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "7" + }, + "19": { + "AFTER_MEAL_TIME:NO_WAIT | female | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "12" + }, + "20": { + "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:12MO | GASTRIC_BAND": "2" + }, + "21": { + "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:6MO | ROUX_EN_Y": "2" + }, + "22": { + "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:NO_SURGERY | LEAN_CONTROL": "4" + }, + "23": { + "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:PRE_SURGERY | GASTRIC_BAND": "2" + }, + "24": { + "AFTER_MEAL_TIME:NO_WAIT | male | POST_SURGERY_TIME:PRE_SURGERY | ROUX_EN_Y": "2" + } +} diff --git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data.json new file mode 100644 index 0000000..574a994 --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data.json @@ -0,0 +1,3572 @@ +{ + "1": { + "study_id": "ST000001", + "analysis_id": "AN000001", + "analysis_summary": "GCMS positive ion mode", + "metabolite_name": "1,2,4-benzenetriol", + "metabolite_id": "ME000097", + "refmet_name": "1,2,4-Trihydroxybenzene", + "units": "Peak height", + "DATA": { + "LabF_115811": "2257", + "LabF_115816": "1718", + "LabF_115821": "1740", + "LabF_115826": "3472", + "LabF_115831": "2054", + "LabF_115836": "1367", + "LabF_115842": "4040", + "LabF_115847": "2432", + "LabF_115852": "2189", + "LabF_115857": "1931", + "LabF_115862": "1307", + "LabF_115867": "2880", + "LabF_115873": "2218", + "LabF_115878": "1754", + "LabF_115883": "1369", + "LabF_115888": "1201", + "LabF_115893": "3324", + "LabF_115898": "1355", + "LabF_115904": "1874", + "LabF_115909": "3566", + "LabF_115914": "1945", + "LabF_115919": "1456", + "LabF_115924": "2004", + "LabF_115929": "1995" + } + }, + "2": { + "study_id": "ST000001", + "analysis_id": "AN000001", + "analysis_summary": "GCMS positive ion mode", + "metabolite_name": "1-monostearin", + "metabolite_id": "ME000096", + "refmet_name": "MG 18:0/0:0/0:0", + "units": "Peak height", + "DATA": { + "LabF_115811": "1035", + "LabF_115816": "789", + "LabF_115821": "875", + "LabF_115826": "224", + "LabF_115831": "641", + "LabF_115836": "693", + "LabF_115842": "393", + "LabF_115847": "705", + "LabF_115852": "100", + "LabF_115857": "481", + "LabF_115862": "265", + "LabF_115867": "120", + "LabF_115873": "1185", + "LabF_115878": "867", + "LabF_115883": "676", + "LabF_115888": "569", + "LabF_115893": "579", + "LabF_115898": "387", + "LabF_115904": "987", + "LabF_115909": "450", + "LabF_115914": "1910", + "LabF_115919": "549", + "LabF_115924": "1032", + "LabF_115929": "902" + } + }, + "3": { + "study_id": "ST000001", + "analysis_id": "AN000001", + "analysis_summary": "GCMS positive ion mode", + "metabolite_name": "2-hydroxyvaleric acid", + "metabolite_id": "ME000098", + "refmet_name": "2-Hydroxyvaleric acid", + "units": "Peak height", + "DATA": { + "LabF_115811": "735", + "LabF_115816": "632", + "LabF_115821": "815", + "LabF_115826": "805", + "LabF_115831": "941", + "LabF_115836": "709", + "LabF_115842": "900", + "LabF_115847": "1778", + "LabF_115852": "1648", + "LabF_115857": "1575", + "LabF_115862": "1466", + "LabF_115867": "1145", + "LabF_115873": "913", + "LabF_115878": "1340", + "LabF_115883": "607", + "LabF_115888": "794", + "LabF_115893": "951", + "LabF_115898": "922", + "LabF_115904": "771", + "LabF_115909": "931", + "LabF_115914": "1114", + "LabF_115919": "509", + "LabF_115924": "516", + "LabF_115929": "803" + } + }, + "4": { + "study_id": "ST000001", + "analysis_id": "AN000001", + "analysis_summary": "GCMS positive ion mode", + "metabolite_name": "3-phosphoglycerate", + "metabolite_id": "ME000095", + "refmet_name": "3-Phosphoglyceric acid", + "units": "Peak height", + "DATA": { + "LabF_115811": "1325", + "LabF_115816": "922", + "LabF_115821": "1235", + "LabF_115826": "1204", + "LabF_115831": "1742", + "LabF_115836": "2109", + "LabF_115842": "3061", + "LabF_115847": "2583", + "LabF_115852": "1182", + "LabF_115857": "2727", + "LabF_115862": "2505", + "LabF_115867": "1437", + "LabF_115873": "1343", + "LabF_115878": "1006", + "LabF_115883": "772", + "LabF_115888": "995", + "LabF_115893": "2449", + "LabF_115898": "2677", + "LabF_115904": "2039", + "LabF_115909": "2005", + "LabF_115914": "1496", + "LabF_115919": "2361", + "LabF_115924": "3282", + "LabF_115929": "2096" + } + }, + "5": { + "study_id": "ST000001", + "analysis_id": "AN000001", + "analysis_summary": "GCMS positive ion mode", + "metabolite_name": "5-hydroxynorvaline NIST", + "metabolite_id": "ME001834", + "refmet_name": "L-2-Amino-5-hydroxypentanoic acid", + "units": "Peak 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b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors.json @@ -0,0 +1,146 @@ +{ + "1": { + "study_id": "ST000001", + "local_sample_id": "LabF_115904", + "subject_type": "Plant", + "factors": "Arabidopsis Genotype:fatb-ko KD; At1g08510 | Plant Wounding Treatment:Control - Non-Wounded" + }, + "2": { + "study_id": "ST000001", + "local_sample_id": "LabF_115909", + "subject_type": "Plant", + "factors": "Arabidopsis Genotype:fatb-ko KD; At1g08510 | Plant Wounding Treatment:Control - Non-Wounded" + }, + "3": { + "study_id": "ST000001", + "local_sample_id": "LabF_115914", + "subject_type": "Plant", + "factors": "Arabidopsis Genotype:fatb-ko KD; At1g08510 | Plant Wounding Treatment:Control - Non-Wounded" + }, + "4": { + "study_id": "ST000001", + "local_sample_id": "LabF_115919", + "subject_type": "Plant", + "factors": "Arabidopsis Genotype:fatb-ko KD; At1g08510 | Plant Wounding Treatment:Control - Non-Wounded" + }, + "5": { + "study_id": "ST000001", + 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--git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary.json new file mode 100644 index 0000000..c7edad0 --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary.json @@ -0,0 +1,14 @@ +{ + "study_id": "ST000001", + "study_title": "Fatb Induction Experiment (FatBIE)", + "study_type": "Genotype treatment", + "institute": "University of California, Davis", + "department": "Davis Genome Center", + "last_name": "Kind", + "first_name": "Tobias", + "email": "tkind@ucdavis.edu", + "phone": "", + "submit_date": "2013-01-15", + "study_summary": "This experiment tests the consequence of a mutation at the FatB gene (At1g08510) in the wound-response of Arabidopsis. The FatB mutant allele (fatb KD J. Ohlrogge (Plant Cell 2003, Vol 15, 1020-1033)) was obtained from Dr. Katayonn Dehesh, University of California, Davis, Davis, CA. This allele is in the Ws background.The standardized growth conditions are as follows: 1. Seeds (between 14 and 16) are sown on media in 100 x 100 x 15mm square Falcon Petri Dishes (Fisher Scientific, catalogue #08-757-11A). Seeds were arranged on the plates in a single horizontal line at the 1-cm mark from the top of the plate.2. Each plate contains between 20 and 25-ml of sterile MS media containing 0.1% (w/v) sucrose.3. Prior to sowing, seeds were sterilized by treating for 1 minute at room temperature with a 300-l solution of 50% (v/v) ethanol, this solution was removed and replaced with a 300-l solution consisting of 1% (v/v) Tween 20 (Fischer BioReagents, catalogue #BP33750), and 50% (v/v) bleach solution (Clorox), and incubated at room temperature for 10-minutes. The seeds were then washed with three changes of 0.3-ml of sterile water.", + "subject_species": "Arabidopsis thaliana" +} diff --git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/data.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/data.json new file mode 100644 index 0000000..fd97135 --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000009/data.json @@ -0,0 +1,50252 @@ +{ + "1": { + "study_id": "ST000009", + "analysis_id": "AN000023", + "analysis_summary": "LC/Electro-spray /QTOF positive ion mode", + "metabolite_name": "10-HYDROXYDECANOATE", + "metabolite_id": "ME642812", + "refmet_name": "10-Hydroxydecanoic acid", + "units": "Peak area", + "DATA": { + "S00008865": "1107792", + "S00008866": "980161", + "S00008867": "2619759", + "S00008868": "2566297", + "S00008869": "1478161", + "S00008870": "1612605", + "S00008871": "2288948", + "S00008872": "2608299", + 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Tricarboxylic Acid and Hexosamine Pathways", + "subject_species": "Homo sapiens", + "institute": "Johns Hopkins" + }, + "1256": { + "study_id": "ST002807", + "analysis_id": "AN004564", + "analysis_display": "Reversed phase POSITIVE ION MODE", + "study_title": "Metabolomic response of river biofilm to cobalt", + "subject_species": "Biofilm microbial community", + "institute": "Muséum Nationale d'Histoire Naturelle" + }, + "1257": { + "study_id": "ST002826", + "analysis_id": "AN004610", + "analysis_display": "HILIC POSITIVE ION MODE", + "study_title": "Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans", + "subject_species": "Homo sapiens", + "institute": "University of Turku" + }, + "1258": { + "study_id": "ST002826", + "analysis_id": "AN004611", + "analysis_display": "HILIC NEGATIVE ION MODE", + "study_title": "Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans", + "subject_species": "Homo sapiens", + "institute": "University of Turku" + }, + "1259": { + "study_id": "ST002826", + "analysis_id": "AN004612", + "analysis_display": "Reversed phase POSITIVE ION MODE", + "study_title": "Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans", + "subject_species": "Homo sapiens", + "institute": "University of Turku" + }, + "1260": { + "study_id": "ST002826", + "analysis_id": "AN004613", + "analysis_display": "Reversed phase NEGATIVE ION MODE", + "study_title": "Cold-stimulated brown adipose tissue activation is related to changes in serum metabolites relevant to NAD+ metabolism in humans", + "subject_species": "Homo sapiens", + "institute": "University of Turku" + }, + "1261": { + "study_id": "ST002832", + "analysis_id": "AN004625", + "analysis_display": "HILIC POSITIVE ION MODE", + "study_title": "Resource competition predicts assembly of in vitro gut bacterial communities- HILIC", + "subject_species": "Bacteroides thetaiotaomicron", + "institute": "Stanford University" + }, + "1262": { + "study_id": "ST002832", + "analysis_id": "AN004626", + "analysis_display": "HILIC NEGATIVE ION MODE", + "study_title": "Resource competition predicts assembly of in vitro gut bacterial communities- HILIC", + "subject_species": "Bacteroides thetaiotaomicron", + "institute": "Stanford University" + }, + "1263": { + "study_id": "ST002833", + "analysis_id": "AN004627", + "analysis_display": "Reversed phase POSITIVE ION MODE", + "study_title": "Resource competition predicts assembly of in vitro gut bacterial communities- 2022-C18", + "subject_species": "Bacteroides thetaiotaomicron", + "institute": "Stanford University" + }, + "1264": { + "study_id": "ST002833", + "analysis_id": "AN004628", + "analysis_display": "Reversed phase NEGATIVE ION MODE", + "study_title": "Resource competition predicts assembly of in vitro gut bacterial communities- 2022-C18", + "subject_species": "Bacteroides thetaiotaomicron", + "institute": "Stanford University" + }, + "1265": { + "study_id": "ST002834", + "analysis_id": "AN004629", + "analysis_display": "Reversed phase POSITIVE ION MODE", + "study_title": "Resource competition predicts assembly of in vitro gut bacterial communities- 2021-C18", + "subject_species": "Bacteroides thetaiotaomicron", + "institute": "Stanford University" + }, + "1266": { + "study_id": "ST002834", + "analysis_id": "AN004630", + "analysis_display": "Reversed phase NEGATIVE ION MODE", + "study_title": "Resource competition predicts assembly of in vitro gut bacterial communities- 2021-C18", + "subject_species": "Bacteroides thetaiotaomicron", + "institute": "Stanford University" + }, + "1267": { + "study_id": "ST002839", + "analysis_id": "AN004645", + "analysis_display": "Reversed phase POSITIVE ION MODE", + "study_title": "Metabolic alteration during ferroptotic process in cancer cells.", + "subject_species": "Homo sapiens", + "institute": "Zhongshan Hospital Fudan University" + }, + "1268": { + "study_id": "ST002839", + "analysis_id": "AN004646", + "analysis_display": "Reversed phase NEGATIVE ION MODE", + "study_title": "Metabolic alteration during ferroptotic process in cancer cells.", + "subject_species": "Homo sapiens", + "institute": "Zhongshan Hospital Fudan University" + }, + "1269": { + "study_id": "ST002845", + "analysis_id": "AN004663", + "analysis_display": "Reversed phase POSITIVE ION MODE", + "study_title": "Methylprednisolone therapy induces differential metabolic trajectories in severe COVID-19 patients", + "subject_species": "Homo sapiens", + "institute": "Federal University of Goiás" + }, + "1270": { + "study_id": "ST002850", + "analysis_id": "AN004668", + "analysis_display": "HILIC NEGATIVE ION MODE", + "study_title": "Bap1 Promotes Osteoclast Function by Metabolic Reprogramming", + "subject_species": "Homo sapiens", + "institute": "Washington University in St. Louis" + }, + "1271": { + "study_id": "ST002850", + "analysis_id": "AN004669", + "analysis_display": "HILIC POSITIVE ION MODE", + "study_title": "Bap1 Promotes Osteoclast Function by Metabolic Reprogramming", + "subject_species": "Homo sapiens", + "institute": "Washington University in St. Louis" + } +} diff --git a/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_title/Diabetes/summary.json b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_title/Diabetes/summary.json new file mode 100644 index 0000000..2ee5059 --- /dev/null +++ b/vignettes/introduction/0/www.metabolomicsworkbench.org/rest/study/study_title/Diabetes/summary.json @@ -0,0 +1,366 @@ +{ + "1": { + "study_id": "ST000057", + "study_title": "Combined Metabolomics and Lipidomics of Type 1 Diabetes (GCMS)", + "study_type": "biomarker study", + "institute": "University of California, Davis", + "department": "Genome and Biomedical Sciences Facility", + "last_name": "Fiehn", + "first_name": "Oliver", + "email": "ofiehn@ucdavis.edu", + "phone": "(530) 754-8258", + "submit_date": "2014-06-11", + "study_summary": "This West Coast Metabolomics Center pilot and feasibility project granted to Graeme Bell  (University of Chicago) and collaborator Manami Hara uses a multi-omics approach to investigate the metabolome (primary metabolites), lipidome (complex lipids) and signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice which progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice (n=71) were assessed as diabetic or non-diabetic based on their fasting (4hr) blood glucose levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and 41 normoglycemic animals. The primary objective of this study was to identify candidate biomarkers associated with beta-cell destruction/survival and T1D progression.", + "subject_species": "Mus musculus" + }, + "2": { + "study_id": "ST000075", + "study_title": "Combined Metabolomics and Lipidomics of Type 1 Diabetes (QTOF)", + "study_type": "biomarker study", + "institute": "University of California, Davis", + "department": "Genome and Biomedical Sciences Facility", + "last_name": "Fiehn", + "first_name": "Oliver", + "email": "ofiehn@ucdavis.edu", + "phone": "(530) 754-8258", + "submit_date": "2014-06-11", + "study_summary": "This West Coast Metabolomics Center pilot and feasibility project granted to Graeme Bell  (University of Chicago) and collaborator Manami Hara uses a multi-omics approach to investigate the metabolome (primary metabolites), lipidome (complex lipids) and signaling lipids (oxylipins) in the plasma of Non-obese Diabetic (NOD) mice which progressed to Type 1 Diabetes Mellitus (T1D) and those that did not. NOD Mice (n=71) were assessed as diabetic or non-diabetic based on their fasting (4hr) blood glucose levels at sacrifice, which defined 30 hyperglycemic (glucose = 250 mg/dL) and 41 normoglycemic animals. The primary objective of this study was to identify candidate biomarkers associated with beta-cell destruction/survival and T1D progression.", + "subject_species": "Mus musculus" + }, + "3": { + "study_id": "ST000091", + "study_title": "Quantitative Metabolomics by 1H-NMR and LC-MS/MS Confirms Altered Metabolic Pathways in Diabetes", + "study_type": "Pre- and Post- insulin study with matched controls", + "institute": "Mayo Clinic", + "department": "Endocrinology", + "last_name": "Nair", + "first_name": "Sreekumaran", + "email": "nair@mayo.edu", + "phone": "--", + "submit_date": "2014-07-15", + "study_summary": "We obtained plasma samples from 7 c-peptide negative type 1 diabetic individuals (T1D) and 7 non-diabetic controls (Con) that were matched for age (T1D = 31.1±2.9 yrs, Con = 30.2±3.4 yrs), body mass (T1D = 80.2±4.7kg, Con = 81.9±7.4 kg) and BMI (T1D = 26.5±1.2 kg/m2, Con = 25.2±1.3 kg/m2). Type 1 diabetic people were studied while treated with insulin and also after 8 hours of insulin deprivation", + "subject_species": "Homo sapiens" + }, + "4": { + "study_id": "ST000398", + "study_title": "Metabolic profiling of maternal urine can aid clinical management of Gestational Diabetes Mellitus (GDM)", + "study_type": "Search for non-treated and treated GDM biomarkers in urine", + "institute": "University of Aveiro", + "department": "CICECO-Department of Chemistry", + "last_name": "Gil", + "first_name": "Ana", + "email": "agil@ua.pt", + "phone": "none", + "submit_date": "2016-04-20", + "study_summary": "NMR metabolomics study of maternal urine of 1) GDM women at the time of diagnosis and before treatment, to define the urine metabolic profile of untreated GDM, and of 2) GDM women treated using diet control alone or with the addition of insulin, to identify treatment-resistant and treatment-responsive metabolic pathways and, hence, evaluate treatment efficacy, and 3) GDM treatment prediction at the time of diagnosis, with the aim of finding potential predictive markers of future treatment requirements based on each individual metabotype.", + "subject_species": "Homo sapiens" + }, + "5": { + "study_id": "ST000421", + "study_title": "Type 1 Diabetes poor glycemic control versus control samples", + "study_type": "Plasma metabolites in T1 diabetes", + "institute": "Mayo Clinic", + "department": "Endocrinology", + "last_name": "Nair", + "first_name": "Sreekumaran", + "email": "Nair.K@mayo.edu", + "phone": "507-285-2415", + "submit_date": "2016-07-15", + "study_summary": "The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.", + "subject_species": "Homo sapiens" + }, + "6": { + "study_id": "ST000422", + "study_title": "Type 1 Diabetes good glycemic control and controls samples", + "study_type": "Plasma metabolites in T1 diabetes", + "institute": "Mayo Clinic", + "department": "Endocrinology", + "last_name": "Nair", + "first_name": "Sreekumaran", + "email": "Nair.K@mayo.edu", + "phone": "507-285-2415", + "submit_date": "2016-07-01", + "study_summary": "The objective of the study was to determine whether T1D with good glycemic control have persistent abnormalities of metabolites and pathways that exist in T1D with poor glycemic control.", + "subject_species": "Homo sapiens" + }, + "7": { + "study_id": "ST000467", + "study_title": "Metabolomics of Saliva Samples Obtained from Subjects with Diabetes", + "study_type": "", + "institute": "University of North Carolina", + "department": "Discovery-Sciences-Technology (DST)", + "last_name": "Sumner", + "first_name": "Susan", + "email": "susan_sumner\r\n@unc.edu", + "phone": "704-250-5066", + "submit_date": "2016-09-02", + "study_summary": "In this research, were are investigating the metabolic profile changes associated with well- and poorly-controlled type 1 and 2 diabetes and if there are distinct metabolite compounds that may be associated with glycemic control. The PI of the study collected whole unstimulated saliva samples were from subjects with well- and poorly-controlled type 1 and type 2 diabetes. Subjects were selected based on the level of A1C (<7= well-controlled and >7 = poorly controlled). Saliva samples were shipped to RTI RCMRC for a broad spectrum reverse phase metabolomics analysis.", + "subject_species": "Homo sapiens" + }, + "8": { + "study_id": "ST000530", + "study_title": "Effects of herb DG and KK01 on Type 2 Diabetes Mellitus (T2DM) through Lipidomics", + "study_type": "LC-MS lipidomics", + "institute": "University of North Carolina", + "department": "Systems and Translational Sciences", + "last_name": "Sumner", + "first_name": "Susan", + "email": "susan_sumner@unc.edu", + "phone": "704-250-5066", + "submit_date": "2016-12-30", + "study_summary": "According to the results in animal test, KK01 is effective in controlling blood glucose increase with comparable effect as metformin and rosiglitazone. This study will conduct lipid profile comparison for serum samples generated from the animal tests. The comparison will be based on the following groups: 1) db/db mice + DG-high dose; 2) db/db mice +DG-low dose; 3) db/db mice + KK01-high dose; 4) db/db mice + KK01-low dose; 5) db/db mice + metformin; 6) db/db mice + rosiglitazone; 7) db/db mice + saline (disease model); and 8) wild type mice + saline (healthy model). The determined lipid marker(s) will be applied to elucidate the drug target(s) and mechanisms of DG and KK01. Furthermore, comparison of target(s) between KK01 and the first line drugs in diabetic treatment, e.g., metformin and rosiglitazone, will facilitate the finding of featured pathway(s) of KK01 differentiated from the established drugs. Comparison of drug target(s) between KK01 and DG can help to understand the synergistic effects of multiple constituents in the herb.", + "subject_species": "Mus musculus" + }, + "9": { + "study_id": "ST000540", + "study_title": "Kidney tissue metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.", + "study_type": "Metabolomics", + "institute": "RTI International", + "department": "Discovery-Science-Technology", + "last_name": "Sumner", + "first_name": "Susan", + "email": "susan_sumner@unc.edu", + "phone": "704-250-5000", + "submit_date": "2017-01-20", + "study_summary": "This metabolomics study evaluated kidney tissue from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.", + "subject_species": "Mus musculus" + }, + "10": { + "study_id": "ST000541", + "study_title": "Canine Diabetes - Preliminary Evaluation of Testing Methods", + "study_type": "Single time point blood collection", + "institute": "University of Florida", + "department": "SECIM", + "last_name": "O'Kell", + "first_name": "Allison", + "email": "aokell@ufl.edu", + "phone": "352-392-2235", + "submit_date": "2017-01-10", + "study_summary": "Blood was collected from diabetic dogs and healthy control dogs. Diabetic dogs and control dogs were breed matched where possible. Timing of blood collection after a meal was matched as best as possible. Serum was frozen at -80C.", + "subject_species": "Canis lupus familiaris" + }, + "11": { + "study_id": "ST000558", + "study_title": "Plasma metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model", + "study_type": "", + "institute": "RTI International", + "department": "", + "last_name": "Sumner", + "first_name": "Susan", + "email": "susan_sumner@unc.edu", + "phone": "704-250-5000", + "submit_date": "2017-02-17", + "study_summary": "This metabolomics study evaluated plasma from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.", + "subject_species": "Mus musculus" + }, + "12": { + "study_id": "ST000559", + "study_title": "Urine metabolomic profiling of diabetic nephropathy in the steptozotocin induced type-1 diabetes mouse model.", + "study_type": "", + "institute": "RTI International", + "department": "", + "last_name": "Sumner", + "first_name": "Susan", + "email": "susan_sumner@unc.edu", + "phone": "704-250-5000", + "submit_date": "2017-02-17", + "study_summary": "This metabolomics study evaluated urine from wild-type and meprin β knockout mice after induction of diabetes with streptozotocin or treatment with sodium citrate control to understand how these factors influence the metabotype.", + "subject_species": "Mus musculus" + }, + "13": { + "study_id": "ST000568", + "study_title": "Metabolomic study on a schizophrenia and type 2 diabetes susceptibility gene", + "study_type": "", + "institute": "Shanghai Jiao Tong University Affiliated Sixth People’s Hospital", + "department": "", + "last_name": "Zhang", + "first_name": "Yinan", + "email": "zhyn@sjtu.edu.cn", + "phone": "86-21-24056374", + "submit_date": "2017-01-15", + "study_summary": "a comprehensive serum metabolomic analysis in healthy subjects with different genotypes of rs12742393 (n=49 for AA, AC, and CC, respectively) using gas chromatography–time-of-flight mass spectrometry and ultra-performance liquid chromatography quadruple time-of-flight mass spectrometry.", + "subject_species": "Homo sapiens" + }, + "14": { + "study_id": "ST000909", + "study_title": "Metabolomics Linking Air Pollution, Obesity and Type 2 Diabetes", + "study_type": "Untargeted high-resolution mass spectrometry profiling", + "institute": "Emory University", + "department": "School of Medicine, Division of Pulmonary, Allergy, Critical Care Medicine", + "last_name": "Walker", + "first_name": "Douglas", + "email": "douglas.walker@emory.edu", + "phone": "(404) 727 5984", + "submit_date": "2017-12-05", + "study_summary": "The overall goal of this proposal is to use blood non-targeted high resolution metabolomics (HRM) to investigate the hypothesis that regional air pollution (NO2, PM2.5 and O3) and traffic-related air pollution exposures (traffic-related particulate matter components including EC2.5 and PM2.5 transition metals, and CALINE model-predicted NOx) alter key metabolic pathway(s) and that these alterations are associated with obesity and type 2 diabetes-related traits during the important developmental period of adolesence in the ongoing prospective Chidlren's Health study (CHS). Specific Aim 1 will examine the adverse impact of environmental chemicals in fasting blood samples measured by HRM on obesity (i.e., total body fat and body mass index (BMI)), metabolic dysfunction (e.g., fasting glucose and insulin concentrations and insulin resistance), and obesity-induced inflammation (i.e., leptin) among 104 Southern California adolescents enrolled in the CHS. Specific Aim 2 will examine associations of childhood exposures to PM2.5 and traffic-related air pollutants (i.e., CALINE model-predicted NOx) with biological metabolites identified in fasting blood samples using HRM among 104 adolescents in the CHS. Specific Aim 3 will investigate the metabolic pathways linking air pollution exposures and obesity and type 2 diabetes-related traits using pathway analysis under bayesian hierarchical model among 104 adolescents in the CHS.", + "subject_species": "Homo sapiens" + }, + "15": { + "study_id": "ST001253", + "study_title": "Phenotyping Mouse blood metabolites in day and night in type 2 diabetes", + "study_type": "time course in a 24hr period", + "institute": "Indiana University School of Medicine", + "department": "Ophthalmology", + "last_name": "Beli", + "first_name": "Eleni", + "email": "e.beli@qub.ac.uk", + "phone": "5176144409", + "submit_date": "2019-09-24", + "study_summary": "This experiment compares the metabolites in control db/m and diabetic db/db in day and night.", + "subject_species": "Mus musculus" + }, + "16": { + "study_id": "ST001411", + "study_title": "Plasma metabolites of lipid metabolism associate with diabetic polyneuropathy in a cohort with screen-tested type 2 diabetes: ADDITION-Denmark", + "study_type": "", + "institute": "University of Michigan", + "department": "", + "last_name": "Feldman", + "first_name": "Eva", + "email": "efeldman@med.umich.edu", + "phone": "7347637274", + "submit_date": "2020-06-22", + "study_summary": "The global rise in type 2 diabetes (T2D) is associated with a concomitant increase in diabetic complications. Diabetic polyneuropathy (DPN), the most frequent T2D complication, is characterized by sensory peripheral nerve damage. Although managing glucose effectively slows DPN progression in type 1 diabetes patients, it has limited efficacy in neuropathic T2D patients. The metabolic syndrome (MetS) recently emerged as a major risk factor for DPN; however, the metabolites associated with MetS that correlate with DPN are unknown. We conducted a global plasma metabolomics analysis from a cohort of patients enrolled in the Anglo-Danish-Dutch study of Intensive Treatment of Diabetes in Primary Care (ADDITION), including healthy control subjects, T2D patients, and T2D DPN patients. We identified 15 total plasma metabolites that were altered in T2D DPN patients, including lipids, amino acids, and energy-related metabolites. We evaluated the correlation between these metabolites and all lipid species to identify major changes in both plasma free fatty acids and complex lipids in T2D DPN patients, and found significant alterations in the abundance of long-chain saturated fatty acids, acylcarnitines, and sphingolipids. Our study suggests that DPN in T2D is associated with novel alterations in plasma metabolites related to lipid metabolism.", + "subject_species": "Homo sapiens" + }, + "17": { + "study_id": "ST001436", + "study_title": "Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet induced diabetes", + "study_type": "Supplementation of mice with probiotic bacteria", + "institute": "Oregon State University", + "department": "Pharmaceutical Sciences", + "last_name": "Morgun", + "first_name": "Andriy", + "email": "andriy.morgun@oregonstate.edu", + "phone": "1 541 737 8047", + "submit_date": "2020-07-28", + "study_summary": "For WD + Microbes 1 and WD + Microbes 3 experiments, C57BL/6 mice were fed western diet or western diet supplemented with Lactobacillus gasseri or Lactobacillus johnsonii for 8 weeks and serum was collected from each mice. For Pooled_1 (control group, western diet only), and Pooled_2 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For Pooled_3 (western diet + Lactobacillus johnsonii) group, serum from 4 mice was pooled. For Pooled_7 (control group, western diet only), Pooled_8 (western diet + Lactobacillus gasseri) and Pooled_9 (western diet + Lactobacillus johnsonii) groups, serum from 6 mice each was pooled. For WD + Microbes 6 experiment, C57BL/6 mice were fed western diet for 8 weeks. Then, one group (n = 5) of mice was supplemented with Lactobacillus gasseri for 12 weeks along with continuation of western diet and serum was collected. For Pooled_10 (control group, western diet only) and Pooled_11 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For GF + WD + LG experiment, C57BL/6 germ free mice were fed western diet or western diet supplemented with Lactobacillus gasseri for 2 weeks. For Pooled_12 (control, western diet only) and Pooled_13 (western diet + Lactobacillus gasseri) groups, serum from 2 mice each was pooled.", + "subject_species": "Mus musculus" + }, + "18": { + "study_id": "ST001642", + "study_title": "Lipidomics in high-risk subjects for the identification of integrated biomarker signatures of type 1 diabetes", + "study_type": "", + "institute": "University of Miami", + "department": "", + "last_name": "Bhattacharya", + "first_name": "Sanjoy", + "email": "sbhattacharya@med.miami.edu", + "phone": "305-482-4103", + "submit_date": "2021-01-06", + "study_summary": "We present the lipidome of plasma collected from high-risk type 1 diabetes subjects. The methyl tert-butyl ether (MTBE) method was used for lipid extraction, followed by high performance liquid chromatography (HPLC) tandem mass spectrometry (LC-MS/MS) using a Q Exactive Orbitrap mass spectrometer and an Accela 600 HPLC. Lipid species were identified and quantified by analyzing the raw files in LipidSearch 4.2. Further analysis was conducted using Graphpad Prism and Ingenuity Pathway Analysis (IPA).", + "subject_species": "Homo sapiens" + }, + "19": { + "study_id": "ST001643", + "study_title": "Deletion of the diabetes candidate gene Slc16a13 in mice", + "study_type": "", + "institute": "University of California, Davis", + "department": "West Coast Metabolomics Center", + "last_name": "Birkenfeld", + "first_name": "Andreas", + "email": "Andreas.Birkenfeld@med.uni-tuebingen.de", + "phone": "+49(0)7071 84 20257", + "submit_date": "2021-01-06", + "study_summary": "The metabolome of plasma and liver lysates of Slc16a13 knockout mice was analyzed. Genome-wide association studies identified SLC16A13 as novel target gene in type 2 diabetes. The SLC16A13 gene encodes for SLC16A13/MCT13, a member of the solute carrier 16 family of monocarboxylate transporters. So far, biology and physiological function of SLC16A13 is unknown. Deletion of Slc16a13 is hypothezised to affect intrahepatocellular monocarboxylate availability, that drives increased oxidative phosphorylation, while reducing hepatic lipid content, thereby attenuating hepatic insulin resistance.", + "subject_species": "Mus musculus" + }, + "20": { + "study_id": "ST001742", + "study_title": "Metabolomic Analysis of Canine Diabetes (part-I)", + "study_type": "Single time point blood collection", + "institute": "University of Florida", + "department": "", + "last_name": "O'Kell", + "first_name": "Allison", + "email": "aokell@ufl.edu", + "phone": "3522944471", + "submit_date": "2021-03-31", + "study_summary": "Blood was collected from diabetic dogs and healthy control dogs. Diabetic dogs and control dogs were breed matched where possible. Timing of blood collection after a meal was matched as best as posible. Serum was frozen at -80C.", + "subject_species": "Canis lupus familiaris" + }, + "21": { + "study_id": "ST001754", + "study_title": "Metabolomic Analysis of Canine Diabetes (part-II)", + "study_type": "Single time point blood collection", + "institute": "University of Florida", + "department": "", + "last_name": "O'Kell", + "first_name": "Allison", + "email": "aokell@ufl.edu", + "phone": "352-294-4471", + "submit_date": "2021-04-01", + "study_summary": "Blood was collected from diabetic dogs and healthy control dogs. Diabetic dogs and control dogs were breed matched where possible. Timing of blood collection after a meal was matched as best as posible. Serum was frozen at -80C.", + "subject_species": "Canis lupus familiaris" + }, + "22": { + "study_id": "ST001905", + "study_title": "Metabolomic profiling of saliva in diabetes patients", + "study_type": "", + "institute": "Osaka University", + "department": "", + "last_name": "Sakanaka", + "first_name": "Akito", + "email": "sakanaka@dent.osaka-u.ac.jp", + "phone": "+81668792922", + "submit_date": "2021-08-15", + "study_summary": "We performed comprehensive profiling of plasma and salivary metabolomes, and investigated multivariate covariations with clinical markers of oral and cardiometabolic health in healthy subjects and type 2 diabetes patients. The key findings highlight the potential utility of salivary metabolites for reflecting cardiometabolic changes, including hyperglycemia and dyslipidemia. Our study shows that analysis of panels of salivary metabolites may become an attractive alternative to blood testing for screening of metabolic disorders.", + "subject_species": "Homo sapiens" + }, + "23": { + "study_id": "ST001906", + "study_title": "Metabolomic profiling of plasma in diabetes patients", + "study_type": "", + "institute": "Osaka University", + "department": "", + "last_name": "Sakanaka", + "first_name": "Akito", + "email": "sakanaka@dent.osaka-u.ac.jp", + "phone": "+81668792922", + "submit_date": "2021-08-15", + "study_summary": "We performed comprehensive profiling of plasma and salivary metabolomes, and investigated multivariate covariations with clinical markers of oral and cardiometabolic health in healthy subjects and type 2 diabetes patients. The key findings highlight the potential utility of salivary metabolites for reflecting cardiometabolic changes, including hyperglycemia and dyslipidemia. Our study shows that analysis of panels of salivary metabolites may become an attractive alternative to blood testing for screening of metabolic disorders.", + "subject_species": "Homo sapiens" + }, + "24": { + "study_id": "ST001932", + "study_title": "Perfluorinated compounds and high fat diet in relation to CVD-relevant metabolomic pathways in the SEARCH for Diabetes in Youth study", + "study_type": "", + "institute": "Emory University", + "department": "School of Medicine", + "last_name": "Tran", + "first_name": "ViLinh", + "email": "vtran6@emory.edu", + "phone": "4047275091", + "submit_date": "2021-10-06", + "study_summary": "This project aims to evaluate the association between environmental exposure to perfluorinated alkyl substances (PFCs) and the development of risk factors for cardiometabolic disease in youth diagnosed with diabetes in the SEARCH Cohort Study. The longitudinal study of newly diagnosed cases of type 1 and type 2 diabetes examines serum metabolome changes at baseline and follow-up at approximately 5 years (all >3 years from baseline). Exposures to PFCs and biological effects characterized by serum metabolome changes will be associated with known cardiometabolic risk factors in youth diagnosed with diabetes.", + "subject_species": "Homo sapiens" + }, + "25": { + "study_id": "ST001935", + "study_title": "Metabolomic profiling of spontaneous macaque model for diabetes mellitus", + "study_type": "", + "institute": "Xiamen University", + "department": "", + "last_name": "Yang", + "first_name": "Zhu", + "email": "yangzhu@gmail.com", + "phone": "(+852)34115162", + "submit_date": "2021-09-18", + "study_summary": "The prevalence of diabetes mellitus has been increasing for decades worldwide. To develop safe and potent therapeutics, insights into the mechanisms underlying its pathogenesis are urgently needed. We reported the multi-omics profiling of the liver and sera of both peripheral blood and hepatic portal vein blood from Macaca fascicularis with spontaneous diabetes mellitus with a chow diet. The other two groups of the monkeys fed with chow diet and high-sugar high-fat (HSHF) diet, respectively, were included for comparison. These multi-omics datasets can provide a comprehensive picture of the molecular changes caused by diabetes in primates. Analyses of various omics datasets revealed the alterations of high consistency. Correlation between transcripts and proteins derived from the same genes was observed across individuals for most genes, especially the ones of differential expression. As a result, we found that distinct patterns of the metabolome, proteome, and transcriptome between spontaneous diabetes and HSHF diet-induced diabetes compared with healthy individuals.", + "subject_species": "Macaca fascicularis" + }, + "26": { + "study_id": "ST001948", + "study_title": "Metabolites Associated with Gestational Diabetes in Plasma", + "study_type": "Case:Control ancillary analysis of RCT", + "institute": "California Polytechnic State University", + "department": "Food Science and Nutrition", + "last_name": "La Frano", + "first_name": "Michael", + "email": "mlafrano@calpoly.edu", + "phone": "18057566233", + "submit_date": "2021-10-13", + "study_summary": "Gestational diabetes mellitus (GDM) significantly increases maternal and fetal health risks, but factors predictive of GDM are poorly understood. Plasma metabolomics analyses were conducted in early pregnancy to identify potential biomarkers for early prediction of Gestational Diabetes Mellitus (GDM). Sixty-eight pregnant women with overweight/obesity from a clinical trial of a lifestyle intervention were included. Participants who developed GDM (n=34; GDM group) were matched on treatment group, age, body mass index, and ethnicity with those who did not develop GDM (n=34; Non-GDM group). Blood draws were completed early in pregnancy (10-16 weeks). Plasma samples were analyzed by UPLC-MS using three metabolomics assays. ", + "subject_species": "Homo sapiens" + } +} diff --git a/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000025/untarg_factors.json b/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000025/untarg_factors.json new file mode 100644 index 0000000..108df62 --- /dev/null +++ b/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/analysis_id/AN000025/untarg_factors.json @@ -0,0 +1,41 @@ +{ + "1": { + "FCS:FCS | Hours:72 | REFED:NO_REFED | TGF:NO_TGF": "3" + }, + "2": { + "FCS:FCS | Hours:72 | REFED:NO_REFED | TGF:TGF": "3" + }, + "3": { + "FCS:NO_FCS | Hours:0 | REFED:NO_REFED | TGF:NO_TGF": "3" + }, + "4": { + "FCS:NO_FCS | Hours:12 | REFED:NO_REFED | TGF:NO_TGF": "3" + }, + "5": { + "FCS:NO_FCS | Hours:12 | REFED:NO_REFED | TGF:TGF": "3" + }, + "6": { + "FCS:NO_FCS | Hours:24 | REFED:NO_REFED | TGF:NO_TGF": "3" + }, + "7": { + "FCS:NO_FCS | Hours:24 | REFED:NO_REFED | TGF:TGF": "3" + }, + "8": { + "FCS:NO_FCS | Hours:2 | REFED:NO_REFED | TGF:NO_TGF": "3" + }, + "9": { + "FCS:NO_FCS | Hours:2 | REFED:NO_REFED | TGF:TGF": "3" + }, + "10": { + "FCS:NO_FCS | Hours:72 | REFED:NO_REFED | TGF:NO_TGF": "3" + }, + "11": { + "FCS:NO_FCS | Hours:72 | REFED:NO_REFED | TGF:TGF": "3" + }, + "12": { + "FCS:NO_FCS | Hours:72 | REFED:REFED_48 | TGF:NO_TGF": "3" + }, + "13": { + "FCS:NO_FCS | Hours:72 | REFED:REFED_48 | TGF:TGF": "3" + } +} diff --git a/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000010/summary.json b/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000010/summary.json new file mode 100644 index 0000000..06a11c5 --- /dev/null +++ b/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ST000010/summary.json @@ -0,0 +1,14 @@ +{ + "study_id": "ST000010", + "study_title": "Lung Cancer Cells 4", + "study_type": "MS analysis (Untargeted)", + "institute": "University of Michigan", + "department": "", + "last_name": "Keshamouni", + "first_name": "Venkat", + "email": "vkeshamo@umich.edu", + "phone": "", + "submit_date": "2013-04-03", + "study_summary": "In cancer cells, the process of epithelial–mesenchymal transition (EMT) confers migratory and invasive capacity, resistance to apoptosis, drug resistance, evasion of host immune surveillance and tumor stem cell traits. Cells undergoing EMT may represent tumor cells with metastatic potential. Characterizing the EMT secretome may identify biomarkers to monitor EMT in tumor progression and provide a prognostic signature to predict patient survival. Utilizing a transforming growth factor-β-induced cell culture model of EMT, we quantitatively profiled differentially secreted proteins, by GeLC-tandem mass spectrometry. Integrating with the corresponding transcriptome, we derived an EMT-associated secretory phenotype (EASP) comprising of proteins that were differentially upregulated both at protein and mRNA levels. Four independent primary tumor-derived gene expression data sets of lung cancers were used for survival analysis by the random survival forests (RSF) method. Analysis of 97-gene EASP expression in human lung adenocarcinoma tumors revealed strong positive correlations with lymph node metastasis, advanced tumor stage and histological grade. RSF analysis built on a training set (n = 442), including age, sex and stage as variables, stratified three independent lung cancer data sets into low-, medium- and high-risk groups with significant differences in overall survival. We further refined EASP to a 20 gene signature (rEASP) based on variable importance scores from RSF analysis. Similar to EASP, rEASP predicted survival of both adenocarcinoma and squamous carcinoma patients. More importantly, it predicted survival in the early-stage cancers. These results demonstrate that integrative analysis of the critical biological process of EMT provides mechanism-based and clinically relevant biomarkers with significant prognostic value.\nResearch is published, core data not used but project description is relevant:\nhttp://www.jimmunol.org/content/194/12/5789.long\n", + "subject_species": "Homo sapiens" +} diff --git a/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json b/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json new file mode 100644 index 0000000..4331d34 --- /dev/null +++ b/vignettes/structToolbox_example/0/www.metabolomicsworkbench.org/rest/study/study_id/ignored/untarg_studies.json @@ -0,0 +1,10170 @@ +{ + "1": { + "study_id": "ST000009", + "analysis_id": "AN000023", + "analysis_display": "LC/Electro-spray /QTOF positive ion mode", + "study_title": "Mixed meal tolerance", + "subject_species": "Homo sapiens", + "institute": "University of Michigan" + }, + "2": { + "study_id": "ST000009", + "analysis_id": "AN000024", + "analysis_display": "LC/Electro-spray /QTOF negative ion mode", + "study_title": "Mixed meal tolerance", + "subject_species": "Homo sapiens", + "institute": "University of Michigan" + }, + "3": { + "study_id": "ST000010", + "analysis_id": "AN000025", + "analysis_display": "LC/Electro-spray /QTOF positive ion mode", + "study_title": "Lung Cancer Cells 4", + "subject_species": "Homo sapiens", + "institute": "University of Michigan" + }, + "4": { + "study_id": "ST000010", + "analysis_id": "AN000026", + "analysis_display": "LC/Electro-spray /QTOF negative ion mode", + "study_title": "Lung Cancer Cells 4", + "subject_species": "Homo sapiens", + "institute": "University of Michigan" + }, + "5": { + "study_id": "ST000045", + "analysis_id": "AN000072", + "analysis_display": "MS positive ion mode/C18", + "study_title": "Plasma metabolomics: Comparison of non-diabetic controls with T1D patients", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "6": { + "study_id": "ST000045", + "analysis_id": "AN000073", + "analysis_display": "MS positive ion mode/HILIC", + "study_title": "Plasma metabolomics: Comparison of non-diabetic controls with T1D patients", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "7": { + "study_id": "ST000045", + "analysis_id": "AN000074", + "analysis_display": "MS negative ion mode/C18", + "study_title": "Plasma metabolomics: Comparison of non-diabetic controls with T1D patients", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "8": { + "study_id": "ST000045", + "analysis_id": "AN000075", + "analysis_display": "MS negative ion mode/HILIC", + "study_title": "Plasma metabolomics: Comparison of non-diabetic controls with T1D patients", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "9": { + "study_id": "ST000046", + "analysis_id": "AN000076", + "analysis_display": "MS positive ion mode/C18", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (plasma)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "10": { + "study_id": "ST000046", + "analysis_id": "AN000077", + "analysis_display": "MS positive ion mode/HILIC", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (plasma)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "11": { + "study_id": "ST000046", + "analysis_id": "AN000078", + "analysis_display": "MS negative ion mode/C18", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (plasma)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "12": { + "study_id": "ST000046", + "analysis_id": "AN000079", + "analysis_display": "MS negative ion mode/HILIC", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (plasma)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "13": { + "study_id": "ST000047", + "analysis_id": "AN000080", + "analysis_display": "MS positive ion mode/C18", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (CSF)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "14": { + "study_id": "ST000047", + "analysis_id": "AN000081", + "analysis_display": "MS positive ion mode/HILIC", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (CSF)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "15": { + "study_id": "ST000047", + "analysis_id": "AN000082", + "analysis_display": "MS negative ion mode/C18", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (CSF)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "16": { + "study_id": "ST000047", + "analysis_id": "AN000083", + "analysis_display": "MS negative ion mode/HILIC", + "study_title": "Identification of altered metabolic pathways in Alzheimer's disease, mild cognitive impairment and cognitively normals using Metabolomics (CSF)", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "17": { + "study_id": "ST000072", + "analysis_id": "AN000113", + "analysis_display": "ESI/QTOF positive ion mode", + "study_title": "Effect of diet and age on ovarian metabolome (via tissue)", + "subject_species": "Macaca fascicularis", + "institute": "University of North Carolina" + }, + "18": { + "study_id": "ST000072", + "analysis_id": "AN000114", + "analysis_display": "ESI/QTOF negative ion mode", + "study_title": "Effect of diet and age on ovarian metabolome (via tissue)", + "subject_species": "Macaca fascicularis", + "institute": "University of North Carolina" + }, + "19": { + "study_id": "ST000074", + "analysis_id": "AN000117", + "analysis_display": "ESI/QTOF positive ion mode", + "study_title": "Genetic effects of high fat diet on mouse fecal metabolomics", + "subject_species": "Mus musculus", + "institute": "University of North Carolina" + }, + "20": { + "study_id": "ST000074", + "analysis_id": "AN000118", + "analysis_display": "ESI/QTOF negative ion mode", + "study_title": "Genetic effects of high fat diet on mouse fecal metabolomics", + "subject_species": "Mus musculus", + "institute": "University of North Carolina" + }, + "21": { + "study_id": "ST000090", + "analysis_id": "AN000143", + "analysis_display": "MS positive ion mode", + "study_title": "Caloric Restriction vs drugs", + "subject_species": "Mus musculus", + "institute": "University of Michigan" + }, + "22": { + "study_id": "ST000090", + "analysis_id": "AN000144", + "analysis_display": "MS negative ion mode", + "study_title": "Caloric Restriction vs drugs", + "subject_species": "Mus musculus", + "institute": "University of Michigan" + }, + "23": { + "study_id": "ST000163", + "analysis_id": "AN000255", + "analysis_display": "HESI positive ion mode", + "study_title": "Metabolomics of 50 healthy humans and common marmosets (MetabNet)", + "subject_species": "Homo sapiens;Callithrix jacchus", + "institute": "Emory University" + }, + "24": { + "study_id": "ST000232", + "analysis_id": "AN000347", + "analysis_display": "ESI positive ion mode", + "study_title": "Untargeted metabolomic analysis of the small intestinal content of malnourished mice", + "subject_species": "Mus musculus", + "institute": "University of Victoria" + }, + "25": { + "study_id": "ST000232", + "analysis_id": "AN000348", + "analysis_display": "ESI negative ion mode", + "study_title": "Untargeted metabolomic analysis of the small intestinal content of malnourished mice", + "subject_species": "Mus musculus", + "institute": "University of Victoria" + }, + "26": { + "study_id": "ST000235", + "analysis_id": "AN000353", + "analysis_display": "ESI positive ion mode", + "study_title": "Sprague Dawley rats Nicotine alters brain oxidative metabolism", + "subject_species": "Rattus norvegicus", + "institute": "University of Florida" + }, + "27": { + "study_id": "ST000235", + "analysis_id": "AN000354", + "analysis_display": "ESI negative ion mode", + "study_title": "Sprague Dawley rats Nicotine alters brain oxidative metabolism", + "subject_species": "Rattus norvegicus", + "institute": "University of Florida" + }, + "28": { + "study_id": "ST000239", + "analysis_id": "AN000369", + "analysis_display": "ESI positive ion mode", + "study_title": "Sexual antagonism in exuded non-volatile metabolites in C. purpureus", + "subject_species": "Ceratodon purpureus", + "institute": "University of Florida" + }, + "29": { + "study_id": "ST000239", + "analysis_id": "AN000370", + "analysis_display": "ESI Negative ion mode", + "study_title": "Sexual antagonism in exuded non-volatile metabolites in C. purpureus", + "subject_species": "Ceratodon purpureus", + "institute": "University of Florida" + }, + "30": { + "study_id": "ST000240", + "analysis_id": "AN000371", + "analysis_display": "HESI positive ion mode", + "study_title": "Global LC-MS of Ozone Stress in Maize: GLCMS", + "subject_species": "Zea mays", + "institute": "University of Florida" + }, + "31": { + "study_id": "ST000240", + "analysis_id": "AN000372", + "analysis_display": "HESI negative ion mode", + "study_title": "Global LC-MS of Ozone Stress in Maize: GLCMS", + "subject_species": "Zea mays", + "institute": "University of Florida" + }, + "32": { + "study_id": "ST000242", + "analysis_id": "AN000375", + "analysis_display": "C18 ESI positive ion mode", + "study_title": "Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole M2 medium", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "33": { + "study_id": "ST000242", + "analysis_id": "AN000376", + "analysis_display": "C18 ESI negative ion mode", + "study_title": "Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole M2 medium", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "34": { + "study_id": "ST000242", + "analysis_id": "AN000377", + "analysis_display": "HILIC ESI positive ion mode", + "study_title": "Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole M2 medium", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "35": { + "study_id": "ST000242", + "analysis_id": "AN000378", + "analysis_display": "HILIC ESI negative ion mode", + "study_title": "Whole unconditioned medium (Defined culture media, M199),Whole M1 medium,Whole M2 medium", + "subject_species": "Homo sapiens", + "institute": "Mayo Clinic" + }, + "36": { + "study_id": "ST000244", + "analysis_id": "AN000381", + "analysis_display": "ESI positive ion mode", + "study_title": "Metabolomic Diagnosis in Horse", + "subject_species": "Equus caballus", + "institute": "University of Florida" + }, + "37": { + "study_id": "ST000244", + "analysis_id": "AN000382", + "analysis_display": "ESI negative ion mode", + "study_title": "Metabolomic Diagnosis in Horse", + "subject_species": "Equus caballus", + "institute": "University of Florida" + }, + "38": { + "study_id": "ST000270", + "analysis_id": "AN000432", + "analysis_display": "ESI positive ion mode", + "study_title": "Metabolomics in AML", + "subject_species": "Homo sapiens", + "institute": "University of Florida" + }, + "39": { + "study_id": "ST000270", + "analysis_id": "AN000433", + "analysis_display": "ESI/Orbitrap Negative ion mode", + "study_title": "Metabolomics in AML", + "subject_species": "Homo sapiens", + "institute": "University of Florida" + }, + "40": { + "study_id": "ST000286", + "analysis_id": "AN000454", + "analysis_display": "ESI Positive ion mode", + "study_title": "Mouse skeletal myotube chronic low-frequency stimulation", + "subject_species": "Mus musculus", + "institute": "University of Florida" + }, + "41": { + "study_id": "ST000286", + "analysis_id": "AN000455", + "analysis_display": "ESI Negative ion mode", + "study_title": "Mouse skeletal myotube chronic low-frequency stimulation", + "subject_species": "Mus musculus", + "institute": "University of Florida" + }, + "42": { + "study_id": "ST000288", + "analysis_id": "AN000458", + "analysis_display": "ESI Positive mode", + "study_title": "Metabolomic profiling of AML Cell Lines", + "subject_species": "Homo sapiens", + "institute": "University of Florida" + }, + "43": { + "study_id": "ST000288", + "analysis_id": "AN000459", + "analysis_display": "ESI Negative mode", + "study_title": "Metabolomic profiling of AML Cell Lines", + "subject_species": "Homo sapiens", + "institute": "University of Florida" + }, + "44": { + "study_id": "ST000289", + "analysis_id": "AN000460", + "analysis_display": "ESI Positive mode", + "study_title": "PPDK RNAi effects in endosperm metabolite pools", + "subject_species": "Zea mays", + "institute": "University of Florida" + }, + "45": { + "study_id": "ST000289", + "analysis_id": "AN000461", + "analysis_display": "ESI Negative mode", + "study_title": "PPDK RNAi effects in endosperm metabolite pools", + "subject_species": "Zea mays", + "institute": "University of Florida" + }, + "46": { + "study_id": "ST000290", + "analysis_id": "AN000462", + "analysis_display": "ESI Positive mode", + "study_title": "2014 Biotron Experiment Metabolites", + "subject_species": "Zea mays", + "institute": "University of Florida" + }, + "47": { + "study_id": "ST000290", + "analysis_id": "AN000463", + "analysis_display": "ESI Negative mode", + "study_title": "2014 Biotron Experiment Metabolites", + "subject_species": "Zea mays", + "institute": "University of Florida" + }, + "48": { + "study_id": "ST000291", + "analysis_id": "AN000464", + "analysis_display": "ESI Positive mode", + "study_title": "LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice", + "subject_species": "Homo sapiens", + "institute": "University of Florida" + }, + "49": { + "study_id": "ST000291", + "analysis_id": "AN000465", + "analysis_display": "ESI Negative mode", + "study_title": "LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice", + "subject_species": "Homo sapiens", + "institute": "University of Florida" + }, + "50": { + "study_id": "ST000292", + "analysis_id": "AN000466", + "analysis_display": "ESI Positive mode", + "study_title": "LC-MS 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