{ "bcoid": "GLY_001045", "title": "Human Diabetes Glycomics (ML Ready)", "description": "The Human Diabetes Glycomics (ML Ready) dataset contains abundance information on the plasma N-glycome ...", "filename_list": "human_proteoform_ml_ready_diabetes_glycomic.csv", "filename": "human_proteoform_ml_ready_diabetes_glycomic.csv", "filetype": "csv", "categories": { "species": [ "Homo sapiens" ], "molecule": [ "Proteoform" ], "tag": [ "Diabetes glycomic study" ], "file_type": [ "csv" ], "usability": [ "Machine Learning" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "4002080252...", "FinnRisk..." ], [ "4002122536...", "FinnRisk..." ] ], "headers": [ "Sample...", "Cohort..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "Sample" }, { "type": "string", "label": "Cohort" }, { "type": "string", "label": "BL_AGE" }, { "type": "string", "label": "DIAB_AGE" }, { "type": "string", "label": "GP1_G83367MW" }, { "type": "string", "label": "GP2_G69449MU_G95184RD" }, { "type": "string", "label": "GP3_G83155SV" }, { "type": "string", "label": "GP4_G92683CO" }, { "type": "string", "label": "GP5_G62110XZ" }, { "type": "string", "label": "GP6_G94649QB_G44147IO" }, { "type": "string", "label": "GP7_G16377ZV" }, { "type": "string", "label": "GP8_G60878GV" }, { "type": "string", "label": "GP9_G60878GV" }, { "type": "string", "label": "GP10_G50303DJ" }, { "type": "string", "label": "GP11_G74112GC" }, { "type": "string", "label": "GP12_G17434DR" }, { "type": "string", "label": "GP13_G69867DA" }, { "type": "string", "label": "GP14_G52069SB" }, { "type": "string", "label": "GP15_G20343BM" }, { "type": "string", "label": "GP16_G31213WS" }, { "type": "string", "label": "GP17_G02849EL" }, { "type": "string", "label": "GP18_G91519IS" }, { "type": "string", "label": "GP19_G73813HX" }, { "type": "string", "label": "GP20_G87442NP" }, { "type": "string", "label": "GP21_G95602TE" }, { "type": "string", "label": "GP22_G34520RB" }, { "type": "string", "label": "GP23_G43679GQ" }, { "type": "string", "label": "GP24_G40510IW" }, { "type": "string", "label": "GP25_G43679GQ" }, { "type": "string", "label": "GP26_G20746DT" }, { "type": "string", "label": "GP27_G53916LT" }, { "type": "string", "label": "GP28_G75079FY" }, { "type": "string", "label": "GP29_G46440UD" }, { "type": "string", "label": "GP30_G59722IA" }, { "type": "string", "label": "GP31_G62220SM" }, { "type": "string", "label": "GP32_G67579EM" }, { "type": "string", "label": "GP33_G67579EM" }, { "type": "string", "label": "GP34_G53972TI_G67579EM" }, { "type": "string", "label": "GP35_G78494LP" }, { "type": "string", "label": "GP36_G53972TI" }, { "type": "string", "label": "GP37_G94649DT" }, { "type": "string", "label": "GP38_G12638YK" }, { "type": "string", "label": "GP39_G12638YK" }, { "type": "string", "label": "GP40_G42752DG" }, { "type": "string", "label": "GP41_G16933RK" }, { "type": "string", "label": "GP42_G16933RK" }, { "type": "string", "label": "GP43_G16933RK" }, { "type": "string", "label": "GP44_G09503CT" }, { "type": "string", "label": "GP45_G58170TE" }, { "type": "string", "label": "GP46_G92164ET" }, { "type": "string", "label": "DIABETES" } ], [ "4002080252", "FinnRisk", "55.425", "57.914", "0.016117543", "0.072337091", "0.002571769", "0.045732195", "3.306536179", "1.466414739", "0.056500309", "4.104060707", "2.48862935", "1.501083086", "1.077958737", "0.684379786", "0.078062741", "4.419775322", "0.963071407", "0.84101438", "0.882493985", "0.076572836", "8.50362312", "0.381232962", "6.479537828", "2.2373325", "2.769472535", "1.133307927", "26.85132263", "0.767373623", "6.474634808", "4.603362955", "1.475636797", "0.079695833", "1.402411565", "0.865194439", "0.580548817", "4.130133093", "0.223745791", "0.550068486", "1.574027557", "3.533020323", "0.43510067", "0.498498337", "0.407195851", "0.321716346", "0.528682933", "0.311148508", "0.486702638", "0.311958971", "1" ], [ "4002122536", "FinnRisk", "63.091", "67.912", "0.02117314", "0.153304231", "0.005156101", "0.082790947", "9.82514388", "2.218289179", "0.064144963", "4.702867076", "2.291542451", "1.31662304", "0.97607611", "0.684601895", "0.068060157", "2.625813595", "0.678217843", "0.811254861", "0.836959484", "0.065711596", "8.730155433", "0.264849785", "5.306888707", "1.897648573", "2.733008111", "1.052433036", "26.7989278", "0.648553609", "5.795037805", "3.534629059", "1.341160785", "0.070047828", "1.200994802", "0.653308103", "0.538682029", "4.251119752", "0.186489456", "0.41743131", "1.468835347", "2.817053845", "0.352064873", "0.305025172", "0.367101032", "0.336453141", "0.517333071", "0.302511897", "0.406640698", "0.277884392", "0" ] ] }, "readme": "Name\n - Human Diabetes Glycomics (ML Ready)\n\nVersion\n - v-2.8.1\n\nCreated on\n - 2024-07-23T00:43:32\n\nModified on\n - 2024-07-23T00:50:48.524Z\n\nCreated by\n - Karina Martinez [karinamartinez@gwu.edu]\n\nAuthors\n - Olga Gornik [ogornik@pharma.hr], Nadja Rudman [najda.rudman@gmail.com]\n\nChecksum\n - \n\nUsability Domain\n - The Human Diabetes Glycomics (ML Ready) dataset contains abundance information on the plasma N-glycome of individuals participating in the FinRisk study and can be used to predict risk of incident diabetes within a 10 year follow up period. Baseline samples were analyzed from 37 individuals who developed type 2 diabetes within 10 years and 37 sex and age matched individuals who remained normoglycaemic. HILIC-UPLC chromatograms were separated into 46 peaks, and were assigned to the most abundant glycan structures in each peak (see Fig 1 of Ref 1). The data was provided by Dr. Olga Gornik, Faculty of Pharmacy and Biochemistry, University of Zagreb and cleaned by the GlyGen team to make ready for machine learning algorithms. If you use this dataset please provide proper attribution to the source publication [1] and GlyGen.\n - References: 1) Keser T, Gornik I, Vu\u010dkovi\u0107 F, Selak N, Pavi\u0107 T, Luki\u0107 E, Gudelj I, Ga\u0161parovi\u0107 H, Bio\u010dina B, Tilin T, Wennerstr\u00f6m A, M\u00e4nnist\u00f6 S, Salomaa V, Havulinna A, Wang W, Wilson JF, Chaturvedi N, Perola M, Campbell H, Lauc G, Gornik O. Increased plasma N-glycome complexity is associated with higher risk of type 2 diabetes. Diabetologia. 2017;60(12):2352-2360. doi:10.1007/s00125-017-4426-9. PMID:28905229.\n - Content: This dataset consists of 74 instances with 51 columns. A description of the headers follows. Sample: The unique identifier of the patient. Cohort: The study cohort. BL_AGE: Age at baseline. DIAB_AGE: Age at follow up. GP*_*: Glycan peak number and GlyTouCan accession mapped to each peak based on the glycan topology.\n - Processing scripts, exploratory data analysis and models trained on this dataset can be found at https://github.com/glygener/glygen-machine-learning/tree/main/diabetes_glycomic\n\nDescription Domain\n Keywords\n - N-glycome\n - Publications\n - Citations\n - PubMed\n - Diabetes\n - Machine Learning\n - Data Science\n - Artificial Intelligence\n - AI\n\n Pipeline Steps\n - Step-1: Processing script that formats the data, drops redundant columns and derived traits, and maps GlyTouCan accessions to peak numbers.\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/diabetes_preprocessing.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Output Subdomain\n Name: human_proteoform_ml_ready_diabetes_glycomic.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/human_proteoform_ml_ready_diabetes_glycomic.csv\n Name: human_proteoform_ml_ready_diabetes_glycomic.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.8.1/reviewed/human_proteoform_ml_ready_diabetes_glycomic.stat.csv\n\nFields\n Name: \"Sample\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"Cohort\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"BL_AGE\"\n Description: \"\"\n Unique Values: \"72\"\n Name: \"DIAB_AGE\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP1_G83367MW\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP2_G69449MU_G95184RD\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP3_G83155SV\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP4_G92683CO\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP5_G62110XZ\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP6_G94649QB_G44147IO\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP7_G16377ZV\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP8_G60878GV\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP9_G60878GV\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP10_G50303DJ\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP11_G74112GC\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP12_G17434DR\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP13_G69867DA\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP14_G52069SB\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP15_G20343BM\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP16_G31213WS\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP17_G02849EL\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP18_G91519IS\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP19_G73813HX\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP20_G87442NP\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP21_G95602TE\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP22_G34520RB\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP23_G43679GQ\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP24_G40510IW\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP25_G43679GQ\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP26_G20746DT\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP27_G53916LT\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP28_G75079FY\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP29_G46440UD\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP30_G59722IA\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP31_G62220SM\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP32_G67579EM\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP33_G67579EM\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP34_G53972TI_G67579EM\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP35_G78494LP\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP36_G53972TI\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP37_G94649DT\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP38_G12638YK\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP39_G12638YK\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP40_G42752DG\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP41_G16933RK\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP42_G16933RK\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP43_G16933RK\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP44_G09503CT\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP45_G58170TE\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"GP46_G92164ET\"\n Description: \"\"\n Unique Values: \"74\"\n Name: \"DIABETES\"\n Description: \"\"\n Unique Values: \"2\"", "downloadurl": "/ln2data/releases/data/v-2.8.1/reviewed/human_proteoform_ml_ready_diabetes_glycomic.csv" }