examples/thermodynamic_metabolic_model/data.json from KarrLab/obj_tables

examples/thermodynamic_metabolic_model/data.json
Summary

Maintainability

Test Coverage

Issues
{"Compartment": [{"__id": 0, "__type": "Compartment", "id": "c", "name": "cytosol"}, {"__id": 1, "__type": "Compartment", "id": "e", "name": "extracellular space"}], "Metabolite": [{"__id": 2, "__type": "Metabolite", "id": "2ddg6p", "formula": {"C": 6.0, "H": 8.0, "O": 9.0, "P": 1.0}, "name": "2-dehydro-3-deoxy-D-gluconate 6-phosphate"}, {"__id": 3, "__type": "Metabolite", "id": "2pg", "formula": {"C": 3.0, "H": 4.0, "O": 7.0, "P": 1.0}, "name": "D-Glycerate 2-phosphate"}, {"__id": 4, "__type": "Metabolite", "id": "3pg", "formula": {"C": 3.0, "H": 4.0, "O": 7.0, "P": 1.0}, "name": "3-Phospho-D-glycerate"}, {"__id": 5, "__type": "Metabolite", "id": "6pgc", "formula": {"C": 6.0, "H": 10.0, "O": 10.0, "P": 1.0}, "name": "6-Phospho-D-gluconate"}, {"__id": 6, "__type": "Metabolite", "id": "6pgl", "formula": {"C": 6.0, "H": 9.0, "O": 9.0, "P": 1.0}, "name": "6-phospho-D-glucono-1,5-lactone"}, {"__id": 7, "__type": "Metabolite", "id": "13dpg", "formula": {"C": 3.0, "H": 4.0, "O": 10.0, "P": 2.0}, "name": "3-Phospho-D-glyceroyl phosphate"}, {"__id": 8, "__type": "Metabolite", "id": "ac", "formula": {"C": 2.0, "H": 3.0, "O": 2.0}, "name": "Acetate"}, {"__id": 9, "__type": "Metabolite", "id": "acald", "formula": {"C": 2.0, "H": 4.0, "O": 1.0}, "name": "Acetaldehyde"}, {"__id": 10, "__type": "Metabolite", "id": "accoa", "formula": {"C": 23.0, "H": 34.0, "N": 7.0, "O": 17.0, "P": 3.0, "S": 1.0}, "name": "Acetyl-CoA"}, {"__id": 11, "__type": "Metabolite", "id": "acon-C", "formula": {"C": 6.0, "H": 3.0, "O": 6.0}, "name": "cis-Aconitate"}, {"__id": 12, "__type": "Metabolite", "id": "actp", "formula": {"C": 2.0, "H": 3.0, "O": 5.0, "P": 1.0}, "name": "Acetyl phosphate"}, {"__id": 13, "__type": "Metabolite", "id": "adp", "formula": {"C": 10.0, "H": 12.0, "N": 5.0, "O": 10.0, "P": 2.0}, "name": "Adenosine diphosphate"}, {"__id": 14, "__type": "Metabolite", "id": "akg", "formula": {"C": 5.0, "H": 4.0, "O": 5.0}, "name": "2-Oxoglutarate"}, {"__id": 15, "__type": "Metabolite", "id": "amp", "formula": {"C": 10.0, "H": 12.0, "N": 5.0, "O": 7.0, "P": 1.0}, "name": "Adenosine monophosphate"}, {"__id": 16, "__type": "Metabolite", "id": "atp", "formula": {"C": 10.0, "H": 12.0, "N": 5.0, "O": 13.0, "P": 3.0}, "name": "Adenosine triphosphate"}, {"__id": 17, "__type": "Metabolite", "id": "cit", "formula": {"C": 6.0, "H": 5.0, "O": 7.0}, "name": "Citrate"}, {"__id": 18, "__type": "Metabolite", "id": "co2", "formula": {"C": 1.0, "O": 2.0}, "name": "CO2"}, {"__id": 19, "__type": "Metabolite", "id": "coa", "formula": {"C": 21.0, "H": 32.0, "N": 7.0, "O": 16.0, "P": 3.0, "S": 1.0}, "name": "Coenzyme A"}, {"__id": 20, "__type": "Metabolite", "id": "dhap", "formula": {"C": 3.0, "H": 5.0, "O": 6.0, "P": 1.0}, "name": "Dihydroxyacetone phosphate"}, {"__id": 21, "__type": "Metabolite", "id": "e4p", "formula": {"C": 4.0, "H": 7.0, "O": 7.0, "P": 1.0}, "name": "D-Erythrose 4-phosphate"}, {"__id": 22, "__type": "Metabolite", "id": "etoh", "formula": {"C": 2.0, "H": 6.0, "O": 1.0}, "name": "Ethanol"}, {"__id": 23, "__type": "Metabolite", "id": "f1p", "formula": {"C": 6.0, "H": 11.0, "O": 9.0, "P": 1.0}, "name": "Fructose-1-phosphate"}, {"__id": 24, "__type": "Metabolite", "id": "f6p", "formula": {"C": 6.0, "H": 11.0, "O": 9.0, "P": 1.0}, "name": "D-Fructose 6-phosphate"}, {"__id": 25, "__type": "Metabolite", "id": "fdp", "formula": {"C": 6.0, "H": 10.0, "O": 12.0, "P": 2.0}, "name": "D-Fructose 1,6-bisphosphate"}, {"__id": 26, "__type": "Metabolite", "id": "for", "formula": {"C": 1.0, "H": 1.0, "O": 2.0}, "name": "Formate"}, {"__id": 27, "__type": "Metabolite", "id": "fru", "formula": {"C": 6.0, "H": 12.0, "O": 6.0}, "name": "D-Fructose"}, {"__id": 28, "__type": "Metabolite", "id": "fum", "formula": {"C": 4.0, "H": 2.0, "O": 4.0}, "name": "Fumarate"}, {"__id": 29, "__type": "Metabolite", "id": "g1p", "formula": {"C": 6.0, "H": 11.0, "O": 9.0, "P": 1.0}, "name": "D-Glucose 1-phosphate"}, {"__id": 30, "__type": "Metabolite", "id": "g3p", "formula": {"C": 3.0, "H": 5.0, "O": 6.0, "P": 1.0}, "name": "Glyceraldehyde 3-phosphate"}, {"__id": 31, "__type": "Metabolite", "id": "g6p", "formula": {"C": 6.0, "H": 11.0, "O": 9.0, "P": 1.0}, "name": "D-Glucose 6-phosphate"}, {"__id": 32, "__type": "Metabolite", "id": "gal", "formula": {"C": 6.0, "H": 12.0, "O": 6.0}, "name": "Galactose"}, {"__id": 33, "__type": "Metabolite", "id": "gal1p", "formula": {"C": 6.0, "H": 11.0, "O": 9.0, "P": 1.0}, "name": "Galactose-1-phosphate"}, {"__id": 34, "__type": "Metabolite", "id": "glc-D", "formula": {"C": 6.0, "H": 12.0, "O": 6.0}, "name": "D-Glucose"}, {"__id": 35, "__type": "Metabolite", "id": "glcn", "formula": {"C": 6.0, "H": 11.0, "O": 7.0}, "name": "Gluconate"}, {"__id": 36, "__type": "Metabolite", "id": "gln-L", "formula": {"C": 5.0, "H": 10.0, "N": 2.0, "O": 3.0}, "name": "L-Glutamine"}, {"__id": 37, "__type": "Metabolite", "id": "glu-L", "formula": {"C": 5.0, "H": 8.0, "N": 1.0, "O": 4.0}, "name": "L-Glutamate"}, {"__id": 38, "__type": "Metabolite", "id": "glx", "formula": {"C": 2.0, "H": 1.0, "O": 3.0}, "name": "Glyoxylate"}, {"__id": 39, "__type": "Metabolite", "id": "glyc", "formula": {"C": 3.0, "H": 8.0, "O": 3.0}, "name": "Glycerol"}, {"__id": 40, "__type": "Metabolite", "id": "glyc3p", "formula": {"C": 3.0, "H": 7.0, "O": 6.0, "P": 1.0}, "name": "Glycerol 3-phosphate"}, {"__id": 41, "__type": "Metabolite", "id": "h", "formula": {"H": 1.0}, "name": "H+"}, {"__id": 42, "__type": "Metabolite", "id": "h2o", "formula": {"H": 2.0, "O": 1.0}, "name": "H2O"}, {"__id": 43, "__type": "Metabolite", "id": "icit", "formula": {"C": 6.0, "H": 5.0, "O": 7.0}, "name": "Isocitrate"}, {"__id": 44, "__type": "Metabolite", "id": "lac-D", "formula": {"C": 3.0, "H": 5.0, "O": 3.0}, "name": "D-Lactate"}, {"__id": 45, "__type": "Metabolite", "id": "mal-L", "formula": {"C": 4.0, "H": 4.0, "O": 5.0}, "name": "L-Malate"}, {"__id": 46, "__type": "Metabolite", "id": "nad", "formula": {"C": 21.0, "H": 26.0, "N": 7.0, "O": 14.0, "P": 2.0}, "name": "Nicotinamide adenine dinucleotide"}, {"__id": 47, "__type": "Metabolite", "id": "nadh", "formula": {"C": 21.0, "H": 27.0, "N": 7.0, "O": 14.0, "P": 2.0}, "name": "Nicotinamide adenine dinucleotide - reduced"}, {"__id": 48, "__type": "Metabolite", "id": "nadp", "formula": {"C": 21.0, "H": 25.0, "N": 7.0, "O": 17.0, "P": 3.0}, "name": "Nicotinamide adenine dinucleotide phosphate"}, {"__id": 49, "__type": "Metabolite", "id": "nadph", "formula": {"C": 21.0, "H": 26.0, "N": 7.0, "O": 17.0, "P": 3.0}, "name": "Nicotinamide adenine dinucleotide phosphate - reduced"}, {"__id": 50, "__type": "Metabolite", "id": "nh4", "formula": {"H": 4.0, "N": 1.0}, "name": "Ammonium"}, {"__id": 51, "__type": "Metabolite", "id": "o2", "formula": {"O": 2.0}, "name": "O2"}, {"__id": 52, "__type": "Metabolite", "id": "oaa", "formula": {"C": 4.0, "H": 2.0, "O": 5.0}, "name": "Oxaloacetate"}, {"__id": 53, "__type": "Metabolite", "id": "pep", "formula": {"C": 3.0, "H": 2.0, "O": 6.0, "P": 1.0}, "name": "Phosphoenolpyruvate"}, {"__id": 54, "__type": "Metabolite", "id": "pi", "formula": {"H": 1.0, "O": 4.0, "P": 1.0}, "name": "Phosphate"}, {"__id": 55, "__type": "Metabolite", "id": "pyr", "formula": {"C": 3.0, "H": 3.0, "O": 3.0}, "name": "Pyruvate"}, {"__id": 56, "__type": "Metabolite", "id": "q8", "formula": {"C": 49.0, "H": 74.0, "O": 4.0}, "name": "Ubiquinone-8"}, {"__id": 57, "__type": "Metabolite", "id": "q8h2", "formula": {"C": 49.0, "H": 76.0, "O": 4.0}, "name": "Ubiquinol-8"}, {"__id": 58, "__type": "Metabolite", "id": "r5p", "formula": {"C": 5.0, "H": 9.0, "O": 8.0, "P": 1.0}, "name": "alpha-D-Ribose 5-phosphate"}, {"__id": 59, "__type": "Metabolite", "id": "ru5p-D", "formula": {"C": 5.0, "H": 9.0, "O": 8.0, "P": 1.0}, "name": "D-Ribulose 5-phosphate"}, {"__id": 60, "__type": "Metabolite", "id": "s7p", "formula": {"C": 7.0, "H": 13.0, "O": 10.0, "P": 1.0}, "name": "Sedoheptulose 7-phosphate"}, {"__id": 61, "__type": "Metabolite", "id": "succ", "formula": {"C": 4.0, "H": 4.0, "O": 4.0}, "name": "Succinate"}, {"__id": 62, "__type": "Metabolite", "id": "succoa", "formula": {"C": 25.0, "H": 35.0, "N": 7.0, "O": 19.0, "P": 3.0, "S": 1.0}, "name": "Succinyl-CoA"}, {"__id": 63, "__type": "Metabolite", "id": "xu5p-D", "formula": {"C": 5.0, "H": 9.0, "O": 8.0, "P": 1.0}, "name": "D-Xylulose 5-phosphate"}], "Reaction": [{"__id": 64, "__type": "Reaction", "id": "ACKr", "delta_g_acetate": -15.2590407588472, "delta_g_acetate_uncertainty": 0.117068558170239, "delta_g_fructose": 9.53451876934678, "delta_g_fructose_uncertainty": 0.311060205085736, "delta_g_galactose": 8.60571345873037, "delta_g_galactose_uncertainty": 0.0731164403823461, "delta_g_gluconate": -11.943647706081, "delta_g_gluconate_uncertainty": 0.118141373385484, "delta_g_glucose": -17.9896304132158, "delta_g_glucose_uncertainty": 0.0571933812647855, "delta_g_glycerol": -11.8766590894163, "delta_g_glycerol_uncertainty": 0.122850894266402, "delta_g_pyruvate": -16.526070814056, "delta_g_pyruvate_uncertainty": 0.131053648537917, 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Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson B\u00d8.", "end_page": null, "issue": 1.0, "journal": "Mol Syst Biol.", "pubmed_id": 17593909.0, "start_page": null, "title": "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.", "volume": 3.0}], "_documentMetadata": {"objTablesVersion": "1.0.9", "date": "2020-06-02 16:01:35", "comment": "Data obtained from Gerosa et al., Cell Systems, 2015, DOI: 10.1016/j.cels.2015.09.008"}, "_classMetadata": {"Compartment": {"class": "Compartment", "name": "Compartments"}, "Metabolite": {"class": "Metabolite", "name": "Metabolites"}, "Reaction": {"class": "Reaction", "name": "Reactions"}, "Reference": {"class": "Reference", "name": "References", "format": "row"}}}