diff --git a/mira/modeling/amr/regnet.py b/mira/modeling/amr/regnet.py index 6c82a0c8a..fa996170b 100644 --- a/mira/modeling/amr/regnet.py +++ b/mira/modeling/amr/regnet.py @@ -147,6 +147,8 @@ def __init__(self, model: Model): self.transitions.append(transition_dict) for key, param in model.parameters.items(): + if param.placeholder: + continue param_dict = {'id': str(key)} if param.value: param_dict['value'] = param.value diff --git a/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py b/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py index e447dd1a8..456c1ab17 100644 --- a/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py +++ b/scripts/covid19_diseasemaps/process_covid19_diseasemaps.py @@ -1,5 +1,6 @@ import json import tqdm +from mira.metamodel import Annotations from mira.modeling.amr.regnet import template_model_to_regnet_json from mira.sources.sif import template_model_from_sif_url @@ -20,6 +21,15 @@ for model in tqdm.tqdm(models): url = f'{SIF_URL_BASE}/{model}_stable.sif' tm = template_model_from_sif_url(url) + tm.annotations = Annotations( + name=model, + description=("A submodel of the COVID-10 Disease Map " + f"focusing on {model}"), + pathogens=["ncbitaxon:2697049"], + diseases=["doid:0080600"], + hosts=["ncbitaxon:9606"], + references=["pubmed:34664389"] + ) regnet = template_model_to_regnet_json(tm) - with open(f'{model}.json', 'w') as fh: + with open(f'regnet_amr/{model}.json', 'w') as fh: json.dump(regnet, fh, indent=1) diff --git a/scripts/covid19_diseasemaps/regnet_amr/Apoptosis.json b/scripts/covid19_diseasemaps/regnet_amr/Apoptosis.json new file mode 100644 index 000000000..efa40d973 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Apoptosis.json @@ -0,0 +1,543 @@ +{ + "header": { + "name": "Apoptosis", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Apoptosis", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "BAD/BBC3/BCL2L11_complex", + "name": "BAD/BBC3/BCL2L11_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2/MCL1/BCL2L1_complex", + "name": "BCL2/MCL1/BCL2L1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAX", + "name": "BAX", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a", + "name": "Orf7a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E", + "name": "E", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAD", + "name": "BAD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FAS/FASL_complex", + "name": "FAS/FASL_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FADD", + "name": "FADD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FASLG", + "name": "FASLG", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TNF/TNFRSF1A_complex", + "name": "TNF/TNFRSF1A_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRADD/FADD_complex", + "name": "TRADD/FADD_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TNF", + "name": "TNF", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP8", + "name": "CASP8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRADD", + "name": "TRADD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Apoptosome_complex", + "name": "Apoptosome_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP9_cell_active", + "name": "CASP9_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CYCS", + "name": "CYCS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "APAF1", + "name": "APAF1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP9_cell", + "name": "CASP9_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AKT1", + "name": "AKT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M", + "name": "M", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BID", + "name": "BID", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK14", + "name": "MAPK14", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a", + "name": "Orf3a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP7", + "name": "CASP7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Apoptosis_phenotype", + "name": "Apoptosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP3", + "name": "CASP3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf6", + "name": "Orf6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S", + "name": "S", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf8a", + "name": "Orf8a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "N", + "name": "N", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3b", + "name": "Orf3b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b", + "name": "Orf9b", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "BAD/BBC3/BCL2L11_complex", + "target": "BCL2/MCL1/BCL2L1_complex", + "sign": false + }, + { + "id": "t2", + "source": "BAX", + "target": "BCL2/MCL1/BCL2L1_complex", + "sign": false + }, + { + "id": "t3", + "source": "BCL2/MCL1/BCL2L1_complex", + "target": "Orf7a", + "sign": false + }, + { + "id": "t4", + "source": "BCL2/MCL1/BCL2L1_complex", + "target": "E", + "sign": false + }, + { + "id": "t5", + "source": "BCL2/MCL1/BCL2L1_complex", + "target": "BAD", + "sign": false + }, + { + "id": "t6", + "source": "FADD", + "target": "FAS/FASL_complex", + "sign": true + }, + { + "id": "t7", + "source": "FAS/FASL_complex", + "target": "FASLG", + "sign": true + }, + { + "id": "t8", + "source": "TRADD/FADD_complex", + "target": "TNF/TNFRSF1A_complex", + "sign": true + }, + { + "id": "t9", + "source": "TNF/TNFRSF1A_complex", + "target": "TNF", + "sign": true + }, + { + "id": "t10", + "source": "BAX", + "target": "BAD/BBC3/BCL2L11_complex", + "sign": true + }, + { + "id": "t11", + "source": "CASP8", + "target": "TRADD/FADD_complex", + "sign": true + }, + { + "id": "t12", + "source": "TRADD/FADD_complex", + "target": "FADD", + "sign": true + }, + { + "id": "t13", + "source": "CASP8", + "target": "FADD", + "sign": true + }, + { + "id": "t14", + "source": "TRADD/FADD_complex", + "target": "TRADD", + "sign": true + }, + { + "id": "t15", + "source": "CASP9_cell_active", + "target": "Apoptosome_complex", + "sign": true + }, + { + "id": "t16", + "source": "Apoptosome_complex", + "target": "CYCS", + "sign": true + }, + { + "id": "t17", + "source": "Apoptosome_complex", + "target": "APAF1", + "sign": true + }, + { + "id": "t18", + "source": "Apoptosome_complex", + "target": "CASP9_cell", + "sign": true + }, + { + "id": "t19", + "source": "Apoptosome_complex", + "target": "AKT1", + "sign": false + }, + { + "id": "t20", + "source": "BAD", + "target": "AKT1", + "sign": false + }, + { + "id": "t21", + "source": "CASP9_cell_active", + "target": "AKT1", + "sign": false + }, + { + "id": "t22", + "source": "AKT1", + "target": "M", + "sign": false + }, + { + "id": "t23", + "source": "CYCS", + "target": "BAX", + "sign": true + }, + { + "id": "t24", + "source": "BAX", + "target": "BID", + "sign": true + }, + { + "id": "t25", + "source": "CYCS", + "target": "MAPK14", + "sign": true + }, + { + "id": "t26", + "source": "MAPK14", + "target": "Orf3a", + "sign": true + }, + { + "id": "t27", + "source": "CASP8", + "target": "Orf3a", + "sign": true + }, + { + "id": "t28", + "source": "Apoptosis_phenotype", + "target": "CASP7", + "sign": true + }, + { + "id": "t29", + "source": "CASP7", + "target": "CASP9_cell_active", + "sign": true + }, + { + "id": "t30", + "source": "CASP3", + "target": "CASP9_cell_active", + "sign": true + }, + { + "id": "t31", + "source": "CASP7", + "target": "CASP8", + "sign": true + }, + { + "id": "t32", + "source": "CASP3", + "target": "CASP8", + "sign": true + }, + { + "id": "t33", + "source": "BID", + "target": "CASP8", + "sign": true + }, + { + "id": "t34", + "source": "Apoptosis_phenotype", + "target": "CASP3", + "sign": true + }, + { + "id": "t35", + "source": "Apoptosis_phenotype", + "target": "Orf6", + "sign": true + }, + { + "id": "t36", + "source": "Apoptosis_phenotype", + "target": "S", + "sign": true + }, + { + "id": "t37", + "source": "Apoptosis_phenotype", + "target": "Orf8a", + "sign": true + }, + { + "id": "t38", + "source": "Apoptosis_phenotype", + "target": "N", + "sign": true + }, + { + "id": "t39", + "source": "Apoptosis_phenotype", + "target": "Orf3b", + "sign": true + }, + { + "id": "t40", + "source": "Apoptosis_phenotype", + "target": "Orf9b", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Coagulation-pathway.json b/scripts/covid19_diseasemaps/regnet_amr/Coagulation-pathway.json new file mode 100644 index 000000000..b34c2d3be --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Coagulation-pathway.json @@ -0,0 +1,2232 @@ +{ + "header": { + "name": "Coagulation-pathway", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Coagulation-pathway", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "KNG1:KLKB1_complex", + "name": "KNG1:KLKB1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Kininogen", + "name": "Kininogen", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Kallikrein", + "name": "Kallikrein", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Bradykinin", + "name": "Bradykinin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "KLKB1", + "name": "KLKB1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F12a", + "name": "F12a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Small_peptide", + "name": "Small_peptide", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Plasmin", + "name": "Plasmin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "KNG1", + "name": "KNG1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F5a:F10a_complex", + "name": "F5a:F10a_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thrombin_blood", + "name": "Thrombin_blood", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F10a", + "name": "F10a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F5a", + "name": "F5a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F9a", + "name": "F9a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F8:F9_complex", + "name": "F8:F9_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F8a", + "name": "F8a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SERPINE1", + "name": "SERPINE1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PLAT:SERPINE1_complex", + "name": "PLAT:SERPINE1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PLAT_blood_active", + "name": "PLAT_blood_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PLAU", + "name": "PLAU", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PLAT_blood", + "name": "PLAT_blood", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SARS-CoV-2_infection_phenotype", + "name": "SARS-CoV-2_infection_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fibrinogen_complex", + "name": "Fibrinogen_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TAT_complex_complex", + "name": "TAT_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5b-9_complex_endothelium,_vascular", + "name": "C5b-9_complex_endothelium,_vascular", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "SERPINF2:Plasmin_complex", + "name": "SERPINF2:Plasmin_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F8", + "name": "F8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "angiotensin_II_simple_molecule", + "name": "angiotensin_II_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Antithrombin", + "name": "Antithrombin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PROC", + "name": "PROC", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "D-dimer", + "name": "D-dimer", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TNF", + "name": "TNF", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL6", + "name": "IL6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL1B", + "name": "IL1B", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5a", + "name": "C5a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thrombomodulin", + "name": "Thrombomodulin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL8", + "name": "IL8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL2RA", + "name": "IL2RA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C4d", + "name": "C4d", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2_endothelium,_vascular", + "name": "ACE2_endothelium,_vascular", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fibrin_monomer", + "name": "Fibrin_monomer", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CRP", + "name": "CRP", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "VWF", + "name": "VWF", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MASP2", + "name": "MASP2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "aldosterone_simple_molecule_blood", + "name": "aldosterone_simple_molecule_blood", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Hypokalemia_phenotype", + "name": "Hypokalemia_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fibrinogen:GP6_complex", + "name": "Fibrinogen:GP6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thrombin_blood_active", + "name": "Thrombin_blood_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thrombin:Thrombomodulin_complex", + "name": "Thrombin:Thrombomodulin_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F11", + "name": "F11", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F11a", + "name": "F11a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TAFI", + "name": "TAFI", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5b:C6:C7:C8A:C8B:C8G_complex", + "name": "C5b:C6:C7:C8A:C8B:C8G_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5b:C6:C7_complex", + "name": "C5b:C6:C7_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C8A:C8B:C8G_complex", + "name": "C8A:C8B:C8G_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C3b:Bb:C3b_complex", + "name": "C3b:Bb:C3b_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5b", + "name": "C5b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C3b", + "name": "C3b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C3b:Bb_complex", + "name": "C3b:Bb_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C3a", + "name": "C3a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5b:C6_complex", + "name": "C5b:C6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C7", + "name": "C7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Plasminogen", + "name": "Plasminogen", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thrombosis_phenotype_blood", + "name": "Thrombosis_phenotype_blood", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5b-9_deposition_phenotype", + "name": "C5b-9_deposition_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C9", + "name": "C9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C6", + "name": "C6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C2a:C4b_complex", + "name": "C2a:C4b_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C4b", + "name": "C4b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C2a", + "name": "C2a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2:Spike_complex", + "name": "ACE2:Spike_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SARS-CoV-2_viral_entry_phenotype", + "name": "SARS-CoV-2_viral_entry_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2_blood", + "name": "ACE2_blood", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S", + "name": "S", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SERPINF2", + "name": "SERPINF2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "platelet_activation_phenotype", + "name": "platelet_activation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GP6", + "name": "GP6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GP6:alpha2:beta1_complex", + "name": "GP6:alpha2:beta1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GP6:alpha2beta1:VWF_complex", + "name": "GP6:alpha2beta1:VWF_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ITGA2:ITGAB1_complex", + "name": "ITGA2:ITGAB1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F12", + "name": "F12", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F10", + "name": "F10", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Bradykinin(1-5)", + "name": "Bradykinin(1-5)", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE", + "name": "ACE", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F9", + "name": "F9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Heparin_simple_molecule", + "name": "Heparin_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "angiotensin_I-7_simple_molecule", + "name": "angiotensin_I-7_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AGTR1_platelet", + "name": "AGTR1_platelet", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AGTR1_blood", + "name": "AGTR1_blood", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "angiotensin_I_simple_molecule", + "name": "angiotensin_I_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AGT", + "name": "AGT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "REN", + "name": "REN", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Prorenin", + "name": "Prorenin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "aldosterone_simple_molecule_endothelium,_vascular", + "name": "aldosterone_simple_molecule_endothelium,_vascular", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F5", + "name": "F5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Prothrombin", + "name": "Prothrombin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fibrin_polymer", + "name": "Fibrin_polymer", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAS1", + "name": "MAS1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NR3C2", + "name": "NR3C2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thrombosis_phenotype_human_host", + "name": "Thrombosis_phenotype_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cytokine_storm_phenotype", + "name": "cytokine_storm_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C5", + "name": "C5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C4d_deposition_phenotype", + "name": "C4d_deposition_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C3", + "name": "C3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MASP1", + "name": "MASP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C2b", + "name": "C2b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MBL2", + "name": "MBL2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C4", + "name": "C4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C4a", + "name": "C4a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MASP2_deposition_phenotype", + "name": "MASP2_deposition_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "C2", + "name": "C2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CFI", + "name": "CFI", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "septal_capillary_necrosis_phenotype", + "name": "septal_capillary_necrosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "apoptosis_phenotype", + "name": "apoptosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "platelet_aggregation_phenotype", + "name": "platelet_aggregation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F13a", + "name": "F13a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "thrombus_formation_phenotype", + "name": "thrombus_formation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "K+_ion", + "name": "K+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACTH_simple_molecule", + "name": "ACTH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "vascular_remodeling_phenotype", + "name": "vascular_remodeling_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "vascular_inflammation_phenotype", + "name": "vascular_inflammation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "Kininogen", + "target": "KNG1:KLKB1_complex", + "sign": true + }, + { + "id": "t2", + "source": "Kallikrein", + "target": "KNG1:KLKB1_complex", + "sign": true + }, + { + "id": "t3", + "source": "Bradykinin", + "target": "KNG1:KLKB1_complex", + "sign": true + }, + { + "id": "t4", + "source": "KNG1:KLKB1_complex", + "target": "KLKB1", + "sign": true + }, + { + "id": "t5", + "source": "F12a", + "target": "KLKB1", + "sign": true + }, + { + "id": "t6", + "source": "Small_peptide", + "target": "KLKB1", + "sign": true + }, + { + "id": "t7", + "source": "Plasmin", + "target": "KLKB1", + "sign": true + }, + { + "id": "t8", + "source": "Kallikrein", + "target": "KLKB1", + "sign": true + }, + { + "id": "t9", + "source": "KNG1:KLKB1_complex", + "target": "KNG1", + "sign": true + }, + { + "id": "t10", + "source": "Thrombin_blood", + "target": "F5a:F10a_complex", + "sign": true + }, + { + "id": "t11", + "source": "F5a:F10a_complex", + "target": "F10a", + "sign": true + }, + { + "id": "t12", + "source": "F5a:F10a_complex", + "target": "F5a", + "sign": true + }, + { + "id": "t13", + "source": "F8:F9_complex", + "target": "F9a", + "sign": true + }, + { + "id": "t14", + "source": "Small_peptide", + "target": "F9a", + "sign": true + }, + { + "id": "t15", + "source": "F10a", + "target": "F9a", + "sign": true + }, + { + "id": "t16", + "source": "F8:F9_complex", + "target": "F8a", + "sign": true + }, + { + "id": "t17", + "source": "PLAT:SERPINE1_complex", + "target": "SERPINE1", + "sign": true + }, + { + "id": "t18", + "source": "PLAT_blood_active", + "target": "SERPINE1", + "sign": false + }, + { + "id": "t19", + "source": "PLAU", + "target": "SERPINE1", + "sign": false + }, + { + "id": "t20", + "source": "PLAT:SERPINE1_complex", + "target": "PLAT_blood", + "sign": true + }, + { + "id": "t21", + "source": "PLAT_blood_active", + "target": "PLAT_blood", + "sign": true + }, + { + "id": "t22", + "source": "PLAT:SERPINE1_complex", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t23", + "source": "Fibrinogen_complex", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t24", + "source": "TAT_complex_complex", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t25", + "source": "C5b-9_complex_endothelium,_vascular", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t26", + "source": "SERPINF2:Plasmin_complex", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t27", + "source": "F8", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t28", + "source": "angiotensin_II_simple_molecule", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t29", + "source": "Antithrombin", + "target": "SARS-CoV-2_infection_phenotype", + "sign": false + }, + { + "id": "t30", + "source": "PROC", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t31", + "source": "D-dimer", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t32", + "source": "TNF", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t33", + "source": "IL6", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t34", + "source": "IL1B", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t35", + "source": "C5a", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t36", + "source": "Thrombomodulin", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t37", + "source": "IL8", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t38", + "source": "IL2RA", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t39", + "source": "C4d", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t40", + "source": "ACE2_endothelium,_vascular", + "target": "SARS-CoV-2_infection_phenotype", + "sign": false + }, + { + "id": "t41", + "source": "Fibrin_monomer", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t42", + "source": "CRP", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t43", + "source": "VWF", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t44", + "source": "MASP2", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t45", + "source": "aldosterone_simple_molecule_blood", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t46", + "source": "Hypokalemia_phenotype", + "target": "SARS-CoV-2_infection_phenotype", + "sign": true + }, + { + "id": "t47", + "source": "Fibrinogen:GP6_complex", + "target": "Fibrinogen_complex", + "sign": true + }, + { + "id": "t48", + "source": "Fibrin_monomer", + "target": "Fibrinogen_complex", + "sign": true + }, + { + "id": "t49", + "source": "TAT_complex_complex", + "target": "Antithrombin", + "sign": true + }, + { + "id": "t50", + "source": "Small_peptide", + "target": "Antithrombin", + "sign": false + }, + { + "id": "t51", + "source": "F10a", + "target": "Antithrombin", + "sign": false + }, + { + "id": "t52", + "source": "Thrombin_blood_active", + "target": "Antithrombin", + "sign": false + }, + { + "id": "t53", + "source": "TAT_complex_complex", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t54", + "source": "Thrombin:Thrombomodulin_complex", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t55", + "source": "Small_peptide", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t56", + "source": "F11", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t57", + "source": "F11a", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t58", + "source": "F8a", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t59", + "source": "TAFI", + "target": "Thrombin_blood_active", + "sign": true + }, + { + "id": "t60", + "source": "F5a", + "target": "Thrombin:Thrombomodulin_complex", + "sign": false + }, + { + "id": "t61", + "source": "Fibrin_monomer", + "target": "Thrombin:Thrombomodulin_complex", + "sign": false + }, + { + "id": "t62", + "source": "Thrombin:Thrombomodulin_complex", + "target": "Thrombomodulin", + "sign": true + }, + { + "id": "t63", + "source": "C5b-9_complex_endothelium,_vascular", + "target": "C5b:C6:C7:C8A:C8B:C8G_complex", + "sign": true + }, + { + "id": "t64", + "source": "C5b:C6:C7:C8A:C8B:C8G_complex", + "target": "C5b:C6:C7_complex", + "sign": true + }, + { + "id": "t65", + "source": "C5b:C6:C7:C8A:C8B:C8G_complex", + "target": "C8A:C8B:C8G_complex", + "sign": true + }, + { + "id": "t66", + "source": "C5a", + "target": "C3b:Bb:C3b_complex", + "sign": true + }, + { + "id": "t67", + "source": "C5b", + "target": "C3b:Bb:C3b_complex", + "sign": true + }, + { + "id": "t68", + "source": "C3b:Bb:C3b_complex", + "target": "C3b", + "sign": true + }, + { + "id": "t69", + "source": "C3b:Bb:C3b_complex", + "target": "C3b:Bb_complex", + "sign": true + }, + { + "id": "t70", + "source": "C3a", + "target": "C3b:Bb_complex", + "sign": true + }, + { + "id": "t71", + "source": "C3b", + "target": "C3b:Bb_complex", + "sign": true + }, + { + "id": "t72", + "source": "C5b:C6:C7_complex", + "target": "C5b:C6_complex", + "sign": true + }, + { + "id": "t73", + "source": "C5b:C6:C7_complex", + "target": "C7", + "sign": true + }, + { + "id": "t75", + "source": "Plasminogen", + "target": "C5b-9_complex_endothelium,_vascular", + "sign": true + }, + { + "id": "t76", + "source": "Thrombosis_phenotype_blood", + "target": "C5b-9_complex_endothelium,_vascular", + "sign": true + }, + { + "id": "t77", + "source": "C5b-9_deposition_phenotype", + "target": "C5b-9_complex_endothelium,_vascular", + "sign": true + }, + { + "id": "t78", + "source": "C5b-9_complex_endothelium,_vascular", + "target": "C9", + "sign": true + }, + { + "id": "t79", + "source": "C5b:C6_complex", + "target": "C5b", + "sign": true + }, + { + "id": "t80", + "source": "C5b:C6_complex", + "target": "C6", + "sign": true + }, + { + "id": "t81", + "source": "C5a", + "target": "C2a:C4b_complex", + "sign": true + }, + { + "id": "t82", + "source": "C3a", + "target": "C2a:C4b_complex", + "sign": true + }, + { + "id": "t83", + "source": "C3b", + "target": "C2a:C4b_complex", + "sign": true + }, + { + "id": "t84", + "source": "C5b", + "target": "C2a:C4b_complex", + "sign": true + }, + { + "id": "t85", + "source": "C2a:C4b_complex", + "target": "C4b", + "sign": true + }, + { + "id": "t86", + "source": "C4d", + "target": "C4b", + "sign": true + }, + { + "id": "t87", + "source": "C2a:C4b_complex", + "target": "C2a", + "sign": true + }, + { + "id": "t88", + "source": "SARS-CoV-2_viral_entry_phenotype", + "target": "ACE2:Spike_complex", + "sign": true + }, + { + "id": "t89", + "source": "ACE2:Spike_complex", + "target": "ACE2_blood", + "sign": true + }, + { + "id": "t90", + "source": "ACE2_endothelium,_vascular", + "target": "ACE2_blood", + "sign": true + }, + { + "id": "t91", + "source": "ACE2:Spike_complex", + "target": "S", + "sign": true + }, + { + "id": "t92", + "source": "C5b-9_complex_endothelium,_vascular", + "target": "S", + "sign": true + }, + { + "id": "t93", + "source": "C4d", + "target": "S", + "sign": true + }, + { + "id": "t94", + "source": "SERPINF2:Plasmin_complex", + "target": "Plasmin", + "sign": true + }, + { + "id": "t95", + "source": "D-dimer", + "target": "Plasmin", + "sign": true + }, + { + "id": "t96", + "source": "C5a", + "target": "Plasmin", + "sign": true + }, + { + "id": "t97", + "source": "SERPINF2:Plasmin_complex", + "target": "SERPINF2", + "sign": true + }, + { + "id": "t98", + "source": "platelet_activation_phenotype", + "target": "Fibrinogen:GP6_complex", + "sign": true + }, + { + "id": "t99", + "source": "Fibrinogen:GP6_complex", + "target": "GP6", + "sign": true + }, + { + "id": "t100", + "source": "GP6:alpha2:beta1_complex", + "target": "GP6", + "sign": true + }, + { + "id": "t101", + "source": "platelet_activation_phenotype", + "target": "GP6:alpha2beta1:VWF_complex", + "sign": true + }, + { + "id": "t102", + "source": "GP6:alpha2beta1:VWF_complex", + "target": "GP6:alpha2:beta1_complex", + "sign": true + }, + { + "id": "t103", + "source": "GP6:alpha2beta1:VWF_complex", + "target": "VWF", + "sign": true + }, + { + "id": "t104", + "source": "Thrombosis_phenotype_blood", + "target": "VWF", + "sign": true + }, + { + "id": "t105", + "source": "GP6:alpha2:beta1_complex", + "target": "ITGA2:ITGAB1_complex", + "sign": true + }, + { + "id": "t106", + "source": "F11", + "target": "F12a", + "sign": true + }, + { + "id": "t107", + "source": "F11a", + "target": "F12a", + "sign": true + }, + { + "id": "t108", + "source": "Kallikrein", + "target": "F12a", + "sign": true + }, + { + "id": "t109", + "source": "F12a", + "target": "F12", + "sign": true + }, + { + "id": "t110", + "source": "Small_peptide", + "target": "F12", + "sign": true + }, + { + "id": "t111", + "source": "Small_peptide", + "target": "F10", + "sign": true + }, + { + "id": "t112", + "source": "F10a", + "target": "F10", + "sign": true + }, + { + "id": "t113", + "source": "Small_peptide", + "target": "F8", + "sign": true + }, + { + "id": "t114", + "source": "F8a", + "target": "F8", + "sign": true + }, + { + "id": "t115", + "source": "Small_peptide", + "target": "PROC", + "sign": false + }, + { + "id": "t116", + "source": "F8a", + "target": "PROC", + "sign": false + }, + { + "id": "t117", + "source": "F5a", + "target": "PROC", + "sign": false + }, + { + "id": "t118", + "source": "PLAT_blood_active", + "target": "PROC", + "sign": false + }, + { + "id": "t119", + "source": "Small_peptide", + "target": "Bradykinin", + "sign": true + }, + { + "id": "t120", + "source": "PLAT_blood_active", + "target": "Bradykinin", + "sign": true + }, + { + "id": "t121", + "source": "Bradykinin(1-5)", + "target": "Bradykinin", + "sign": true + }, + { + "id": "t122", + "source": "Small_peptide", + "target": "ACE", + "sign": true + }, + { + "id": "t123", + "source": "angiotensin_II_simple_molecule", + "target": "ACE", + "sign": true + }, + { + "id": "t124", + "source": "Bradykinin(1-5)", + "target": "ACE", + "sign": true + }, + { + "id": "t125", + "source": "F9a", + "target": "F11a", + "sign": true + }, + { + "id": "t126", + "source": "Plasmin", + "target": "F11a", + "sign": true + }, + { + "id": "t127", + "source": "F9a", + "target": "F9", + "sign": true + }, + { + "id": "t128", + "source": "Thrombin_blood_active", + "target": "Thrombin_blood", + "sign": true + }, + { + "id": "t129", + "source": "Fibrin_monomer", + "target": "Thrombin_blood", + "sign": true + }, + { + "id": "t130", + "source": "Thrombin_blood_active", + "target": "Heparin_simple_molecule", + "sign": true + }, + { + "id": "t131", + "source": "PLAT_blood_active", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t132", + "source": "SERPINE1", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t133", + "source": "Thrombosis_phenotype_blood", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t134", + "source": "angiotensin_I-7_simple_molecule", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t135", + "source": "AGTR1_platelet", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t136", + "source": "aldosterone_simple_molecule_blood", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t137", + "source": "AGTR1_blood", + "target": "angiotensin_II_simple_molecule", + "sign": true + }, + { + "id": "t138", + "source": "angiotensin_II_simple_molecule", + "target": "angiotensin_I_simple_molecule", + "sign": true + }, + { + "id": "t139", + "source": "angiotensin_I_simple_molecule", + "target": "AGT", + "sign": true + }, + { + "id": "t140", + "source": "angiotensin_I_simple_molecule", + "target": "REN", + "sign": true + }, + { + "id": "t141", + "source": "REN", + "target": "Prorenin", + "sign": true + }, + { + "id": "t142", + "source": "REN", + "target": "Kallikrein", + "sign": true + }, + { + "id": "t143", + "source": "ACE", + "target": "aldosterone_simple_molecule_blood", + "sign": true + }, + { + "id": "t144", + "source": "SERPINE1", + "target": "aldosterone_simple_molecule_blood", + "sign": true + }, + { + "id": "t145", + "source": "aldosterone_simple_molecule_endothelium,_vascular", + "target": "aldosterone_simple_molecule_blood", + "sign": true + }, + { + "id": "t146", + "source": "Hypokalemia_phenotype", + "target": "aldosterone_simple_molecule_blood", + "sign": true + }, + { + "id": "t147", + "source": "F5a", + "target": "F5", + "sign": true + }, + { + "id": "t148", + "source": "Thrombin_blood", + "target": "Prothrombin", + "sign": true + }, + { + "id": "t149", + "source": "D-dimer", + "target": "Fibrin_polymer", + "sign": true + }, + { + "id": "t150", + "source": "D-dimer", + "target": "TAFI", + "sign": true + }, + { + "id": "t151", + "source": "Plasmin", + "target": "Plasminogen", + "sign": true + }, + { + "id": "t152", + "source": "Plasmin", + "target": "PLAT_blood_active", + "sign": true + }, + { + "id": "t153", + "source": "Plasmin", + "target": "PLAU", + "sign": true + }, + { + "id": "t154", + "source": "PLAT_blood_active", + "target": "angiotensin_I-7_simple_molecule", + "sign": false + }, + { + "id": "t155", + "source": "SERPINE1", + "target": "angiotensin_I-7_simple_molecule", + "sign": false + }, + { + "id": "t156", + "source": "MAS1", + "target": "angiotensin_I-7_simple_molecule", + "sign": true + }, + { + "id": "t157", + "source": "SERPINE1", + "target": "IL6", + "sign": true + }, + { + "id": "t158", + "source": "Thrombosis_phenotype_blood", + "target": "IL6", + "sign": true + }, + { + "id": "t159", + "source": "SERPINE1", + "target": "AGTR1_blood", + "sign": true + }, + { + "id": "t160", + "source": "aldosterone_simple_molecule_blood", + "target": "AGTR1_blood", + "sign": true + }, + { + "id": "t161", + "source": "NR3C2", + "target": "AGTR1_blood", + "sign": true + }, + { + "id": "t162", + "source": "Thrombosis_phenotype_human_host", + "target": "AGTR1_blood", + "sign": true + }, + { + "id": "t163", + "source": "Thrombosis_phenotype_blood", + "target": "TNF", + "sign": true + }, + { + "id": "t164", + "source": "TNF", + "target": "cytokine_storm_phenotype", + "sign": true + }, + { + "id": "t165", + "source": "IL6", + "target": "cytokine_storm_phenotype", + "sign": true + }, + { + "id": "t166", + "source": "IL1B", + "target": "cytokine_storm_phenotype", + "sign": true + }, + { + "id": "t167", + "source": "IL8", + "target": "cytokine_storm_phenotype", + "sign": true + }, + { + "id": "t168", + "source": "IL2RA", + "target": "cytokine_storm_phenotype", + "sign": true + }, + { + "id": "t169", + "source": "Thrombosis_phenotype_blood", + "target": "IL1B", + "sign": true + }, + { + "id": "t170", + "source": "C5a", + "target": "C5", + "sign": true + }, + { + "id": "t171", + "source": "C5b", + "target": "C5", + "sign": true + }, + { + "id": "t172", + "source": "Thrombosis_phenotype_blood", + "target": "IL8", + "sign": true + }, + { + "id": "t173", + "source": "Thrombosis_phenotype_blood", + "target": "IL2RA", + "sign": true + }, + { + "id": "t174", + "source": "Thrombosis_phenotype_blood", + "target": "CRP", + "sign": true + }, + { + "id": "t175", + "source": "Thrombosis_phenotype_blood", + "target": "C4d", + "sign": true + }, + { + "id": "t176", + "source": "C4d_deposition_phenotype", + "target": "C4d", + "sign": true + }, + { + "id": "t177", + "source": "C3a", + "target": "C3", + "sign": true + }, + { + "id": "t178", + "source": "C3b", + "target": "C3", + "sign": true + }, + { + "id": "t179", + "source": "C2a", + "target": "MASP1", + "sign": true + }, + { + "id": "t180", + "source": "C2b", + "target": "MASP1", + "sign": true + }, + { + "id": "t181", + "source": "MASP1", + "target": "MBL2", + "sign": true + }, + { + "id": "t182", + "source": "C4a", + "target": "C4", + "sign": true + }, + { + "id": "t183", + "source": "C4b", + "target": "C4", + "sign": true + }, + { + "id": "t184", + "source": "C4a", + "target": "MASP2", + "sign": true + }, + { + "id": "t185", + "source": "C4b", + "target": "MASP2", + "sign": true + }, + { + "id": "t186", + "source": "MASP2_deposition_phenotype", + "target": "MASP2", + "sign": true + }, + { + "id": "t187", + "source": "C2a", + "target": "C2", + "sign": true + }, + { + "id": "t188", + "source": "C2b", + "target": "C2", + "sign": true + }, + { + "id": "t189", + "source": "C4d", + "target": "CFI", + "sign": true + }, + { + "id": "t190", + "source": "septal_capillary_necrosis_phenotype", + "target": "C4d_deposition_phenotype", + "sign": true + }, + { + "id": "t191", + "source": "apoptosis_phenotype", + "target": "C5b-9_deposition_phenotype", + "sign": true + }, + { + "id": "t192", + "source": "platelet_aggregation_phenotype", + "target": "C5b-9_deposition_phenotype", + "sign": true + }, + { + "id": "t193", + "source": "angiotensin_I-7_simple_molecule", + "target": "ACE2_endothelium,_vascular", + "sign": true + }, + { + "id": "t194", + "source": "Fibrin_polymer", + "target": "Fibrin_monomer", + "sign": true + }, + { + "id": "t195", + "source": "Fibrin_polymer", + "target": "F13a", + "sign": true + }, + { + "id": "t196", + "source": "thrombus_formation_phenotype", + "target": "platelet_activation_phenotype", + "sign": true + }, + { + "id": "t197", + "source": "thrombus_formation_phenotype", + "target": "MAS1", + "sign": false + }, + { + "id": "t198", + "source": "thrombus_formation_phenotype", + "target": "AGTR1_platelet", + "sign": true + }, + { + "id": "t199", + "source": "aldosterone_simple_molecule_blood", + "target": "K+_ion", + "sign": true + }, + { + "id": "t200", + "source": "aldosterone_simple_molecule_blood", + "target": "ACTH_simple_molecule", + "sign": true + }, + { + "id": "t201", + "source": "NR3C2", + "target": "aldosterone_simple_molecule_endothelium,_vascular", + "sign": true + }, + { + "id": "t202", + "source": "vascular_remodeling_phenotype", + "target": "aldosterone_simple_molecule_endothelium,_vascular", + "sign": true + }, + { + "id": "t203", + "source": "vascular_inflammation_phenotype", + "target": "aldosterone_simple_molecule_endothelium,_vascular", + "sign": true + }, + { + "id": "t204", + "source": "Thrombosis_phenotype_human_host", + "target": "NR3C2", + "sign": true + }, + { + "id": "t205", + "source": "K+_ion", + "target": "Hypokalemia_phenotype", + "sign": false + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/ER_Stress.json b/scripts/covid19_diseasemaps/regnet_amr/ER_Stress.json new file mode 100644 index 000000000..ee6c72ff8 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/ER_Stress.json @@ -0,0 +1,3058 @@ +{ + "header": { + "name": "ER_Stress", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on ER_Stress", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "EIF2-P:GDP_complex", + "name": "EIF2-P:GDP_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATF4_rna", + "name": "ATF4_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2S1_phosphorylated", + "name": "EIF2S1_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2S1", + "name": "EIF2S1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2S2", + "name": "EIF2S2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2:GDP_complex", + "name": "EIF2:GDP_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2S3:GDP_complex", + "name": "EIF2S3:GDP_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRAF2:ERN1_complex", + "name": "TRAF2:ERN1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRAF2", + "name": "TRAF2", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "UPR_phenotype", + "name": "UPR_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "XBP1_rna", + "name": "XBP1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAP3K5_phosphorylated", + "name": "MAP3K5_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERN1:Unfolded_space_protein_complex", + "name": "ERN1:Unfolded_space_protein_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAK1:ERN1_complex", + "name": "BAK1:ERN1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAX:ERN1_complex", + "name": "BAX:ERN1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2", + "name": "BCL2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2L1", + "name": "BCL2L1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Persistant_space_ER_space_Stress_phenotype_endoplasmic_reticulum", + "name": "Persistant_space_ER_space_Stress_phenotype_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "name": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2AK3:EIF2AK3_complex", + "name": "EIF2AK3:EIF2AK3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAX_endoplasmic_reticulum", + "name": "BAX_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAK1", + "name": "BAK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SIGMAR1:ITPR3_complex", + "name": "SIGMAR1:ITPR3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+_ion_mitochondrion", + "name": "Ca2+_ion_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "name": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ER_space_stress_phenotype", + "name": "ER_space_stress_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Apoptosis_phenotype_endoplasmic_reticulum", + "name": "Apoptosis_phenotype_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ITPR3", + "name": "ITPR3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "autophagy_phenotype", + "name": "autophagy_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HSPA5_endoplasmic_reticulum", + "name": "HSPA5_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "unfolded_space_protein_space_response_space_(UPR)_phenotype", + "name": "unfolded_space_protein_space_response_space_(UPR)_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN2_endoplasmic_reticulum", + "name": "MFN2_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+space_ER_space_depletion_phenotype", + "name": "Ca2+space_ER_space_depletion_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2:GDP:Met-tRNA_complex", + "name": "EIF2:GDP:Met-tRNA_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ternary_space_Complex_complex", + "name": "Ternary_space_Complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GDP_simple_molecule", + "name": "GDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Met-tRNA_rna", + "name": "Met-tRNA_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GTP_simple_molecule", + "name": "GTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Translation_space_initiation_phenotype", + "name": "Translation_space_initiation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Apoptosis_phenotype_cell", + "name": "Apoptosis_phenotype_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP8:CASP8-ubq:FADD_complex", + "name": "CASP8:CASP8-ubq:FADD_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SQSTM1_space_", + "name": "SQSTM1_space_", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAP1LC3A", + "name": "MAP1LC3A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATG5", + "name": "ATG5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIM13", + "name": "TRIM13", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERN1_endoplasmic_reticulum", + "name": "ERN1_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Unfolded_space_protein", + "name": "Unfolded_space_protein", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATF6_endoplasmic_reticulum", + "name": "ATF6_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "name": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SIGMAR1:HSPA5_complex", + "name": "SIGMAR1:HSPA5_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SIGMAR1_endoplasmic_reticulum", + "name": "SIGMAR1_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype", + "name": "endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "VAPB:RMDN3_complex", + "name": "VAPB:RMDN3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "name": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "VAPB", + "name": "VAPB", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+space_mitochondrial_space_concentration_phenotype", + "name": "Ca2+space_mitochondrial_space_concentration_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+space_cytosolic_space_concentration_phenotype", + "name": "Ca2+space_cytosolic_space_concentration_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RMDN3", + "name": "RMDN3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2B_complex", + "name": "EIF2B_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PACS2-ADAM17_space_interaction_complex", + "name": "PACS2-ADAM17_space_interaction_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADAM17_cell", + "name": "ADAM17_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PACS2_early_space_endosome", + "name": "PACS2_early_space_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADAM17_early_space_endosome", + "name": "ADAM17_early_space_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FIS1:BCAP31_complex", + "name": "FIS1:BCAP31_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCAP31", + "name": "BCAP31", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "p20", + "name": "p20", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FIS1", + "name": "FIS1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mitochondrial_space_outer_space_membrane_space_depolarization_phenotype", + "name": "mitochondrial_space_outer_space_membrane_space_depolarization_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN2:MFN2_complex", + "name": "MFN2:MFN2_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN1:MFN2_complex", + "name": "MFN1:MFN2_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "endoplasmic_space_reticulum_space_organization_phenotype", + "name": "endoplasmic_space_reticulum_space_organization_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN2_mitochondrion", + "name": "MFN2_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERN1:BBC3_complex", + "name": "ERN1:BBC3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERN1:BCL2L11_complex", + "name": "ERN1:BCL2L11_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BBC3", + "name": "BBC3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Persistant_space_ER_space_Stress_phenotype_cell", + "name": "Persistant_space_ER_space_Stress_phenotype_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DDIT3_rna", + "name": "DDIT3_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN1", + "name": "MFN1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MCU:MICU1:MICU2:SMDT1_complex", + "name": "MCU:MICU1:MICU2:SMDT1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mitochondrial_space_calcium_space_uniporter_space_complex_complex", + "name": "Mitochondrial_space_calcium_space_uniporter_space_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MCU", + "name": "MCU", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SMDT1", + "name": "SMDT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MCU2", + "name": "MCU2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MCU1", + "name": "MCU1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2L11_endoplasmic_reticulum", + "name": "BCL2L11_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CAPN1:Ca2+_complex", + "name": "CAPN1:Ca2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cleaved~CASP4", + "name": "cleaved~CASP4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CAPN1", + "name": "CAPN1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+_ion_cell", + "name": "Ca2+_ion_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", + "name": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "name": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2AK3", + "name": "EIF2AK3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+_ion_mitochondrial_matrix", + "name": "Ca2+_ion_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mitochondrial_space_calcium_space_ion_space_transmembrane_space_transport_phenotype", + "name": "mitochondrial_space_calcium_space_ion_space_transmembrane_space_transport_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2", + "name": "ACE2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2:Spike_complex", + "name": "ACE2:Spike_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HSPA5_rna", + "name": "HSPA5_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2,_space_soluble", + "name": "ACE2,_space_soluble", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2,_space_membrane-bound", + "name": "ACE2,_space_membrane-bound", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "pulmonary_fibrosis_phenotype", + "name": "pulmonary_fibrosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "viral_RNA_genome_replication_phenotype", + "name": "viral_RNA_genome_replication_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S", + "name": "S", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HSPA5-Spike_interaction_complex", + "name": "HSPA5-Spike_interaction_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2-SARS-CoV_interaction_complex", + "name": "ACE2-SARS-CoV_interaction_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "viral_entry_into_host_cell_phenotype", + "name": "viral_entry_into_host_cell_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HSPA5_default_compartment", + "name": "HSPA5_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPP1R15A_rna", + "name": "PPP1R15A_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPP1R15A", + "name": "PPP1R15A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPP1R15A_gene", + "name": "PPP1R15A_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATF4", + "name": "ATF4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DDIT3", + "name": "DDIT3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DDIT3_phosphorylated", + "name": "DDIT3_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIB3_rna", + "name": "TRIB3_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP-1_phosphorylated_phosphorylated", + "name": "AP-1_phosphorylated_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERO1A_rna", + "name": "ERO1A_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "release_space_of_space_ER_space_Ca2+_phenotype", + "name": "release_space_of_space_ER_space_Ca2+_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAX_phosphorylated", + "name": "BAX_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATF6_Golgi_apparatus", + "name": "ATF6_Golgi_apparatus", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "ATF6_nucleus", + "name": "ATF6_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ER_space_Stress_phenotype", + "name": "ER_space_Stress_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CDK5", + "name": "CDK5", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "protein_space_ubiquitination_space_and_space_destruction_phenotype", + "name": "protein_space_ubiquitination_space_and_space_destruction_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MBTPS2", + "name": "MBTPS2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MBTPS1", + "name": "MBTPS1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2_rna", + "name": "BCL2_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK14_phosphorylated", + "name": "MAPK14_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATF6:HSPA5_complex", + "name": "ATF6:HSPA5_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ITPR", + "name": "ITPR", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "TMBIM6", + "name": "TMBIM6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERO1A_endoplasmic_reticulum", + "name": "ERO1A_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "hyperoxidation_phenotype", + "name": "hyperoxidation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HSPA5_gene", + "name": "HSPA5_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "XBP1", + "name": "XBP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERAD_phenotype", + "name": "ERAD_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mitochondrial_space_fission_phenotype", + "name": "mitochondrial_space_fission_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mitochondria_space_fragmentation_phenotype", + "name": "mitochondria_space_fragmentation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PACS2_endoplasmic_reticulum", + "name": "PACS2_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2AK2", + "name": "EIF2AK2", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "DNAJC3", + "name": "DNAJC3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DNAJC3_rna", + "name": "DNAJC3_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DDIT3_gene", + "name": "DDIT3_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HYOU1_rna", + "name": "HYOU1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATF4_gene", + "name": "ATF4_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2L11_cell", + "name": "BCL2L11_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2L11_phosphorylated", + "name": "BCL2L11_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPP2CA", + "name": "PPP2CA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIB3", + "name": "TRIB3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIB3_gene", + "name": "TRIB3_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+_ion_endoplasmic_reticulum", + "name": "Ca2+_ion_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ITPR3:HSPA9:VDAC1_complex", + "name": "ITPR3:HSPA9:VDAC1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERO1A_cell", + "name": "ERO1A_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF2AK1", + "name": "EIF2AK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cleaved~CASP9", + "name": "cleaved~CASP9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP9", + "name": "CASP9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cleaved~CASP3", + "name": "cleaved~CASP3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "XBP1_gene", + "name": "XBP1_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2_gene", + "name": "BCL2_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAP3K4_phosphorylated", + "name": "MAP3K4_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK14", + "name": "MAPK14", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK8_phosphorylated", + "name": "MAPK8_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Cell_space_survival_phenotype", + "name": "Cell_space_survival_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "presence_space_of_space_dsRNA_phenotype", + "name": "presence_space_of_space_dsRNA_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAX_cell", + "name": "BAX_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BID_phosphorylated", + "name": "BID_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK8", + "name": "MAPK8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BID", + "name": "BID", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP4", + "name": "CASP4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HYOU1", + "name": "HYOU1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP3", + "name": "CASP3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GCN2:ATP_complex", + "name": "GCN2:ATP_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP-1", + "name": "AP-1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RYR1", + "name": "RYR1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAP3K5", + "name": "MAP3K5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DNAJC3_gene", + "name": "DNAJC3_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN2_rna", + "name": "MFN2_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MFN2_gene", + "name": "MFN2_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAP3K4", + "name": "MAP3K4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HYOU1_gene", + "name": "HYOU1_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ERO1A_gene", + "name": "ERO1A_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2_rna", + "name": "ACE2_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SARS-CoV_infection_phenotype", + "name": "SARS-CoV_infection_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "ATF4_rna", + "target": "EIF2-P:GDP_complex", + "sign": true + }, + { + "id": "t2", + "source": "EIF2-P:GDP_complex", + "target": "EIF2S1_phosphorylated", + "sign": true + }, + { + "id": "t3", + "source": "EIF2S1", + "target": "EIF2S1_phosphorylated", + "sign": true + }, + { + "id": "t4", + "source": "EIF2-P:GDP_complex", + "target": "EIF2S2", + "sign": true + }, + { + "id": "t5", + "source": "EIF2:GDP_complex", + "target": "EIF2S2", + "sign": true + }, + { + "id": "t6", + "source": "EIF2-P:GDP_complex", + "target": "EIF2S3:GDP_complex", + "sign": true + }, + { + "id": "t7", + "source": "EIF2:GDP_complex", + "target": "EIF2S3:GDP_complex", + "sign": true + }, + { + "id": "t8", + "source": "TRAF2", + "target": "TRAF2:ERN1_complex", + "sign": true + }, + { + "id": "t9", + "source": "UPR_phenotype", + "target": "TRAF2:ERN1_complex", + "sign": true + }, + { + "id": "t10", + "source": "XBP1_rna", + "target": "TRAF2:ERN1_complex", + "sign": true + }, + { + "id": "t11", + "source": "MAP3K5_phosphorylated", + "target": "TRAF2:ERN1_complex", + "sign": true + }, + { + "id": "t12", + "source": "TRAF2:ERN1_complex", + "target": "ERN1:Unfolded_space_protein_complex", + "sign": true + }, + { + "id": "t13", + "source": "TRAF2:ERN1_complex", + "target": "TRAF2", + "sign": true + }, + { + "id": "t15", + "source": "MAP3K5_phosphorylated", + "target": "TRAF2", + "sign": true + }, + { + "id": "t16", + "source": "TRAF2:ERN1_complex", + "target": "BAK1:ERN1_complex", + "sign": true + }, + { + "id": "t17", + "source": "TRAF2:ERN1_complex", + "target": "BAX:ERN1_complex", + "sign": true + }, + { + "id": "t18", + "source": "TRAF2:ERN1_complex", + "target": "BCL2", + "sign": false + }, + { + "id": "t19", + "source": "TRAF2:ERN1_complex", + "target": "BCL2L1", + "sign": false + }, + { + "id": "t20", + "source": "TRAF2:ERN1_complex", + "target": "Persistant_space_ER_space_Stress_phenotype_endoplasmic_reticulum", + "sign": false + }, + { + "id": "t21", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "target": "Persistant_space_ER_space_Stress_phenotype_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t22", + "source": "EIF2AK3:EIF2AK3_complex", + "target": "Persistant_space_ER_space_Stress_phenotype_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t23", + "source": "TRAF2:ERN1_complex", + "target": "BAX_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t24", + "source": "TRAF2:ERN1_complex", + "target": "BAK1", + "sign": true + }, + { + "id": "t25", + "source": "Ca2+_ion_mitochondrion", + "target": "SIGMAR1:ITPR3_complex", + "sign": true + }, + { + "id": "t26", + "source": "SIGMAR1:ITPR3_complex", + "target": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "sign": true + }, + { + "id": "t27", + "source": "ER_space_stress_phenotype", + "target": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "sign": false + }, + { + "id": "t28", + "source": "Apoptosis_phenotype_endoplasmic_reticulum", + "target": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "sign": false + }, + { + "id": "t29", + "source": "SIGMAR1:ITPR3_complex", + "target": "ITPR3", + "sign": true + }, + { + "id": "t30", + "source": "autophagy_phenotype", + "target": "ITPR3", + "sign": false + }, + { + "id": "t31", + "source": "SIGMAR1:ITPR3_complex", + "target": "ER_space_stress_phenotype", + "sign": true + }, + { + "id": "t32", + "source": "HSPA5_endoplasmic_reticulum", + "target": "ER_space_stress_phenotype", + "sign": true + }, + { + "id": "t33", + "source": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "target": "ER_space_stress_phenotype", + "sign": true + }, + { + "id": "t34", + "source": "unfolded_space_protein_space_response_space_(UPR)_phenotype", + "target": "ER_space_stress_phenotype", + "sign": true + }, + { + "id": "t35", + "source": "Apoptosis_phenotype_endoplasmic_reticulum", + "target": "ER_space_stress_phenotype", + "sign": true + }, + { + "id": "t36", + "source": "MFN2_endoplasmic_reticulum", + "target": "ER_space_stress_phenotype", + "sign": true + }, + { + "id": "t37", + "source": "SIGMAR1:ITPR3_complex", + "target": "Ca2+space_ER_space_depletion_phenotype", + "sign": true + }, + { + "id": "t38", + "source": "HSPA5_endoplasmic_reticulum", + "target": "Ca2+space_ER_space_depletion_phenotype", + "sign": true + }, + { + "id": "t39", + "source": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "target": "Ca2+space_ER_space_depletion_phenotype", + "sign": true + }, + { + "id": "t40", + "source": "Ternary_space_Complex_complex", + "target": "EIF2:GDP:Met-tRNA_complex", + "sign": true + }, + { + "id": "t41", + "source": "GDP_simple_molecule", + "target": "EIF2:GDP:Met-tRNA_complex", + "sign": true + }, + { + "id": "t42", + "source": "EIF2:GDP:Met-tRNA_complex", + "target": "Met-tRNA_rna", + "sign": true + }, + { + "id": "t43", + "source": "EIF2:GDP:Met-tRNA_complex", + "target": "EIF2:GDP_complex", + "sign": true + }, + { + "id": "t44", + "source": "EIF2:GDP:Met-tRNA_complex", + "target": "Ternary_space_Complex_complex", + "sign": true + }, + { + "id": "t45", + "source": "GTP_simple_molecule", + "target": "Ternary_space_Complex_complex", + "sign": true + }, + { + "id": "t46", + "source": "Translation_space_initiation_phenotype", + "target": "Ternary_space_Complex_complex", + "sign": true + }, + { + "id": "t47", + "source": "EIF2:GDP:Met-tRNA_complex", + "target": "GDP_simple_molecule", + "sign": true + }, + { + "id": "t48", + "source": "GTP_simple_molecule", + "target": "GDP_simple_molecule", + "sign": true + }, + { + "id": "t49", + "source": "Apoptosis_phenotype_cell", + "target": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "sign": true + }, + { + "id": "t50", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "target": "CASP8:CASP8-ubq:FADD_complex", + "sign": true + }, + { + "id": "t51", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "target": "SQSTM1_space_", + "sign": true + }, + { + "id": "t52", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "target": "MAP1LC3A", + "sign": true + }, + { + "id": "t53", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "target": "ATG5", + "sign": true + }, + { + "id": "t54", + "source": "CASP8:FADD:MAP1LC3A:SQSTM1:ATG5_complex", + "target": "TRIM13", + "sign": true + }, + { + "id": "t55", + "source": "ERN1:Unfolded_space_protein_complex", + "target": "ERN1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t56", + "source": "ERN1:Unfolded_space_protein_complex", + "target": "Unfolded_space_protein", + "sign": true + }, + { + "id": "t57", + "source": "EIF2AK3:EIF2AK3_complex", + "target": "Unfolded_space_protein", + "sign": true + }, + { + "id": "t58", + "source": "HSPA5_endoplasmic_reticulum", + "target": "Unfolded_space_protein", + "sign": true + }, + { + "id": "t59", + "source": "ATF6_endoplasmic_reticulum", + "target": "Unfolded_space_protein", + "sign": true + }, + { + "id": "t60", + "source": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "target": "Unfolded_space_protein", + "sign": true + }, + { + "id": "t61", + "source": "HSPA5_endoplasmic_reticulum", + "target": "SIGMAR1:HSPA5_complex", + "sign": true + }, + { + "id": "t62", + "source": "SIGMAR1_mitochondria-associated_endoplasmic_reticulum_membrane", + "target": "SIGMAR1:HSPA5_complex", + "sign": true + }, + { + "id": "t63", + "source": "SIGMAR1:HSPA5_complex", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t64", + "source": "SIGMAR1:HSPA5_complex", + "target": "HSPA5_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t65", + "source": "endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype", + "target": "HSPA5_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t66", + "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "target": "VAPB:RMDN3_complex", + "sign": true + }, + { + "id": "t67", + "source": "VAPB:RMDN3_complex", + "target": "VAPB", + "sign": true + }, + { + "id": "t68", + "source": "Ca2+space_mitochondrial_space_concentration_phenotype", + "target": "VAPB", + "sign": true + }, + { + "id": "t69", + "source": "autophagy_phenotype", + "target": "VAPB", + "sign": false + }, + { + "id": "t70", + "source": "Ca2+space_cytosolic_space_concentration_phenotype", + "target": "VAPB", + "sign": false + }, + { + "id": "t71", + "source": "VAPB:RMDN3_complex", + "target": "RMDN3", + "sign": true + }, + { + "id": "t72", + "source": "Ca2+space_mitochondrial_space_concentration_phenotype", + "target": "RMDN3", + "sign": true + }, + { + "id": "t73", + "source": "autophagy_phenotype", + "target": "RMDN3", + "sign": false + }, + { + "id": "t74", + "source": "Ca2+space_cytosolic_space_concentration_phenotype", + "target": "RMDN3", + "sign": false + }, + { + "id": "t75", + "source": "Ternary_space_Complex_complex", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t76", + "source": "GDP_simple_molecule", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t77", + "source": "Ternary_space_Complex_complex", + "target": "EIF2B_complex", + "sign": true + }, + { + "id": "t78", + "source": "GDP_simple_molecule", + "target": "EIF2B_complex", + "sign": true + }, + { + "id": "t79", + "source": "ADAM17_cell", + "target": "PACS2-ADAM17_space_interaction_complex", + "sign": true + }, + { + "id": "t80", + "source": "PACS2-ADAM17_space_interaction_complex", + "target": "PACS2_early_space_endosome", + "sign": true + }, + { + "id": "t81", + "source": "PACS2-ADAM17_space_interaction_complex", + "target": "ADAM17_early_space_endosome", + "sign": true + }, + { + "id": "t82", + "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "target": "FIS1:BCAP31_complex", + "sign": true + }, + { + "id": "t83", + "source": "FIS1:BCAP31_complex", + "target": "BCAP31", + "sign": true + }, + { + "id": "t84", + "source": "p20", + "target": "BCAP31", + "sign": true + }, + { + "id": "t85", + "source": "FIS1:BCAP31_complex", + "target": "FIS1", + "sign": true + }, + { + "id": "t86", + "source": "Ca2+space_mitochondrial_space_concentration_phenotype", + "target": "FIS1", + "sign": true + }, + { + "id": "t87", + "source": "mitochondrial_space_outer_space_membrane_space_depolarization_phenotype", + "target": "FIS1", + "sign": true + }, + { + "id": "t88", + "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "target": "MFN2:MFN2_complex", + "sign": true + }, + { + "id": "t89", + "source": "MFN2:MFN2_complex", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t90", + "source": "MFN1:MFN2_complex", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t91", + "source": "endoplasmic_space_reticulum_space_organization_phenotype", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t92", + "source": "unfolded_space_protein_space_response_space_(UPR)_phenotype", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t93", + "source": "ER_space_stress_phenotype", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t94", + "source": "Apoptosis_phenotype_endoplasmic_reticulum", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t95", + "source": "endoplasmic_space_reticulum_space_calcium_space_ion_space_homeostasis_phenotype", + "target": "MFN2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t96", + "source": "MFN2:MFN2_complex", + "target": "MFN2_mitochondrion", + "sign": true + }, + { + "id": "t97", + "source": "XBP1_rna", + "target": "ERN1:BBC3_complex", + "sign": true + }, + { + "id": "t98", + "source": "ERN1:BBC3_complex", + "target": "ERN1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t99", + "source": "ERN1:BCL2L11_complex", + "target": "ERN1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t100", + "source": "ERN1:BBC3_complex", + "target": "BBC3", + "sign": true + }, + { + "id": "t101", + "source": "ERN1:BBC3_complex", + "target": "Persistant_space_ER_space_Stress_phenotype_cell", + "sign": false + }, + { + "id": "t102", + "source": "ERN1:BCL2L11_complex", + "target": "Persistant_space_ER_space_Stress_phenotype_cell", + "sign": false + }, + { + "id": "t103", + "source": "DDIT3_rna", + "target": "Persistant_space_ER_space_Stress_phenotype_cell", + "sign": true + }, + { + "id": "t104", + "source": "EIF2:GDP_complex", + "target": "EIF2S1", + "sign": true + }, + { + "id": "t105", + "source": "EIF2S1_phosphorylated", + "target": "EIF2S1", + "sign": true + }, + { + "id": "t106", + "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "target": "MFN1:MFN2_complex", + "sign": true + }, + { + "id": "t107", + "source": "MFN1:MFN2_complex", + "target": "MFN1", + "sign": true + }, + { + "id": "t108", + "source": "Mitochondrial_space_calcium_space_uniporter_space_complex_complex", + "target": "MCU:MICU1:MICU2:SMDT1_complex", + "sign": true + }, + { + "id": "t109", + "source": "MCU:MICU1:MICU2:SMDT1_complex", + "target": "MCU", + "sign": true + }, + { + "id": "t110", + "source": "MCU:MICU1:MICU2:SMDT1_complex", + "target": "SMDT1", + "sign": true + }, + { + "id": "t111", + "source": "MCU:MICU1:MICU2:SMDT1_complex", + "target": "MCU2", + "sign": true + }, + { + "id": "t112", + "source": "MCU:MICU1:MICU2:SMDT1_complex", + "target": "MCU1", + "sign": true + }, + { + "id": "t113", + "source": "XBP1_rna", + "target": "ERN1:BCL2L11_complex", + "sign": true + }, + { + "id": "t114", + "source": "ERN1:BCL2L11_complex", + "target": "BCL2L11_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t115", + "source": "cleaved~CASP4", + "target": "CAPN1:Ca2+_complex", + "sign": true + }, + { + "id": "t116", + "source": "CAPN1:Ca2+_complex", + "target": "CAPN1", + "sign": true + }, + { + "id": "t117", + "source": "CAPN1:Ca2+_complex", + "target": "Ca2+_ion_cell", + "sign": true + }, + { + "id": "t118", + "source": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", + "target": "Ca2+_ion_cell", + "sign": true + }, + { + "id": "t119", + "source": "CAPN1:Ca2+_complex", + "target": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", + "sign": true + }, + { + "id": "t120", + "source": "UPR_phenotype", + "target": "EIF2AK3:EIF2AK3_complex", + "sign": true + }, + { + "id": "t121", + "source": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "target": "EIF2AK3:EIF2AK3_complex", + "sign": true + }, + { + "id": "t122", + "source": "EIF2S1_phosphorylated", + "target": "EIF2AK3:EIF2AK3_complex", + "sign": true + }, + { + "id": "t123", + "source": "EIF2AK3:EIF2AK3_complex", + "target": "EIF2AK3", + "sign": true + }, + { + "id": "t124", + "source": "Ca2+_ion_mitochondrial_matrix", + "target": "Mitochondrial_space_calcium_space_uniporter_space_complex_complex", + "sign": true + }, + { + "id": "t125", + "source": "mitochondrial_space_calcium_space_ion_space_transmembrane_space_transport_phenotype", + "target": "Mitochondrial_space_calcium_space_uniporter_space_complex_complex", + "sign": true + }, + { + "id": "t126", + "source": "ACE2:Spike_complex", + "target": "ACE2", + "sign": true + }, + { + "id": "t127", + "source": "HSPA5_endoplasmic_reticulum", + "target": "ACE2", + "sign": false + }, + { + "id": "t128", + "source": "HSPA5_rna", + "target": "ACE2", + "sign": false + }, + { + "id": "t129", + "source": "ER_space_stress_phenotype", + "target": "ACE2", + "sign": false + }, + { + "id": "t130", + "source": "ACE2,_space_soluble", + "target": "ACE2", + "sign": true + }, + { + "id": "t131", + "source": "ACE2,_space_membrane-bound", + "target": "ACE2", + "sign": true + }, + { + "id": "t132", + "source": "pulmonary_fibrosis_phenotype", + "target": "ACE2", + "sign": false + }, + { + "id": "t133", + "source": "viral_RNA_genome_replication_phenotype", + "target": "ACE2", + "sign": true + }, + { + "id": "t134", + "source": "ACE2:Spike_complex", + "target": "S", + "sign": true + }, + { + "id": "t135", + "source": "HSPA5-Spike_interaction_complex", + "target": "S", + "sign": true + }, + { + "id": "t136", + "source": "ACE2-SARS-CoV_interaction_complex", + "target": "S", + "sign": true + }, + { + "id": "t137", + "source": "HSPA5_rna", + "target": "S", + "sign": true + }, + { + "id": "t138", + "source": "viral_entry_into_host_cell_phenotype", + "target": "HSPA5-Spike_interaction_complex", + "sign": true + }, + { + "id": "t139", + "source": "HSPA5-Spike_interaction_complex", + "target": "HSPA5_default_compartment", + "sign": true + }, + { + "id": "t140", + "source": "viral_entry_into_host_cell_phenotype", + "target": "ACE2-SARS-CoV_interaction_complex", + "sign": true + }, + { + "id": "t141", + "source": "ACE2-SARS-CoV_interaction_complex", + "target": "ACE2,_space_membrane-bound", + "sign": true + }, + { + "id": "t142", + "source": "ACE2-SARS-CoV_interaction_complex", + "target": "ACE2,_space_soluble", + "sign": false + }, + { + "id": "t143", + "source": "viral_entry_into_host_cell_phenotype", + "target": "ACE2,_space_soluble", + "sign": false + }, + { + "id": "t144", + "source": "PPP1R15A", + "target": "PPP1R15A_rna", + "sign": true + }, + { + "id": "t145", + "source": "PPP1R15A_rna", + "target": "PPP1R15A_gene", + "sign": true + }, + { + "id": "t146", + "source": "PPP1R15A_rna", + "target": "ATF4", + "sign": true + }, + { + "id": "t147", + "source": "DDIT3_rna", + "target": "ATF4", + "sign": true + }, + { + "id": "t148", + "source": "PPP1R15A_rna", + "target": "DDIT3", + "sign": true + }, + { + "id": "t149", + "source": "DDIT3_phosphorylated", + "target": "DDIT3", + "sign": true + }, + { + "id": "t150", + "source": "TRIB3_rna", + "target": "DDIT3", + "sign": true + }, + { + "id": "t151", + "source": "AP-1_phosphorylated_phosphorylated", + "target": "DDIT3", + "sign": true + }, + { + "id": "t152", + "source": "ERO1A_rna", + "target": "DDIT3", + "sign": true + }, + { + "id": "t153", + "source": "high_space_Ca2+space_cytosolic_space_concentration_phenotype", + "target": "release_space_of_space_ER_space_Ca2+_phenotype", + "sign": true + }, + { + "id": "t154", + "source": "release_space_of_space_ER_space_Ca2+_phenotype", + "target": "BAX_phosphorylated", + "sign": true + }, + { + "id": "t155", + "source": "Apoptosis_phenotype_cell", + "target": "BAX_phosphorylated", + "sign": true + }, + { + "id": "t157", + "source": "UPR_phenotype", + "target": "ATF6_Golgi_apparatus", + "sign": true + }, + { + "id": "t158", + "source": "ATF6_nucleus", + "target": "ATF6_Golgi_apparatus", + "sign": true + }, + { + "id": "t159", + "source": "ATF6_Golgi_apparatus", + "target": "ATF6_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t160", + "source": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "target": "ATF6_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t161", + "source": "ATF6_Golgi_apparatus", + "target": "ER_space_Stress_phenotype", + "sign": true + }, + { + "id": "t162", + "source": "CDK5", + "target": "ER_space_Stress_phenotype", + "sign": true + }, + { + "id": "t163", + "source": "Persistant_space_ER_space_Stress_phenotype_endoplasmic_reticulum", + "target": "ER_space_Stress_phenotype", + "sign": true + }, + { + "id": "t164", + "source": "ATF6_Golgi_apparatus", + "target": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "sign": false + }, + { + "id": "t165", + "source": "protein_space_ubiquitination_space_and_space_destruction_phenotype", + "target": "retrograde_space_transport_space_from_space_ER_space_to_space_cytosol_phenotype", + "sign": true + }, + { + "id": "t166", + "source": "ATF6_Golgi_apparatus", + "target": "MBTPS2", + "sign": true + }, + { + "id": "t167", + "source": "ATF6_Golgi_apparatus", + "target": "MBTPS1", + "sign": true + }, + { + "id": "t168", + "source": "BCL2_rna", + "target": "DDIT3_phosphorylated", + "sign": false + }, + { + "id": "t169", + "source": "Apoptosis_phenotype_cell", + "target": "DDIT3_phosphorylated", + "sign": true + }, + { + "id": "t170", + "source": "DDIT3_phosphorylated", + "target": "MAPK14_phosphorylated", + "sign": true + }, + { + "id": "t171", + "source": "BAX_phosphorylated", + "target": "MAPK14_phosphorylated", + "sign": true + }, + { + "id": "t172", + "source": "Apoptosis_phenotype_cell", + "target": "MAPK14_phosphorylated", + "sign": true + }, + { + "id": "t173", + "source": "HSPA5_endoplasmic_reticulum", + "target": "ATF6:HSPA5_complex", + "sign": true + }, + { + "id": "t174", + "source": "ATF6_endoplasmic_reticulum", + "target": "ATF6:HSPA5_complex", + "sign": true + }, + { + "id": "t175", + "source": "HSPA5_endoplasmic_reticulum", + "target": "HSPA5_rna", + "sign": true + }, + { + "id": "t177", + "source": "Ca2+_ion_cell", + "target": "ITPR", + "sign": true + }, + { + "id": "t178", + "source": "ITPR", + "target": "TMBIM6", + "sign": true + }, + { + "id": "t179", + "source": "Ca2+_ion_cell", + "target": "TMBIM6", + "sign": true + }, + { + "id": "t180", + "source": "ITPR", + "target": "ERO1A_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t181", + "source": "hyperoxidation_phenotype", + "target": "ERO1A_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t182", + "source": "HSPA5_rna", + "target": "HSPA5_gene", + "sign": true + }, + { + "id": "t183", + "source": "UPR_phenotype", + "target": "XBP1", + "sign": true + }, + { + "id": "t184", + "source": "DDIT3_rna", + "target": "XBP1", + "sign": true + }, + { + "id": "t185", + "source": "ERAD_phenotype", + "target": "XBP1", + "sign": true + }, + { + "id": "t186", + "source": "UPR_phenotype", + "target": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "sign": true + }, + { + "id": "t187", + "source": "ER_space_Stress_phenotype", + "target": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "sign": true + }, + { + "id": "t188", + "source": "mitochondria_space_fragmentation_phenotype", + "target": "mitochondrial_space_fission_phenotype", + "sign": true + }, + { + "id": "t189", + "source": "mitochondrial_space_fission_phenotype", + "target": "PACS2_endoplasmic_reticulum", + "sign": false + }, + { + "id": "t190", + "source": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "target": "PACS2_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t191", + "source": "p20", + "target": "PACS2_endoplasmic_reticulum", + "sign": false + }, + { + "id": "t192", + "source": "EIF2AK2", + "target": "DNAJC3", + "sign": false + }, + { + "id": "t193", + "source": "EIF2S1_phosphorylated", + "target": "DNAJC3", + "sign": false + }, + { + "id": "t194", + "source": "DNAJC3", + "target": "DNAJC3_rna", + "sign": true + }, + { + "id": "t195", + "source": "DDIT3", + "target": "DDIT3_rna", + "sign": true + }, + { + "id": "t196", + "source": "DDIT3_rna", + "target": "DDIT3_gene", + "sign": true + }, + { + "id": "t197", + "source": "DDIT3_rna", + "target": "ATF6_nucleus", + "sign": true + }, + { + "id": "t198", + "source": "XBP1_rna", + "target": "ATF6_nucleus", + "sign": true + }, + { + "id": "t199", + "source": "DNAJC3_rna", + "target": "ATF6_nucleus", + "sign": true + }, + { + "id": "t200", + "source": "HYOU1_rna", + "target": "ATF6_nucleus", + "sign": true + }, + { + "id": "t201", + "source": "ERO1A_rna", + "target": "ATF6_nucleus", + "sign": true + }, + { + "id": "t202", + "source": "ATF4", + "target": "ATF4_rna", + "sign": true + }, + { + "id": "t203", + "source": "ATF4_rna", + "target": "ATF4_gene", + "sign": true + }, + { + "id": "t204", + "source": "BCL2L11_phosphorylated", + "target": "BCL2L11_cell", + "sign": true + }, + { + "id": "t205", + "source": "BCL2L11_cell", + "target": "BCL2L11_phosphorylated", + "sign": true + }, + { + "id": "t206", + "source": "Apoptosis_phenotype_cell", + "target": "BCL2L11_phosphorylated", + "sign": true + }, + { + "id": "t207", + "source": "BCL2L11_cell", + "target": "PPP2CA", + "sign": true + }, + { + "id": "t208", + "source": "TRIB3", + "target": "TRIB3_rna", + "sign": true + }, + { + "id": "t209", + "source": "TRIB3_rna", + "target": "TRIB3_gene", + "sign": true + }, + { + "id": "t210", + "source": "Ca2+_ion_mitochondrial_matrix", + "target": "Ca2+_ion_mitochondrion", + "sign": true + }, + { + "id": "t211", + "source": "Ca2+_ion_mitochondrion", + "target": "Ca2+_ion_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t212", + "source": "Ca2+_ion_cell", + "target": "Ca2+_ion_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t213", + "source": "Ca2+_ion_mitochondrion", + "target": "ITPR3:HSPA9:VDAC1_complex", + "sign": true + }, + { + "id": "t214", + "source": "ERO1A_endoplasmic_reticulum", + "target": "ERO1A_cell", + "sign": true + }, + { + "id": "t215", + "source": "EIF2S1", + "target": "PPP1R15A", + "sign": true + }, + { + "id": "t216", + "source": "EIF2S1", + "target": "EIF2AK1", + "sign": true + }, + { + "id": "t217", + "source": "Apoptosis_phenotype_cell", + "target": "cleaved~CASP9", + "sign": true + }, + { + "id": "t218", + "source": "cleaved~CASP9", + "target": "CASP9", + "sign": true + }, + { + "id": "t219", + "source": "cleaved~CASP9", + "target": "cleaved~CASP4", + "sign": true + }, + { + "id": "t220", + "source": "cleaved~CASP3", + "target": "cleaved~CASP4", + "sign": true + }, + { + "id": "t221", + "source": "autophagy_phenotype", + "target": "mitochondrion-endoplasmic_space_reticulum_space_membrane_space_tethering_space__phenotype", + "sign": false + }, + { + "id": "t222", + "source": "XBP1", + "target": "XBP1_rna", + "sign": true + }, + { + "id": "t223", + "source": "XBP1_rna", + "target": "XBP1_gene", + "sign": true + }, + { + "id": "t224", + "source": "accumulation_space_of_space_misfolded_space_protein_space_in_space_ER_phenotype", + "target": "ERAD_phenotype", + "sign": true + }, + { + "id": "t225", + "source": "BCL2_rna", + "target": "BCL2_gene", + "sign": true + }, + { + "id": "t227", + "source": "MAP3K4_phosphorylated", + "target": "CDK5", + "sign": true + }, + { + "id": "t228", + "source": "MAPK14_phosphorylated", + "target": "MAPK14", + "sign": true + }, + { + "id": "t229", + "source": "MAPK14_phosphorylated", + "target": "MAP3K5_phosphorylated", + "sign": true + }, + { + "id": "t230", + "source": "MAPK8_phosphorylated", + "target": "MAP3K5_phosphorylated", + "sign": true + }, + { + "id": "t231", + "source": "ERO1A_cell", + "target": "ERO1A_rna", + "sign": true + }, + { + "id": "t232", + "source": "Apoptosis_phenotype_cell", + "target": "Cell_space_survival_phenotype", + "sign": true + }, + { + "id": "t233", + "source": "Cell_space_survival_phenotype", + "target": "Apoptosis_phenotype_cell", + "sign": true + }, + { + "id": "t234", + "source": "unfolded_space_protein_space_response_space_(UPR)_phenotype", + "target": "p20", + "sign": true + }, + { + "id": "t236", + "source": "EIF2S1_phosphorylated", + "target": "EIF2AK2", + "sign": true + }, + { + "id": "t237", + "source": "EIF2AK2", + "target": "presence_space_of_space_dsRNA_phenotype", + "sign": true + }, + { + "id": "t238", + "source": "BAX_phosphorylated", + "target": "BAX_cell", + "sign": true + }, + { + "id": "t239", + "source": "BAX_phosphorylated", + "target": "MAPK8_phosphorylated", + "sign": true + }, + { + "id": "t240", + "source": "BID_phosphorylated", + "target": "MAPK8_phosphorylated", + "sign": true + }, + { + "id": "t241", + "source": "AP-1_phosphorylated_phosphorylated", + "target": "MAPK8_phosphorylated", + "sign": true + }, + { + "id": "t242", + "source": "BCL2L11_phosphorylated", + "target": "MAPK8_phosphorylated", + "sign": true + }, + { + "id": "t243", + "source": "MAPK8_phosphorylated", + "target": "MAPK8", + "sign": true + }, + { + "id": "t244", + "source": "MAPK8_phosphorylated", + "target": "MAP3K4_phosphorylated", + "sign": true + }, + { + "id": "t245", + "source": "Apoptosis_phenotype_cell", + "target": "BID_phosphorylated", + "sign": true + }, + { + "id": "t246", + "source": "BID_phosphorylated", + "target": "BID", + "sign": true + }, + { + "id": "t247", + "source": "Apoptosis_phenotype_cell", + "target": "TRIB3", + "sign": true + }, + { + "id": "t248", + "source": "cleaved~CASP4", + "target": "CASP4", + "sign": true + }, + { + "id": "t249", + "source": "HYOU1", + "target": "HYOU1_rna", + "sign": true + }, + { + "id": "t250", + "source": "Apoptosis_phenotype_cell", + "target": "cleaved~CASP3", + "sign": true + }, + { + "id": "t251", + "source": "cleaved~CASP3", + "target": "CASP3", + "sign": true + }, + { + "id": "t252", + "source": "EIF2S1_phosphorylated", + "target": "GCN2:ATP_complex", + "sign": true + }, + { + "id": "t253", + "source": "AP-1_phosphorylated_phosphorylated", + "target": "AP-1", + "sign": true + }, + { + "id": "t254", + "source": "Ca2+_ion_cell", + "target": "RYR1", + "sign": true + }, + { + "id": "t255", + "source": "p20", + "target": "Apoptosis_phenotype_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t256", + "source": "MAP3K5_phosphorylated", + "target": "MAP3K5", + "sign": true + }, + { + "id": "t257", + "source": "DNAJC3_rna", + "target": "DNAJC3_gene", + "sign": true + }, + { + "id": "t258", + "source": "MFN2_endoplasmic_reticulum", + "target": "MFN2_rna", + "sign": true + }, + { + "id": "t259", + "source": "ACE2,_space_soluble", + "target": "ADAM17_cell", + "sign": true + }, + { + "id": "t260", + "source": "ACE2,_space_membrane-bound", + "target": "ADAM17_cell", + "sign": true + }, + { + "id": "t261", + "source": "MFN2_rna", + "target": "MFN2_gene", + "sign": true + }, + { + "id": "t262", + "source": "MAP3K4_phosphorylated", + "target": "MAP3K4", + "sign": true + }, + { + "id": "t263", + "source": "HYOU1_rna", + "target": "HYOU1_gene", + "sign": true + }, + { + "id": "t264", + "source": "ERO1A_rna", + "target": "ERO1A_gene", + "sign": true + }, + { + "id": "t265", + "source": "ACE2_rna", + "target": "viral_entry_into_host_cell_phenotype", + "sign": false + }, + { + "id": "t266", + "source": "viral_entry_into_host_cell_phenotype", + "target": "SARS-CoV_infection_phenotype", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/ETC.json b/scripts/covid19_diseasemaps/regnet_amr/ETC.json new file mode 100644 index 000000000..0da160b54 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/ETC.json @@ -0,0 +1,1630 @@ +{ + "header": { + "name": "ETC", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on ETC", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "TIM_space_complex:Nsp4_complex", + "name": "TIM_space_complex:Nsp4_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "precursor_space_protein_space_N-terminus_space_binding", + "name": "precursor_space_protein_space_N-terminus_space_binding", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_mitochondrion", + "name": "Nsp4_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TIM_space_complex_complex", + "name": "TIM_space_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_space_Synthase_complex", + "name": "ATP_space_Synthase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_mitochondrial_matrix", + "name": "H+_ion_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule", + "name": "ATP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F-ATPase_complex_mitochondrial_matrix", + "name": "F-ATPase_complex_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nsp6", + "name": "Nsp6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F-ATPase:Nsp6_complex", + "name": "F-ATPase:Nsp6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_mitochondrion", + "name": "H+_ion_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mt_space_mRNA_rna", + "name": "mt_space_mRNA_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "name": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mt_space_translation_complex", + "name": "Mt_space_translation_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mt_space_ribosomal_space_proteins_complex", + "name": "Mt_space_ribosomal_space_proteins_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp8-affected_Mt_ribosomal_proteins_complex", + "name": "Nsp8-affected_Mt_ribosomal_proteins_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Complex_space_1_complex", + "name": "Complex_space_1_complex", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "complex_space_2_complex_mitochondrial_matrix", + "name": "complex_space_2_complex_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "complex_space_3_complex", + "name": "complex_space_3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "paraquat_simple_molecule", + "name": "paraquat_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ubiquinol_simple_molecule_mitochondrial_matrix", + "name": "ubiquinol_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAD+_simple_molecule", + "name": "NAD+_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADH_simple_molecule", + "name": "NADH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NDUFA1", + "name": "NDUFA1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NDUFB9", + "name": "NDUFB9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "OXPHOS_space_factors_complex", + "name": "OXPHOS_space_factors_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "complex_space_4_complex", + "name": "complex_space_4_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP5MG", + "name": "ATP5MG", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACAD9", + "name": "ACAD9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ECSIT", + "name": "ECSIT", 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"mt_space_DNA_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MT_space_tRNAs_complex", + "name": "MT_space_tRNAs_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "damaged_space_mt_space_DNA_gene", + "name": "damaged_space_mt_space_DNA_gene", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mt-tRNA_space_synthetase_complex", + "name": "Mt-tRNA_space_synthetase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRMT1", + "name": "TRMT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp8", + "name": "Nsp8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "paraquat_space_dication_complex", + "name": "paraquat_space_dication_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "superoxide_simple_molecule", + "name": "superoxide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_simple_molecule", + "name": "O2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_cell", + "name": "Nsp4_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4:DNAJC11_complex", + "name": "Nsp4:DNAJC11_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DNAJC11", + "name": "DNAJC11", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe3+_ion", + "name": "Fe3+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion", + "name": "Fe2+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "hydroxide_simple_molecule", + "name": "hydroxide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule", + "name": "H2O_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ROS_simple_molecule", + "name": "ROS_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HO_simple_molecule", + "name": "HO_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O2_simple_molecule", + "name": "H2O2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXN2", + "name": "TXN2", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "glutathione_space_disulfide_simple_molecule", + "name": "glutathione_space_disulfide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TFAM", + "name": "TFAM", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mt_space_DNA_space_replication_phenotype", + "name": "mt_space_DNA_space_replication_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MT_space_transcription_complex", + "name": "MT_space_transcription_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9c", + "name": "Orf9c", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SOD1", + "name": "SOD1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mt_space_DNA_space_damage_phenotype", + "name": "mt_space_DNA_space_damage_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mt-DNA_space_repair_complex", + "name": "Mt-DNA_space_repair_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mt-dNTP_space_pool_complex", + "name": "Mt-dNTP_space_pool_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "glutathione_simple_molecule", + "name": "glutathione_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GPX4", + "name": "GPX4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GPX1", + "name": "GPX1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CAT", + "name": "CAT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADP(+)_simple_molecule", + "name": "NADP(+)_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRDX_complex", + "name": "PRDX_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADPH_simple_molecule", + "name": "NADPH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXNRD2", + "name": "TXNRD2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GSR", + "name": "GSR", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP_simple_molecule", + "name": "ADP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pi_simple_molecule", + "name": "Pi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mt_space_replication_complex", + "name": "Mt_space_replication_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TOM_space_complex_complex_mitochondrion", + "name": "TOM_space_complex_complex_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b", + "name": "Orf9b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TIM23_space_complex_complex", + "name": "TIM23_space_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp7", + "name": "Nsp7", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "precursor_space_protein_space_N-terminus_space_binding", + "target": "TIM_space_complex:Nsp4_complex", + "sign": true + }, + { + "id": "t2", + "source": "TIM_space_complex:Nsp4_complex", + "target": "Nsp4_mitochondrion", + "sign": true + }, + { + "id": "t3", + "source": "TIM_space_complex:Nsp4_complex", + "target": "TIM_space_complex_complex", + "sign": true + }, + { + "id": "t4", + "source": "precursor_space_protein_space_N-terminus_space_binding", + "target": "TIM_space_complex_complex", + "sign": true + }, + { + "id": "t5", + "source": "H+_ion_mitochondrial_matrix", + "target": "ATP_space_Synthase_complex", + "sign": true + }, + { + "id": "t6", + "source": "ATP_simple_molecule", + "target": "ATP_space_Synthase_complex", + "sign": true + }, + { + "id": "t7", + "source": "ATP_space_Synthase_complex", + "target": "F-ATPase_complex_mitochondrial_matrix", + "sign": true + }, + { + "id": "t8", + "source": "ATP_space_Synthase_complex", + "target": "Nsp6", + "sign": false + }, + { + "id": "t9", + "source": "F-ATPase:Nsp6_complex", + "target": "Nsp6", + "sign": true + }, + { + "id": "t10", + "source": "ATP_space_Synthase_complex", + "target": "H+_ion_mitochondrion", + "sign": true + }, + { + "id": "t11", + "source": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "target": "mt_space_mRNA_rna", + "sign": true + }, + { + "id": "t12", + "source": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "target": "Mt_space_translation_complex", + "sign": true + }, + { + "id": "t13", + "source": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "target": "Mt_space_ribosomal_space_proteins_complex", + "sign": true + }, + { + "id": "t14", + "source": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "target": "Nsp8-affected_Mt_ribosomal_proteins_complex", + "sign": true + }, + { + "id": "t16", + "source": "complex_space_2_complex_mitochondrial_matrix", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t17", + "source": "complex_space_3_complex", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t18", + "source": "paraquat_simple_molecule", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t19", + "source": "H+_ion_mitochondrial_matrix", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t20", + "source": "H+_ion_mitochondrion", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t21", + "source": "ubiquinol_simple_molecule_mitochondrial_matrix", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t22", + "source": "NAD+_simple_molecule", + "target": "Complex_space_1_complex", + "sign": true + }, + { + "id": "t23", + "source": "Complex_space_1_complex", + "target": "NADH_simple_molecule", + "sign": true + }, + { + "id": "t24", + "source": "H+_ion_mitochondrial_matrix", + "target": "NADH_simple_molecule", + "sign": true + }, + { + "id": "t25", + "source": "NAD+_simple_molecule", + "target": "NADH_simple_molecule", + "sign": true + }, + { + "id": "t26", + "source": "Complex_space_1_complex", + "target": "NDUFA1", + "sign": true + }, + { + "id": "t27", + "source": "Complex_space_1_complex", + "target": "NDUFB9", + "sign": true + }, + { + "id": "t28", + "source": "Complex_space_1_complex", + "target": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "sign": true + }, + { + "id": "t29", + "source": "Complex_space_1_complex", + "target": "OXPHOS_space_factors_complex", + "sign": true + }, + { + "id": "t30", + "source": "complex_space_2_complex_mitochondrial_matrix", + "target": "OXPHOS_space_factors_complex", + "sign": true + }, + { + "id": "t31", + "source": "complex_space_3_complex", + "target": "OXPHOS_space_factors_complex", + "sign": true + }, + { + "id": "t32", + "source": "complex_space_4_complex", + "target": "OXPHOS_space_factors_complex", + "sign": true + }, + { + "id": "t33", + "source": "F-ATPase_complex_mitochondrial_matrix", + "target": "ATP5MG", + "sign": true + }, + { + "id": "t34", + "source": "F-ATPase:Nsp6_complex", + "target": "ATP5MG", + "sign": true + }, + { + "id": "t36", + "source": "OXPHOS_space_factors_complex", + "target": "ACAD9", + "sign": true + }, + { + "id": "t37", + "source": "OXPHOS_space_factors_complex", + "target": "ECSIT", + "sign": true + }, + { + "id": "t38", + "source": "OXPHOS_space_factors_complex", + "target": "NDUFAF7", + "sign": true + }, + { + "id": "t40", + "source": "ubiquinol_simple_molecule_mitochondrial_matrix", + "target": "complex_space_2_complex_mitochondrial_matrix", + "sign": true + }, + { + "id": "t41", + "source": "complex_space_2_complex_mitochondrial_matrix", + "target": "Q_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t42", + "source": "complex_space_3_complex", + "target": "Q_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t43", + "source": "ubiquinol_simple_molecule_mitochondrial_matrix", + "target": "Q_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t44", + "source": "complex_space_2_complex_mitochondrial_matrix", + "target": "SIRT3", + "sign": true + }, + { + "id": "t45", + "source": "SOD2", + "target": "SIRT3", + "sign": true + }, + { + "id": "t46", + "source": "complex_space_4_complex", + "target": "complex_space_3_complex", + "sign": true + }, + { + "id": "t47", + "source": "Q_simple_molecule_mitochondrial_matrix", + "target": "complex_space_3_complex", + "sign": true + }, + { + "id": "t48", + "source": "H+_ion_mitochondrion", + "target": "complex_space_3_complex", + "sign": true + }, + { + "id": "t49", + "source": "O2-_simple_molecule", + "target": "complex_space_3_complex", + "sign": true + }, + { + "id": "t50", + "source": "CYCS_mitochondrial_matrix", + "target": "complex_space_3_complex", + "sign": true + }, + { + "id": "t51", + "source": "complex_space_3_complex", + "target": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "sign": true + }, + { + "id": "t52", + "source": "complex_space_4_complex", + "target": "mtDNA_space_encoded_space_OXPHOS_space_units_complex_mitochondrial_matrix", + "sign": true + }, + { + "id": "t53", + "source": "complex_space_2_complex_mitochondrial_matrix", + "target": "TCA_phenotype", + "sign": true + }, + { + "id": "t54", + "source": "MT_space_tRNAs_complex", + "target": "mt_space_DNA_gene", + "sign": true + }, + { + "id": "t55", + "source": "mt_space_mRNA_rna", + "target": "mt_space_DNA_gene", + "sign": true + }, + { + "id": "t56", + "source": "damaged_space_mt_space_DNA_gene", + "target": "mt_space_DNA_gene", + "sign": true + }, + { + "id": "t57", + "source": "MT_space_tRNAs_complex", + "target": "Mt-tRNA_space_synthetase_complex", + "sign": true + }, + { + "id": "t58", + "source": "MT_space_tRNAs_complex", + "target": "TRMT1", + "sign": true + }, + { + "id": "t59", + "source": "Nsp8-affected_Mt_ribosomal_proteins_complex", + "target": "Nsp8", + "sign": false + }, + { + "id": "t60", + "source": "paraquat_simple_molecule", + "target": "paraquat_space_dication_complex", + "sign": true + }, + { + "id": "t61", + "source": "paraquat_space_dication_complex", + "target": "paraquat_simple_molecule", + "sign": true + }, + { + "id": "t62", + "source": "superoxide_simple_molecule", + "target": "paraquat_simple_molecule", + "sign": true + }, + { + "id": "t63", + "source": "paraquat_space_dication_complex", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t64", + "source": "Q_simple_molecule_mitochondrial_matrix", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t65", + "source": "H+_ion_mitochondrion", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t66", + "source": "superoxide_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t67", + "source": "O2-_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t68", + "source": "CYCS_mitochondrial_matrix", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t69", + "source": "complex_space_4_complex", + "target": "CYCS_mitochondrial_matrix", + "sign": true + }, + { + "id": "t70", + "source": "Nsp4:DNAJC11_complex", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t71", + "source": "Nsp4_mitochondrion", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t72", + "source": "Nsp4:DNAJC11_complex", + "target": "DNAJC11", + "sign": true + }, + { + "id": "t73", + "source": "H+_ion_mitochondrial_matrix", + "target": "Fe3+_ion", + "sign": true + }, + { + "id": "t74", + "source": "Fe2+_ion", + "target": "Fe3+_ion", + "sign": true + }, + { + "id": "t75", + "source": "O2_simple_molecule", + "target": "Fe3+_ion", + "sign": true + }, + { + "id": "t76", + "source": "Fe3+_ion", + "target": "hydroxide_simple_molecule", + "sign": true + }, + { + "id": "t77", + "source": "H+_ion_mitochondrial_matrix", + "target": "hydroxide_simple_molecule", + "sign": true + }, + { + "id": "t78", + "source": "H2O_simple_molecule", + "target": "hydroxide_simple_molecule", + "sign": true + }, + { + "id": "t79", + "source": "ROS_simple_molecule", + "target": "hydroxide_simple_molecule", + "sign": true + }, + { + "id": "t80", + "source": "HO_simple_molecule", + "target": "hydroxide_simple_molecule", + "sign": true + }, + { + "id": "t81", + "source": "superoxide_simple_molecule", + "target": "hydroxide_simple_molecule", + "sign": true + }, + { + "id": "t82", + "source": "Fe3+_ion", + "target": "Fe2+_ion", + "sign": true + }, + { + "id": "t83", + "source": "HO_simple_molecule", + "target": "Fe2+_ion", + "sign": true + }, + { + "id": "t84", + "source": "hydroxide_simple_molecule", + "target": "Fe2+_ion", + "sign": true + }, + { + "id": "t85", + "source": "Fe3+_ion", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t86", + "source": "H+_ion_mitochondrial_matrix", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t87", + "source": "H2O_simple_molecule", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t88", + "source": "ROS_simple_molecule", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t89", + "source": "TXN2", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t90", + "source": "HO_simple_molecule", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t91", + "source": "superoxide_simple_molecule", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t92", + "source": "hydroxide_simple_molecule", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t93", + "source": "glutathione_space_disulfide_simple_molecule", + "target": "H2O2_simple_molecule", + "sign": true + }, + { + "id": "t94", + "source": "paraquat_simple_molecule", + "target": "superoxide_simple_molecule", + "sign": true + }, + { + "id": "t95", + "source": "H2O2_simple_molecule", + "target": "superoxide_simple_molecule", + "sign": true + }, + { + "id": "t96", + "source": "H+_ion_mitochondrial_matrix", + "target": "superoxide_simple_molecule", + "sign": true + }, + { + "id": "t97", + "source": "Fe2+_ion", + "target": "superoxide_simple_molecule", + "sign": true + }, + { + "id": "t98", + "source": "ROS_simple_molecule", + "target": "superoxide_simple_molecule", + "sign": true + }, + { + "id": "t99", + "source": "O2_simple_molecule", + "target": "superoxide_simple_molecule", + "sign": true + }, + { + "id": "t100", + "source": "mt_space_mRNA_rna", + "target": "TFAM", + "sign": true + }, + { + "id": "t101", + "source": "mt_space_DNA_gene", + "target": "TFAM", + "sign": true + }, + { + "id": "t102", + "source": "mt_space_DNA_space_replication_phenotype", + "target": "TFAM", + "sign": true + }, + { + "id": "t103", + "source": "mt_space_mRNA_rna", + "target": "MT_space_transcription_complex", + "sign": true + }, + { + "id": "t104", + "source": "mt_space_mRNA_rna", + "target": "damaged_space_mt_space_DNA_gene", + "sign": false + }, + { + "id": "t105", + "source": "mt_space_DNA_gene", + "target": "damaged_space_mt_space_DNA_gene", + "sign": true + }, + { + "id": "t106", + "source": "ECSIT", + "target": "Orf9c", + "sign": false + }, + { + "id": "t107", + "source": "NDUFA1", + "target": "Orf9c", + "sign": false + }, + { + "id": "t108", + "source": "NDUFB9", + "target": "Orf9c", + "sign": false + }, + { + "id": "t109", + "source": "ACAD9", + "target": "Orf9c", + "sign": false + }, + { + "id": "t110", + "source": "H2O2_simple_molecule", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t111", + "source": "Q_simple_molecule_mitochondrial_matrix", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t112", + "source": "H+_ion_mitochondrion", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t113", + "source": "ATP_simple_molecule", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t114", + "source": "O2-_simple_molecule", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t115", + "source": "CYCS_mitochondrial_matrix", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t116", + "source": "H2O2_simple_molecule", + "target": "SOD1", + "sign": true + }, + { + "id": "t117", + "source": "H2O2_simple_molecule", + "target": "SOD2", + "sign": true + }, + { + "id": "t118", + "source": "mt_space_DNA_gene", + "target": "mt_space_DNA_space_damage_phenotype", + "sign": false + }, + { + "id": "t119", + "source": "damaged_space_mt_space_DNA_gene", + "target": "mt_space_DNA_space_damage_phenotype", + "sign": true + }, + { + "id": "t120", + "source": "mt_space_DNA_gene", + "target": "mt_space_DNA_space_replication_phenotype", + "sign": true + }, + { + "id": "t121", + "source": "mt_space_DNA_gene", + "target": "Mt-DNA_space_repair_complex", + "sign": true + }, + { + "id": "t122", + "source": "mt_space_DNA_gene", + "target": "Mt-dNTP_space_pool_complex", + "sign": true + }, + { + "id": "t123", + "source": "mt_space_DNA_space_replication_phenotype", + "target": "Mt-dNTP_space_pool_complex", + "sign": true + }, + { + "id": "t124", + "source": "H2O_simple_molecule", + "target": "glutathione_simple_molecule", + "sign": true + }, + { + "id": "t125", + "source": "glutathione_space_disulfide_simple_molecule", + "target": "glutathione_simple_molecule", + "sign": true + }, + { + "id": "t126", + "source": "H2O_simple_molecule", + "target": "GPX4", + "sign": true + }, + { + "id": "t127", + "source": "glutathione_space_disulfide_simple_molecule", + "target": "GPX4", + "sign": true + }, + { + "id": "t128", + "source": "H2O_simple_molecule", + "target": "GPX1", + "sign": true + }, + { + "id": "t129", + "source": "glutathione_space_disulfide_simple_molecule", + "target": "GPX1", + "sign": true + }, + { + "id": "t130", + "source": "H2O_simple_molecule", + "target": "CAT", + "sign": true + }, + { + "id": "t131", + "source": "H2O_simple_molecule", + "target": "TXN2", + "sign": true + }, + { + "id": "t133", + "source": "NADP(+)_simple_molecule", + "target": "TXN2", + "sign": true + }, + { + "id": "t134", + "source": "H2O_simple_molecule", + "target": "PRDX_complex", + "sign": true + }, + { + "id": "t135", + "source": "TXN2", + "target": "PRDX_complex", + "sign": true + }, + { + "id": "t136", + "source": "Q_simple_molecule_mitochondrial_matrix", + "target": "CYCS_mitochondrial_matrix", + "sign": true + }, + { + "id": "t137", + "source": "H+_ion_mitochondrion", + "target": "CYCS_mitochondrial_matrix", + "sign": true + }, + { + "id": "t138", + "source": "O2-_simple_molecule", + "target": "CYCS_mitochondrial_matrix", + "sign": true + }, + { + "id": "t140", + "source": "Q_simple_molecule_mitochondrial_matrix", + "target": "ubiquinol_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t141", + "source": "H+_ion_mitochondrion", + "target": "ubiquinol_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t142", + "source": "O2-_simple_molecule", + "target": "ubiquinol_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t143", + "source": "CYCS_mitochondrial_matrix", + "target": "ubiquinol_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t144", + "source": "TXN2", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t145", + "source": "NADP(+)_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t146", + "source": "glutathione_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t147", + "source": "TXN2", + "target": "TXNRD2", + "sign": true + }, + { + "id": "t148", + "source": "NADP(+)_simple_molecule", + "target": "TXNRD2", + "sign": true + }, + { + "id": "t149", + "source": "NADP(+)_simple_molecule", + "target": "glutathione_space_disulfide_simple_molecule", + "sign": true + }, + { + "id": "t150", + "source": "glutathione_simple_molecule", + "target": "glutathione_space_disulfide_simple_molecule", + "sign": true + }, + { + "id": "t151", + "source": "NADP(+)_simple_molecule", + "target": "GSR", + "sign": true + }, + { + "id": "t152", + "source": "glutathione_simple_molecule", + "target": "GSR", + "sign": true + }, + { + "id": "t153", + "source": "ATP_simple_molecule", + "target": "ADP_simple_molecule", + "sign": true + }, + { + "id": "t154", + "source": "ATP_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t155", + "source": "mt_space_DNA_space_replication_phenotype", + "target": "Mt_space_replication_complex", + "sign": true + }, + { + "id": "t156", + "source": "precursor_space_protein_space_N-terminus_space_binding", + "target": "TOM_space_complex_complex_mitochondrion", + "sign": true + }, + { + "id": "t157", + "source": "precursor_space_protein_space_N-terminus_space_binding", + "target": "Orf9b", + "sign": false + }, + { + "id": "t158", + "source": "precursor_space_protein_space_N-terminus_space_binding", + "target": "TIM23_space_complex_complex", + "sign": true + }, + { + "id": "t159", + "source": "NDUFAF7", + "target": "Nsp7", + "sign": false + }, + { + "id": "t160", + "source": "Nsp4_mitochondrion", + "target": "TOM_space_complex_complex_mitochondrion", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/E_protein.json b/scripts/covid19_diseasemaps/regnet_amr/E_protein.json new file mode 100644 index 000000000..ffbac3fdc --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/E_protein.json @@ -0,0 +1,542 @@ +{ + "header": { + "name": "E_protein", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on E_protein", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "histone_complex_nucleus", + "name": "histone_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Chromatin_organization_phenotype", + "name": "Chromatin_organization_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BRD4", + "name": "BRD4", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "CDK9", + "name": "CDK9", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "CCNT1", + "name": "CCNT1", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "BRD2", + "name": "BRD2", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "TBP", + "name": "TBP", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "H4C14", + "name": "H4C14", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H4-16", + "name": "H4-16", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H4C1", + "name": "H4C1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H3C15", + "name": "H3C15", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H3C1", + "name": "H3C1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H4C9", + "name": "H4C9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2BC21", + "name": "H2BC21", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2A", + "name": "H2A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CRB3:PALS1:PATJ_complex_complex", + "name": "CRB3:PALS1:PATJ_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Maintenance_of_tight_junction_phenotype", + "name": "Maintenance_of_tight_junction_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MPP5", + "name": "MPP5", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "E-PALS1_complex", + "name": "E-PALS1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CRB3", + "name": "CRB3", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "PATJ", + "name": "PATJ", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "ASIC1_trimer:H+:STOML3_complex", + "name": "ASIC1_trimer:H+:STOML3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Activity_of_sodium_channels_phenotype", 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"target": "BRD2", + "sign": true + }, + { + "id": "t10", + "source": "histone_complex_nucleus", + "target": "H4C14", + "sign": true + }, + { + "id": "t11", + "source": "histone_complex_nucleus", + "target": "H4-16", + "sign": true + }, + { + "id": "t12", + "source": "histone_complex_nucleus", + "target": "H4C1", + "sign": true + }, + { + "id": "t13", + "source": "histone_complex_nucleus", + "target": "H3C15", + "sign": true + }, + { + "id": "t14", + "source": "histone_complex_nucleus", + "target": "H3C1", + "sign": true + }, + { + "id": "t15", + "source": "histone_complex_nucleus", + "target": "H4C9", + "sign": true + }, + { + "id": "t16", + "source": "histone_complex_nucleus", + "target": "H2BC21", + "sign": true + }, + { + "id": "t17", + "source": "histone_complex_nucleus", + "target": "H2A", + "sign": true + }, + { + "id": "t18", + "source": "Maintenance_of_tight_junction_phenotype", + "target": "CRB3:PALS1:PATJ_complex_complex", + "sign": true + }, + { + "id": "t19", + "source": 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"ATP1A:ATP1B:FXYDs_complex", + "target": "E_cell", + "sign": false + }, + { + "id": "t32", + "source": "E-PALS1_complex", + "target": "E_cell", + "sign": true + }, + { + "id": "t33", + "source": "K+_ion", + "target": "ATP1A:ATP1B:FXYDs_complex", + "sign": true + }, + { + "id": "t34", + "source": "Na+_ion", + "target": "ATP1A:ATP1B:FXYDs_complex", + "sign": true + }, + { + "id": "t35", + "source": "Activity_of_sodium_channels_phenotype", + "target": "ATP1A:ATP1B:FXYDs_complex", + "sign": true + }, + { + "id": "t36", + "source": "Maintenance_of_tight_junction_phenotype", + "target": "E-PALS1_complex", + "sign": true + }, + { + "id": "t37", + "source": "RNA_Polymerase_II-dependent_Transcription__phenotype", + "target": "P-TEFb_complex", + "sign": true + }, + { + "id": "t38", + "source": "P-TEFb_complex", + "target": "CDK9", + "sign": true + }, + { + "id": "t40", + "source": "P-TEFb_complex", + "target": "CCNT1", + "sign": true + }, + { + "id": "t42", + "source": "BRD4", + "target": "E_nucleus", + "sign": false + }, + { + "id": "t43", + "source": "BRD2", + "target": "E_nucleus", + "sign": false + }, + { + "id": "t45", + "source": "BRD2", + "target": "JQ-1_simple_molecule", + "sign": false + }, + { + "id": "t46", + "source": "ASIC1", + "target": "H+_ion", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/HMOX1_Pathway.json b/scripts/covid19_diseasemaps/regnet_amr/HMOX1_Pathway.json new file mode 100644 index 000000000..fc57d8a21 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/HMOX1_Pathway.json @@ -0,0 +1,2600 @@ +{ + "header": { + "name": "HMOX1_Pathway", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on HMOX1_Pathway", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "Nrf2/Maf_complex", + "name": "Nrf2/Maf_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMOX1_rna", + "name": "HMOX1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NRF2_phosphorylated_nucleus", + "name": "NRF2_phosphorylated_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC40A1_rna", + "name": "SLC40A1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FTH1_rna", + "name": "FTH1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FTL_rna", + "name": "FTL_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FECH_rna", + "name": "FECH_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BLVRA_rna", + "name": "BLVRA_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BLVRB_rna", + "name": "BLVRB_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAF", + "name": "MAF", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BACH1/Maf_complex", + "name": "BACH1/Maf_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BACH1", + "name": "BACH1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ubiquitin_Ligase_Complex_complex_cell", + "name": "Ubiquitin_Ligase_Complex_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "E2_ubiquitinated", + "name": "E2_ubiquitinated", + "grounding": { + "identifiers": {}, + "context": 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"identifiers": {}, + "context": {} + } + }, + { + "id": "SLC40A1:CP:Cu2+_complex", + "name": "SLC40A1:CP:Cu2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion_default_compartment", + "name": "Fe2+_ion_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe3+_ion_default_compartment", + "name": "Fe3+_ion_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_default_compartment", + "name": "H2O_simple_molecule_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CAND1", + "name": "CAND1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "holoTF_complex", + "name": "holoTF_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TFRC:holoTF_complex_cell", + "name": "TFRC:holoTF_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Transferrin", + "name": "Transferrin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TFRC:holoTF_complex_endosome", + "name": "TFRC:holoTF_complex_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TFRC", + "name": "TFRC", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TFRC:TF_complex_endosome", + "name": "TFRC:TF_complex_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe3+_ion_endosome", + "name": "Fe3+_ion_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TFRC:TF_complex_cell", + "name": "TFRC:TF_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXNIP:NLRP3_complex", + "name": "TXNIP:NLRP3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_cell_active", + "name": "NLRP3_cell_active", + "grounding": { 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"name": "Bilirubin_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXN_cell", + "name": "TXN_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Pyrin_trimer_complex", + "name": "Pyrin_trimer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PSTPIP1_trimer:Pyrin_trimer_complex", + "name": "PSTPIP1_trimer:Pyrin_trimer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pyrin_trimer:ASC_complex", + "name": "Pyrin_trimer:ASC_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PSTPIP1", + "name": "PSTPIP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_oligomer:ASC_complex", + "name": "NLRP3_oligomer:ASC_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_oligomer:ASC:Caspase1_complex", + "name": "NLRP3_oligomer:ASC:Caspase1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ASC", + "name": "ASC", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP1_cell", + "name": "CASP1_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTSG", + "name": "CTSG", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ferritin_complex", + "name": "Ferritin_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe(3+)O(OH)_simple_molecule", + "name": "Fe(3+)O(OH)_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Bilirubin_simple_molecule_default_compartment", + "name": "Bilirubin_simple_molecule_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ALB/BIL_complex", + "name": "ALB/BIL_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ALB", + "name": "ALB", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Caspase-1_Tetramer_complex", + "name": "Caspase-1_Tetramer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "proIL-1B_cell", + "name": "proIL-1B_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "proIL-18_cell", + "name": "proIL-18_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "IL-1B_cell", + "name": "IL-1B_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-18_cell", + "name": "IL-18_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP1(120-197):CASP1(317-404)_complex", + "name": "CASP1(120-197):CASP1(317-404)_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Heme_simple_molecule_cell", + "name": "Heme_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Biliverdin_simple_molecule", + "name": "Biliverdin_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_cell", + "name": "H2O_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion_cell", + "name": "Fe2+_ion_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "CO_simple_molecule", + "name": "CO_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Heme_simple_molecule_default_compartment", + "name": "Heme_simple_molecule_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP_simple_molecule", + "name": "ADP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pi_simple_molecule", + "name": "Pi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Heme_simple_molecule_mitochondrial_matrix", + "name": "Heme_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dALA_simple_molecule_mitochondrial_matrix", + "name": "dALA_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO2_simple_molecule_mitochondrial_matrix", + "name": "CO2_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CoA-SH_simple_molecule", + "name": "CoA-SH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FLVCR1-2", + "name": "FLVCR1-2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_simple_molecule_cell", + "name": "O2_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADPH_simple_molecule", + "name": "NADPH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMOX1_cell_active", + "name": "HMOX1_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRIN9_simple_molecule_mitochondrial_matrix", + "name": "PRIN9_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_mitochondrial_matrix", + "name": "H+_ion_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion_mitochondrial_matrix", + "name": "Fe2+_ion_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FECH", + "name": "FECH", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pb2+_ion", + "name": "Pb2+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMBL_simple_molecule", + "name": "HMBL_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NH4+_ion", + "name": "NH4+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dALA_simple_molecule_cell", + "name": "dALA_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PBG_simple_molecule", + "name": "PBG_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_cell", + "name": "H+_ion_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ALAD:Zn2+_complex", + "name": "ALAD:Zn2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BLVRB", + "name": "BLVRB", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Reactive_Oxygen_Species_simple_molecule", + "name": "Reactive_Oxygen_Species_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC11A2", + "name": "SLC11A2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion_endosome", + "name": "Fe2+_ion_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MCOLN1", + "name": "MCOLN1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMOX1_cell", + "name": "HMOX1_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ABCC1", + "name": "ABCC1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ORF9c", + "name": "ORF9c", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "miRNA-155_rna", + "name": "miRNA-155_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRIN9_simple_molecule_mitochondrion", + "name": "PRIN9_simple_molecule_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SUCC-CoA_simple_molecule", + "name": "SUCC-CoA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Gly_simple_molecule", + "name": "Gly_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ALAS1:ALAS2_complex", + "name": "ALAS1:ALAS2_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Panhematin_drug", + "name": "Panhematin_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "URO3_simple_molecule", + "name": "URO3_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMBS:DIPY_complex", + "name": "HMBS:DIPY_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPRO3_simple_molecule_cell", + "name": "COPRO3_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UROS", + "name": "UROS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPRO3_simple_molecule_mitochondrion", + "name": "COPRO3_simple_molecule_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UROD", + "name": "UROD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPGEN9_simple_molecule", + "name": "PPGEN9_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO2_simple_molecule_mitochondrion", + "name": "CO2_simple_molecule_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O2_simple_molecule", + "name": "H2O2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_simple_molecule_mitochondrion", + "name": "O2_simple_molecule_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CPOX", + "name": "CPOX", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPO:FAD_complex", + "name": "PPO:FAD_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Lipid_Peroxide_simple_molecule", + "name": "Lipid_Peroxide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ferroptosis_phenotype", + "name": "Ferroptosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Lipid_alcohol_simple_molecule", + "name": "Lipid_alcohol_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Poly-unsaturated_fatty_acid_simple_molecule", + "name": "Poly-unsaturated_fatty_acid_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC40A1:HEPH:Cu2+_complex", + "name": "SLC40A1:HEPH:Cu2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "e-_ion_default_compartment", + "name": "e-_ion_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CYBRD1:Heme_complex", + "name": "CYBRD1:Heme_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_simple_molecule_default_compartment", + "name": "O2_simple_molecule_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_default_compartment", + "name": "H+_ion_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GPX4", + "name": "GPX4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ORF3a", + "name": "ORF3a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PKC", + "name": "PKC", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CK2", + "name": "CK2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FLVCR1-1", + "name": "FLVCR1-1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule", + "name": "ATP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ABCG2", + "name": "ABCG2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "e-_ion_endosome", + "name": "e-_ion_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "STEAP3", + "name": "STEAP3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_rna", + "name": "NLRP3_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nf-KB_Complex_complex", + "name": "Nf-KB_Complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-1B_default_compartment", + "name": "IL-1B_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-18_default_compartment", + "name": "IL-18_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SARS_E", + "name": "SARS_E", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PAMPs_phenotype", + "name": "PAMPs_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DAMPs_phenotype", + "name": "DAMPs_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SARS_Orf3a", + "name": "SARS_Orf3a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_Elicitor_Small_Molecules_simple_molecule", + "name": "NLRP3_Elicitor_Small_Molecules_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_Elicitor_Proteins", + "name": "NLRP3_Elicitor_Proteins", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "HMOX1_rna", + "target": "Nrf2/Maf_complex", + "sign": true + }, + { + "id": "t2", + "source": "Nrf2/Maf_complex", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t3", + "source": "SLC40A1_rna", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t4", + "source": "FTH1_rna", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t5", + "source": "FTL_rna", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t6", + "source": "FECH_rna", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t7", + "source": "BLVRA_rna", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t8", + "source": "BLVRB_rna", + "target": "NRF2_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t9", + "source": "Nrf2/Maf_complex", + "target": "MAF", + "sign": true + }, + { + "id": "t10", + "source": "BACH1/Maf_complex", + "target": "MAF", + "sign": true + }, + { + "id": "t11", + "source": "HMOX1_rna", + "target": "BACH1/Maf_complex", + "sign": false + }, + { + "id": "t12", + "source": "BACH1/Maf_complex", + "target": "BACH1", + "sign": true + }, + { + "id": "t14", + "source": "Ubiquitin_Ligase_Complex_complex_cell", + "target": "E2_ubiquitinated", + "sign": true + }, + { + "id": "t15", + "source": "NRF2_ubiquitinated", + "target": "Ubiquitin_Ligase_Complex_complex_cell", + "sign": true + }, + { + "id": "t16", + "source": "Ubiquitin_Ligase_Complex_complex_cell", + "target": "NRF2:KEAP1_complex", + "sign": true + }, + { + "id": "t17", + "source": "NRF2:KEAP1_complex", + "target": "NRF2_empty", + "sign": true + }, + { + "id": "t18", + "source": "NRF2_phosphorylated_cell", + "target": "NRF2_empty", + "sign": true + }, + { + "id": "t19", + "source": "NRF2:KEAP1_complex", + "target": "KEAP1", + "sign": true + }, + { + "id": "t20", + "source": "NRF2:KEAP1_complex", + "target": "Dimethly_fumarate_drug", + "sign": false + }, + { + "id": "t21", + "source": "Ubiquitin_Ligase_Complex_complex_cell", + "target": "Neddylated_CUL3:RBX1_complex", + "sign": true + }, + { + "id": "t22", + "source": "Neddylated_CUL3:RBX1_complex", + "target": "CUL3:RBX1_complex", + "sign": true + }, + { + "id": "t23", + "source": "Fe2+_ion_default_compartment", + "target": "SLC40A1:CP:Cu2+_complex", + "sign": true + }, + { + "id": "t24", + "source": "Fe3+_ion_default_compartment", + "target": "SLC40A1:CP:Cu2+_complex", + "sign": true + }, + { + "id": "t25", + "source": "H2O_simple_molecule_default_compartment", + "target": "SLC40A1:CP:Cu2+_complex", + "sign": true + }, + { + "id": "t26", + "source": "SLC40A1:CP:Cu2+_complex", + "target": "SLC40A1_rna", + "sign": true + }, + { + "id": "t27", + "source": "Ubiquitin_Ligase_Complex_complex_cell", + "target": "CAND1", + "sign": false + }, + { + "id": "t28", + "source": "TFRC:holoTF_complex_cell", + "target": "holoTF_complex", + "sign": true + }, + { + "id": "t29", + "source": "holoTF_complex", + "target": "Fe3+_ion_default_compartment", + "sign": true + }, + { + "id": "t30", + "source": "Fe2+_ion_default_compartment", + "target": "Fe3+_ion_default_compartment", + "sign": true + }, + { + "id": "t31", + "source": "holoTF_complex", + "target": "Transferrin", + "sign": true + }, + { + "id": "t32", + "source": "TFRC:holoTF_complex_endosome", + "target": "TFRC:holoTF_complex_cell", + "sign": true + }, + { + "id": "t33", + "source": "TFRC:holoTF_complex_cell", + "target": "TFRC", + "sign": true + }, + { + "id": "t34", + "source": "TFRC:TF_complex_endosome", + "target": "TFRC:holoTF_complex_endosome", + "sign": true + }, + { + "id": "t35", + "source": "Fe3+_ion_endosome", + "target": "TFRC:holoTF_complex_endosome", + "sign": true + }, + { + "id": "t36", + "source": "TFRC:TF_complex_cell", + "target": "TFRC:TF_complex_endosome", + "sign": true + }, + { + "id": "t37", + "source": "Transferrin", + "target": "TFRC:TF_complex_cell", + "sign": true + }, + { + "id": "t38", + "source": "TFRC", + "target": "TFRC:TF_complex_cell", + "sign": true + }, + { + "id": "t39", + "source": "NLRP3_cell_active", + "target": "TXNIP:NLRP3_complex", + "sign": true + }, + { + "id": "t40", + "source": "TXNIP:NLRP3_complex", + "target": "NLRP3_cell", + "sign": true + }, + { + "id": "t41", + "source": "NLRP3:SUGT1:HSP90_complex", + "target": "NLRP3_cell", + "sign": true + }, + { + "id": "t42", + "source": "NLRP3_cell_active", + "target": "NLRP3_cell", + "sign": true + }, + { + "id": "t43", + "source": "TXNIP:NLRP3_complex", + "target": "TXNIP", + "sign": true + }, + { + "id": "t44", + "source": "Thioredoxin:TXNIP_complex", + "target": "TXNIP", + "sign": true + }, + { + "id": "t45", + "source": "SUGT1:HSP90AB1_complex", + "target": "NLRP3:SUGT1:HSP90_complex", + "sign": true + }, + { + "id": "t46", + "source": "NLRP3_cell", + "target": "NLRP3:SUGT1:HSP90_complex", + "sign": true + }, + { + "id": "t47", + "source": "NLRP3:SUGT1:HSP90_complex", + "target": "SUGT1:HSP90AB1_complex", + "sign": true + }, + { + "id": "t48", + "source": "NADP+_simple_molecule", + "target": "BLVRA:Zn2+_complex", + "sign": true + }, + { + "id": "t49", + "source": "Bilirubin_simple_molecule_cell", + "target": "BLVRA:Zn2+_complex", + "sign": true + }, + { + "id": "t50", + "source": "BLVRA:Zn2+_complex", + "target": "BLVRA_rna", + "sign": true + }, + { + "id": "t51", + "source": "TXNIP", + "target": "Thioredoxin:TXNIP_complex", + "sign": true + }, + { + "id": "t52", + "source": "TXN_cell", + "target": "Thioredoxin:TXNIP_complex", + "sign": true + }, + { + "id": "t53", + "source": "Thioredoxin:TXNIP_complex", + "target": "TXN_cell", + "sign": true + }, + { + "id": "t55", + "source": "PSTPIP1_trimer:Pyrin_trimer_complex", + "target": "Pyrin_trimer_complex", + "sign": true + }, + { + "id": "t56", + "source": "Pyrin_trimer:ASC_complex", + "target": "Pyrin_trimer_complex", + "sign": true + }, + { + "id": "t57", + "source": "PSTPIP1_trimer:Pyrin_trimer_complex", + "target": "PSTPIP1", + "sign": true + }, + { + "id": "t58", + "source": "NLRP3_oligomer:ASC:Caspase1_complex", + "target": "NLRP3_oligomer:ASC_complex", + "sign": true + }, + { + "id": "t59", + "source": "NLRP3_oligomer:ASC_complex", + "target": "NLRP3_cell_active", + "sign": true + }, + { + "id": "t60", + "source": "NLRP3_oligomer:ASC_complex", + "target": "ASC", + "sign": true + }, + { + "id": "t61", + "source": "Pyrin_trimer:ASC_complex", + "target": "ASC", + "sign": true + }, + { + "id": "t62", + "source": "NLRP3_oligomer:ASC_complex", + "target": "NLRP3_oligomer:ASC:Caspase1_complex", + "sign": true + }, + { + "id": "t63", + "source": "CASP1_cell", + "target": "NLRP3_oligomer:ASC:Caspase1_complex", + "sign": true + }, + { + "id": "t64", + "source": "NLRP3_oligomer:ASC_complex", + "target": "CTSG", + "sign": true + }, + { + "id": "t65", + "source": "CASP1_cell", + "target": "CTSG", + "sign": true + }, + { + "id": "t66", + "source": "NLRP3_oligomer:ASC:Caspase1_complex", + "target": "CASP1_cell", + "sign": true + }, + { + "id": "t67", + "source": "Fe(3+)O(OH)_simple_molecule", + "target": "Ferritin_complex", + "sign": true + }, + { + "id": "t68", + "source": "Ferritin_complex", + "target": "FTH1_rna", + "sign": true + }, + { + "id": "t69", + "source": "Ferritin_complex", + "target": "FTL_rna", + "sign": true + }, + { + "id": "t70", + "source": "ALB/BIL_complex", + "target": "Bilirubin_simple_molecule_default_compartment", + "sign": true + }, + { + "id": "t71", + "source": "ALB/BIL_complex", + "target": "ALB", + "sign": true + }, + { + "id": "t72", + "source": "proIL-1B_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t73", + "source": "proIL-18_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t74", + "source": "IL-1B_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t75", + "source": "IL-18_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t76", + "source": "Caspase-1_Tetramer_complex", + "target": "CASP1(120-197):CASP1(317-404)_complex", + "sign": true + }, + { + "id": "t77", + "source": "CASP1(120-197):CASP1(317-404)_complex", + "target": "CASP1_cell", + "sign": true + }, + { + "id": "t78", + "source": "Biliverdin_simple_molecule", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t79", + "source": "H2O_simple_molecule_cell", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t80", + "source": "NADP+_simple_molecule", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t81", + "source": "Fe2+_ion_cell", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t82", + "source": "CO_simple_molecule", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t83", + "source": "Heme_simple_molecule_default_compartment", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t84", + "source": "ADP_simple_molecule", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t85", + "source": "Pi_simple_molecule", + "target": "Heme_simple_molecule_cell", + "sign": true + }, + { + "id": "t86", + "source": "Heme_simple_molecule_cell", + "target": "Heme_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t87", + "source": "dALA_simple_molecule_mitochondrial_matrix", + "target": "Heme_simple_molecule_mitochondrial_matrix", + "sign": false + }, + { + "id": "t88", + "source": "CO2_simple_molecule_mitochondrial_matrix", + "target": "Heme_simple_molecule_mitochondrial_matrix", + "sign": false + }, + { + "id": "t89", + "source": "CoA-SH_simple_molecule", + "target": "Heme_simple_molecule_mitochondrial_matrix", + "sign": false + }, + { + "id": "t90", + "source": "Heme_simple_molecule_cell", + "target": "FLVCR1-2", + "sign": true + }, + { + "id": "t91", + "source": "NADP+_simple_molecule", + "target": "Biliverdin_simple_molecule", + "sign": true + }, + { + "id": "t92", + "source": "Bilirubin_simple_molecule_cell", + "target": "Biliverdin_simple_molecule", + "sign": true + }, + { + "id": "t93", + "source": "Biliverdin_simple_molecule", + "target": "O2_simple_molecule_cell", + "sign": true + }, + { + "id": "t94", + "source": "H2O_simple_molecule_cell", + "target": "O2_simple_molecule_cell", + "sign": true + }, + { + "id": "t95", + "source": "NADP+_simple_molecule", + "target": "O2_simple_molecule_cell", + "sign": true + }, + { + "id": "t96", + "source": "Fe2+_ion_cell", + "target": "O2_simple_molecule_cell", + "sign": true + }, + { + "id": "t97", + "source": "CO_simple_molecule", + "target": "O2_simple_molecule_cell", + "sign": true + }, + { + "id": "t98", + "source": "Fe(3+)O(OH)_simple_molecule", + "target": "O2_simple_molecule_cell", + "sign": true + }, + { + "id": "t99", + "source": "Biliverdin_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t100", + "source": "H2O_simple_molecule_cell", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t101", + "source": "NADP+_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t102", + "source": "Fe2+_ion_cell", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t103", + "source": "CO_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t104", + "source": "Bilirubin_simple_molecule_cell", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t105", + "source": "Biliverdin_simple_molecule", + "target": "HMOX1_cell_active", + "sign": true + }, + { + "id": "t106", + "source": "H2O_simple_molecule_cell", + "target": "HMOX1_cell_active", + "sign": true + }, + { + "id": "t107", + "source": "NADP+_simple_molecule", + "target": "HMOX1_cell_active", + "sign": true + }, + { + "id": "t108", + "source": "Fe2+_ion_cell", + "target": "HMOX1_cell_active", + "sign": true + }, + { + "id": "t109", + "source": "CO_simple_molecule", + "target": "HMOX1_cell_active", + "sign": true + }, + { + "id": "t110", + "source": "Heme_simple_molecule_mitochondrial_matrix", + "target": "PRIN9_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t111", + "source": "H+_ion_mitochondrial_matrix", + "target": "PRIN9_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t112", + "source": "Heme_simple_molecule_mitochondrial_matrix", + "target": "Fe2+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t113", + "source": "H+_ion_mitochondrial_matrix", + "target": "Fe2+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t114", + "source": "Heme_simple_molecule_mitochondrial_matrix", + "target": "FECH", + "sign": true + }, + { + "id": "t115", + "source": "H+_ion_mitochondrial_matrix", + "target": "FECH", + "sign": true + }, + { + "id": "t116", + "source": "Heme_simple_molecule_mitochondrial_matrix", + "target": "Pb2+_ion", + "sign": false + }, + { + "id": "t117", + "source": "H+_ion_mitochondrial_matrix", + "target": "Pb2+_ion", + "sign": false + }, + { + "id": "t118", + "source": "HMBL_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t119", + "source": "NH4+_ion", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t120", + "source": "Heme_simple_molecule_default_compartment", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t121", + "source": "ADP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t122", + "source": "Pi_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t123", + "source": "H2O_simple_molecule_cell", + "target": "dALA_simple_molecule_cell", + "sign": true + }, + { + "id": "t124", + "source": "PBG_simple_molecule", + "target": "dALA_simple_molecule_cell", + "sign": true + }, + { + "id": "t125", + "source": "H+_ion_cell", + "target": "dALA_simple_molecule_cell", + "sign": true + }, + { + "id": "t126", + "source": "H2O_simple_molecule_cell", + "target": "ALAD:Zn2+_complex", + "sign": true + }, + { + "id": "t127", + "source": "PBG_simple_molecule", + "target": "ALAD:Zn2+_complex", + "sign": true + }, + { + "id": "t128", + "source": "H+_ion_cell", + "target": "ALAD:Zn2+_complex", + "sign": true + }, + { + "id": "t129", + "source": "NADP+_simple_molecule", + "target": "BLVRB", + "sign": true + }, + { + "id": "t130", + "source": "Bilirubin_simple_molecule_cell", + "target": "BLVRB", + "sign": true + }, + { + "id": "t132", + "source": "Fe2+_ion_default_compartment", + "target": "Fe2+_ion_cell", + "sign": true + }, + { + "id": "t133", + "source": "Fe(3+)O(OH)_simple_molecule", + "target": "Fe2+_ion_cell", + "sign": true + }, + { + "id": "t134", + "source": "Reactive_Oxygen_Species_simple_molecule", + "target": "Fe2+_ion_cell", + "sign": true + }, + { + "id": "t135", + "source": "Fe2+_ion_cell", + "target": "Fe2+_ion_default_compartment", + "sign": true + }, + { + "id": "t136", + "source": "Fe3+_ion_default_compartment", + "target": "Fe2+_ion_default_compartment", + "sign": true + }, + { + "id": "t137", + "source": "H2O_simple_molecule_default_compartment", + "target": "Fe2+_ion_default_compartment", + "sign": true + }, + { + "id": "t138", + "source": "Fe2+_ion_cell", + "target": "SLC11A2", + "sign": true + }, + { + "id": "t139", + "source": "Fe2+_ion_cell", + "target": "Fe2+_ion_endosome", + "sign": true + }, + { + "id": "t140", + "source": "Fe2+_ion_cell", + "target": "MCOLN1", + "sign": true + }, + { + "id": "t141", + "source": "HMOX1_cell_active", + "target": "HMOX1_cell", + "sign": true + }, + { + "id": "t142", + "source": "HMOX1_cell", + "target": "HMOX1_rna", + "sign": true + }, + { + "id": "t143", + "source": "Reactive_Oxygen_Species_simple_molecule", + "target": "CO_simple_molecule", + "sign": false + }, + { + "id": "t144", + "source": "Bilirubin_simple_molecule_default_compartment", + "target": "Bilirubin_simple_molecule_cell", + "sign": true + }, + { + "id": "t145", + "source": "BLVRB", + "target": "BLVRB_rna", + "sign": true + }, + { + "id": "t146", + "source": "Bilirubin_simple_molecule_default_compartment", + "target": "ABCC1", + "sign": true + }, + { + "id": "t147", + "source": "ABCC1", + "target": "ORF9c", + "sign": true + }, + { + "id": "t148", + "source": "NRF2_phosphorylated_nucleus", + "target": "NRF2_phosphorylated_cell", + "sign": true + }, + { + "id": "t149", + "source": "BACH1", + "target": "miRNA-155_rna", + "sign": false + }, + { + "id": "t150", + "source": "FECH", + "target": "FECH_rna", + "sign": true + }, + { + "id": "t151", + "source": "PRIN9_simple_molecule_mitochondrial_matrix", + "target": "PRIN9_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t152", + "source": "dALA_simple_molecule_mitochondrial_matrix", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t153", + "source": "CO2_simple_molecule_mitochondrial_matrix", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t154", + "source": "CoA-SH_simple_molecule", + "target": "H+_ion_mitochondrial_matrix", + "sign": true + }, + { + "id": "t155", + "source": "dALA_simple_molecule_cell", + "target": "dALA_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t156", + "source": "dALA_simple_molecule_mitochondrial_matrix", + "target": "SUCC-CoA_simple_molecule", + "sign": true + }, + { + "id": "t157", + "source": "CO2_simple_molecule_mitochondrial_matrix", + "target": "SUCC-CoA_simple_molecule", + "sign": true + }, + { + "id": "t158", + "source": "CoA-SH_simple_molecule", + "target": "SUCC-CoA_simple_molecule", + "sign": true + }, + { + "id": "t159", + "source": "dALA_simple_molecule_mitochondrial_matrix", + "target": "Gly_simple_molecule", + "sign": true + }, + { + "id": "t160", + "source": "CO2_simple_molecule_mitochondrial_matrix", + "target": "Gly_simple_molecule", + "sign": true + }, + { + "id": "t161", + "source": "CoA-SH_simple_molecule", + "target": "Gly_simple_molecule", + "sign": true + }, + { + "id": "t162", + "source": "dALA_simple_molecule_mitochondrial_matrix", + "target": "ALAS1:ALAS2_complex", + "sign": true + }, + { + "id": "t163", + "source": "CO2_simple_molecule_mitochondrial_matrix", + "target": "ALAS1:ALAS2_complex", + "sign": true + }, + { + "id": "t164", + "source": "CoA-SH_simple_molecule", + "target": "ALAS1:ALAS2_complex", + "sign": true + }, + { + "id": "t165", + "source": "dALA_simple_molecule_mitochondrial_matrix", + "target": "Panhematin_drug", + "sign": false + }, + { + "id": "t166", + "source": "CO2_simple_molecule_mitochondrial_matrix", + "target": "Panhematin_drug", + "sign": false + }, + { + "id": "t167", + "source": "CoA-SH_simple_molecule", + "target": "Panhematin_drug", + "sign": false + }, + { + "id": "t168", + "source": "HMBL_simple_molecule", + "target": "PBG_simple_molecule", + "sign": true + }, + { + "id": "t169", + "source": "NH4+_ion", + "target": "PBG_simple_molecule", + "sign": true + }, + { + "id": "t170", + "source": "Fe(3+)O(OH)_simple_molecule", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t171", + "source": "URO3_simple_molecule", + "target": "HMBL_simple_molecule", + "sign": true + }, + { + "id": "t172", + "source": "HMBL_simple_molecule", + "target": "HMBS:DIPY_complex", + "sign": true + }, + { + "id": "t173", + "source": "NH4+_ion", + "target": "HMBS:DIPY_complex", + "sign": true + }, + { + "id": "t174", + "source": "COPRO3_simple_molecule_cell", + "target": "URO3_simple_molecule", + "sign": true + }, + { + "id": "t175", + "source": "URO3_simple_molecule", + "target": "UROS", + "sign": true + }, + { + "id": "t176", + "source": "COPRO3_simple_molecule_mitochondrion", + "target": "COPRO3_simple_molecule_cell", + "sign": true + }, + { + "id": "t177", + "source": "COPRO3_simple_molecule_cell", + "target": "UROD", + "sign": true + }, + { + "id": "t178", + "source": "PPGEN9_simple_molecule", + "target": "COPRO3_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t179", + "source": "CO2_simple_molecule_mitochondrion", + "target": "COPRO3_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t180", + "source": "H2O2_simple_molecule", + "target": "COPRO3_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t181", + "source": "PRIN9_simple_molecule_mitochondrion", + "target": "PPGEN9_simple_molecule", + "sign": true + }, + { + "id": "t182", + "source": "H2O2_simple_molecule", + "target": "PPGEN9_simple_molecule", + "sign": true + }, + { + "id": "t183", + "source": "PPGEN9_simple_molecule", + "target": "O2_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t184", + "source": "PRIN9_simple_molecule_mitochondrion", + "target": "O2_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t185", + "source": "CO2_simple_molecule_mitochondrion", + "target": "O2_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t186", + "source": "H2O2_simple_molecule", + "target": "O2_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t187", + "source": "PPGEN9_simple_molecule", + "target": "CPOX", + "sign": true + }, + { + "id": "t188", + "source": "CO2_simple_molecule_mitochondrion", + "target": "CPOX", + "sign": true + }, + { + "id": "t189", + "source": "H2O2_simple_molecule", + "target": "CPOX", + "sign": true + }, + { + "id": "t190", + "source": "PRIN9_simple_molecule_mitochondrion", + "target": "PPO:FAD_complex", + "sign": true + }, + { + "id": "t191", + "source": "H2O2_simple_molecule", + "target": "PPO:FAD_complex", + "sign": true + }, + { + "id": "t192", + "source": "Ferroptosis_phenotype", + "target": "Lipid_Peroxide_simple_molecule", + "sign": true + }, + { + "id": "t193", + "source": "Lipid_alcohol_simple_molecule", + "target": "Lipid_Peroxide_simple_molecule", + "sign": true + }, + { + "id": "t194", + "source": "Lipid_Peroxide_simple_molecule", + "target": "Poly-unsaturated_fatty_acid_simple_molecule", + "sign": true + }, + { + "id": "t195", + "source": "Lipid_Peroxide_simple_molecule", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t196", + "source": "TXNIP", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t197", + "source": "TXN_cell", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t198", + "source": "NLRP3_cell_active", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t199", + "source": "Fe2+_ion_default_compartment", + "target": "SLC40A1:HEPH:Cu2+_complex", + "sign": true + }, + { + "id": "t200", + "source": "Fe3+_ion_default_compartment", + "target": "SLC40A1:HEPH:Cu2+_complex", + "sign": true + }, + { + "id": "t201", + "source": "H2O_simple_molecule_default_compartment", + "target": "SLC40A1:HEPH:Cu2+_complex", + "sign": true + }, + { + "id": "t202", + "source": "Fe2+_ion_default_compartment", + "target": "e-_ion_default_compartment", + "sign": true + }, + { + "id": "t203", + "source": "Fe2+_ion_default_compartment", + "target": "CYBRD1:Heme_complex", + "sign": true + }, + { + "id": "t204", + "source": "Fe3+_ion_default_compartment", + "target": "O2_simple_molecule_default_compartment", + "sign": true + }, + { + "id": "t205", + "source": "H2O_simple_molecule_default_compartment", + "target": "O2_simple_molecule_default_compartment", + "sign": true + }, + { + "id": "t206", + "source": "Fe3+_ion_default_compartment", + "target": "H+_ion_default_compartment", + "sign": true + }, + { + "id": "t207", + "source": "H2O_simple_molecule_default_compartment", + "target": "H+_ion_default_compartment", + "sign": true + }, + { + "id": "t208", + "source": "Lipid_alcohol_simple_molecule", + "target": "GPX4", + "sign": true + }, + { + "id": "t209", + "source": "HMOX1_cell_active", + "target": "ORF3a", + "sign": true + }, + { + "id": "t210", + "source": "NRF2_phosphorylated_cell", + "target": "PKC", + "sign": true + }, + { + "id": "t211", + "source": "NRF2_phosphorylated_cell", + "target": "CK2", + "sign": true + }, + { + "id": "t212", + "source": "Heme_simple_molecule_default_compartment", + "target": "FLVCR1-1", + "sign": true + }, + { + 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"https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on IFN-lambda", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "receptor_complex_complex_cell", + "name": "receptor_complex_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Ifn_lambda_complex", + "name": "Ifn_lambda_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "STAT1_phosphorylated", + "name": "STAT1_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "STAT2_phosphorylated", + "name": "STAT2_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ISGF3_complex", + "name": "ISGF3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ISGs_rna", + "name": 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000000000..334375e56 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Interferon1.json @@ -0,0 +1,2101 @@ +{ + "header": { + "name": "Interferon1", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Interferon1", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "IFNA1_IFNAR_complex", + "name": "IFNA1_IFNAR_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "JAK1_TYK2_complex", + "name": "JAK1_TYK2_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNAR_complex", + "name": "IFNAR_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNB1_IFNAR_complex", + "name": "IFNB1_IFNAR_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNA1_extracellular_space", + "name": "IFNA1_extracellular_space", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Viral_dsRNA_rna_cell", + "name": "Viral_dsRNA_rna_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "type_I_IFN_response_phenotype", + "name": "type_I_IFN_response_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TLR4_TRIF_TRAM_complex", + "name": "TLR4_TRIF_TRAM_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAP1", + "name": "NAP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IRAK1/4", + "name": "IRAK1/4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MYD88_TRAM_complex", + "name": "MYD88_TRAM_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIF", + "name": "TRIF", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": 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{ + "identifiers": {}, + "context": {} + } + }, + { + "id": "ISG15_rna", + "name": "ISG15_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "JAK1", + "name": "JAK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TYK2", + "name": "TYK2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP-1_complex_cell", + "name": "AP-1_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP-1_complex_nucleus", + "name": "AP-1_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "JUN", + "name": "JUN", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FOS", + "name": "FOS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E", + "name": "E", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_inflammasome_complex", + "name": "NLRP3_inflammasome_complex", + 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"identifiers": {}, + "context": {} + } + }, + { + "id": "TLR9", + "name": "TLR9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Viral_dsRNA_rna_endosome", + "name": "Viral_dsRNA_rna_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRAF3_TANK_TBK1_IKKepsilon_complex", + "name": "TRAF3_TANK_TBK1_IKKepsilon_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IRF7_phosphorylated", + "name": "IRF7_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRAF3_TBK1_IKBKE_complex_cell_active", + "name": "TRAF3_TBK1_IKBKE_complex_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TANK", + "name": "TANK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TLR3_TRIF_RIPK1_complex", + "name": "TLR3_TRIF_RIPK1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": 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"grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Proinflammatory_cytokine_expression_Inflammation_phenotype", + "name": "Proinflammatory_cytokine_expression_Inflammation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNA1_rna", + "name": "IFNA1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MNS_drug", + "name": "MNS_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK14", + "name": "MAPK14", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAPK8", + "name": "MAPK8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAP3K7", + "name": "MAP3K7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TAB1/2_TRAF6_TAK1_complex", + "name": "TAB1/2_TRAF6_TAK1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RIP1", + "name": "RIP1", + "grounding": { 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"id": "IkB", + "name": "IkB", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IRF3_homodimer_complex_cell", + "name": "IRF3_homodimer_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IRF7_homodimer_complex", + "name": "IRF7_homodimer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ISG15", + "name": "ISG15", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GRL0617_drug", + "name": "GRL0617_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNB1_cell", + "name": "IFNB1_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNA1_cell", + "name": "IFNA1_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "OAS1_cell", + "name": "OAS1_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ITCH", + "name": "ITCH", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp13", + "name": "Nsp13", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp1", + "name": "Nsp1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7b", + "name": "Orf7b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a", + "name": "Orf3a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6", + "name": "Nsp6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a", + "name": "Orf7a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "OAS2_cell", + "name": "OAS2_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "OAS3_cell", + "name": "OAS3_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf8_complex", + "name": "Orf8_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b", + "name": "Orf9b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIM25", + "name": "TRIM25", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RNF135", + "name": "RNF135", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Viral_replication_phenotype", + "name": "Viral_replication_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "JAK1_TYK2_complex", + "target": "IFNA1_IFNAR_complex", + "sign": true + }, + { + "id": "t2", + "source": "IFNA1_IFNAR_complex", + "target": "IFNAR_complex", + "sign": true + }, + { + "id": "t3", + "source": "IFNB1_IFNAR_complex", + "target": "IFNAR_complex", + "sign": true + }, + { + "id": "t4", + "source": "IFNA1_IFNAR_complex", + "target": "IFNA1_extracellular_space", + "sign": true + }, + { + "id": "t5", + "source": "Viral_dsRNA_rna_cell", + "target": "IFNA1_extracellular_space", + "sign": false + }, + { + "id": "t6", + "source": "type_I_IFN_response_phenotype", + "target": "IFNA1_extracellular_space", + "sign": true + }, + { + "id": "t7", + "source": "NAP1", + "target": "TLR4_TRIF_TRAM_complex", + "sign": true + }, + { + "id": "t8", + "source": "TLR4_TRIF_TRAM_complex", + "target": "IRAK1/4", + "sign": true + }, + { + "id": "t9", + "source": "MYD88_TRAM_complex", + "target": "IRAK1/4", + "sign": true + }, + { + "id": "t10", + "source": "TLR4_TRIF_TRAM_complex", + "target": "TRIF", + "sign": true + }, + { + "id": "t11", + "source": "TLR3_TRIF_complex", + "target": "TRIF", + "sign": true + }, + { + "id": "t12", + "source": "JAK1_TYK2_complex", + "target": "IFNB1_IFNAR_complex", + "sign": true + }, + { + "id": "t13", + "source": "IFNB1_IFNAR_complex", + "target": "IFNB1_extracellular_space", + "sign": true + }, + { + "id": "t14", + "source": "Viral_dsRNA_rna_cell", + "target": "IFNB1_extracellular_space", + "sign": false + }, + { + "id": "t15", + "source": "type_I_IFN_response_phenotype", + "target": "IFNB1_extracellular_space", + "sign": true + }, + { + "id": "t16", + "source": "ISRE_complex", + "target": "STAT1/2_IRF9_complex", + "sign": true + }, + { + "id": "t17", + "source": "STAT1/2_IRF9_complex", + "target": "STAT1_phosphorylated", + "sign": true + }, + { + "id": "t18", + "source": "STAT1/2_IRF9_complex", + "target": "IRF9", + "sign": true + }, + { + "id": "t19", + "source": "STAT1/2_IRF9_complex", + "target": "STAT2_phosphorylated", + "sign": true + }, + { + "id": "t20", + "source": "STAT1/2_IRF9_complex", + "target": "Orf6", + "sign": false + }, + { + "id": "t21", + "source": "ISRE_complex", + "target": "Orf6", + "sign": false + }, + { + "id": "t22", + "source": "IRF3_homodimer_complex_nucleus", + "target": "Orf6", + "sign": false + }, + { + "id": "t23", + "source": "IRF3_phosphorylated", + "target": "Orf6", + "sign": false + }, + { + "id": "t24", + "source": "STAT1/2_IRF9_complex", + "target": "TREML4", + "sign": true + }, + { 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"target": "TYK2", + "sign": true + }, + { + "id": "t36", + "source": "AP-1_complex_nucleus", + "target": "AP-1_complex_cell", + "sign": true + }, + { + "id": "t37", + "source": "AP-1_complex_cell", + "target": "JUN", + "sign": true + }, + { + "id": "t38", + "source": "AP-1_complex_cell", + "target": "FOS", + "sign": true + }, + { + "id": "t39", + "source": "AP-1_complex_cell", + "target": "E", + "sign": true + }, + { + "id": "t40", + "source": "NLRP3_inflammasome_complex", + "target": "E", + "sign": true + }, + { + "id": "t41", + "source": "AP-1_complex_cell", + "target": "MAPK8/14_complex", + "sign": true + }, + { + "id": "t42", + "source": "p50_p65_complex_nucleus", + "target": "p50_p65_complex_cell", + "sign": true + }, + { + "id": "t43", + "source": "p50_p65_complex_cell", + "target": "IkB_p50_p65_complex_cell", + "sign": true + }, + { + "id": "t44", + "source": "IkB_phosphorylated", + "target": "IkB_p50_p65_complex_cell", + "sign": true + }, + { + "id": "t45", + "source": 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"id": "t55", + "source": "TBK1", + "target": "IKBKE", + "sign": true + }, + { + "id": "t56", + "source": "TBK1_IKBKE_complex", + "target": "TRAF3", + "sign": true + }, + { + "id": "t57", + "source": "TRAF3_TBK1_IKBKE_complex_cell", + "target": "TRAF3", + "sign": true + }, + { + "id": "t58", + "source": "TBK1_IKBKE_complex", + "target": "Nsp3", + "sign": false + }, + { + "id": "t59", + "source": "ISG15_Nsp3_complex", + "target": "Nsp3", + "sign": true + }, + { + "id": "t60", + "source": "TRAF6_ubiquitinated", + "target": "Nsp3", + "sign": false + }, + { + "id": "t61", + "source": "ISG_expression_antiviral_response_phenotype", + "target": "Nsp3", + "sign": false + }, + { + "id": "t62", + "source": "TRAF3", + "target": "Nsp3", + "sign": false + }, + { + "id": "t63", + "source": "IKBKE", + "target": "Nsp3", + "sign": false + }, + { + "id": "t64", + "source": "IRF3_phosphorylated", + "target": "Nsp3", + "sign": false + }, + { + "id": "t65", + "source": "TBK1_IKBKE_complex", + "target": 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"id": "t115", + "source": "IRF3_phosphorylated", + "target": "Nsp15", + "sign": false + }, + { + "id": "t116", + "source": "IFIH1", + "target": "Nsp15", + "sign": false + }, + { + "id": "t117", + "source": "Proinflammatory_cytokine_expression_Inflammation_phenotype", + "target": "NLRP3_inflammasome_complex", + "sign": true + }, + { + "id": "t118", + "source": "NLRP3_inflammasome_complex", + "target": "p50_p65_complex_nucleus", + "sign": true + }, + { + "id": "t119", + "source": "IFNB1_rna", + "target": "p50_p65_complex_nucleus", + "sign": true + }, + { + "id": "t120", + "source": "IFNA1_rna", + "target": "p50_p65_complex_nucleus", + "sign": true + }, + { + "id": "t121", + "source": "ISG_expression_antiviral_response_phenotype", + "target": "p50_p65_complex_nucleus", + "sign": true + }, + { + "id": "t122", + "source": "Proinflammatory_cytokine_expression_Inflammation_phenotype", + "target": "p50_p65_complex_nucleus", + "sign": true + }, + { + "id": "t123", + "source": 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a/scripts/covid19_diseasemaps/regnet_amr/JNK_pathway.json b/scripts/covid19_diseasemaps/regnet_amr/JNK_pathway.json new file mode 100644 index 000000000..e27f9e5ff --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/JNK_pathway.json @@ -0,0 +1,304 @@ +{ + "header": { + "name": "JNK_pathway", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on JNK_pathway", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "JNK_complex_cell", + "name": "JNK_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "AP-1_complex", + "name": "AP-1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCL2_phosphorylated", + "name": "BCL2_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": 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"source": "BCL2_phosphorylated", + "target": "JNK_complex_cell", + "sign": true + }, + { + "id": "t3", + "source": "ATF2_phosphorylated", + "target": "JNK_complex_cell", + "sign": true + }, + { + "id": "t4", + "source": "TP53_phosphorylated", + "target": "JNK_complex_cell", + "sign": true + }, + { + "id": "t6", + "source": "JNK_complex_cell", + "target": "MAP2K4_phosphorylated", + "sign": true + }, + { + "id": "t7", + "source": "JNK_complex_cell", + "target": "MAP2K7_phosphorylated", + "sign": true + }, + { + "id": "t8", + "source": "JNK_complex_cell", + "target": "7a", + "sign": true + }, + { + "id": "t9", + "source": "JNK_complex_cell", + "target": "3a", + "sign": true + }, + { + "id": "t10", + "source": "JNK_complex_cell", + "target": "S", + "sign": true + }, + { + "id": "t11", + "source": "MAP2K7_phosphorylated", + "target": "MLK1/2/3_complex", + "sign": true + }, + { + "id": "t12", + "source": "MLK1/2/3_complex", + "target": "SARS-CoV-1_proteins_complex", + "sign": true + }, + { + "id": "t13", + "source": "MEKK1/4_complex", + "target": "SARS-CoV-1_proteins_complex", + "sign": true + }, + { + "id": "t14", + "source": "MAP2K4_phosphorylated", + "target": "SARS-CoV-1_proteins_complex", + "sign": true + }, + { + "id": "t15", + "source": "MAP2K7_phosphorylated", + "target": "SARS-CoV-1_proteins_complex", + "sign": true + }, + { + "id": "t16", + "source": "Innate_Immunity_phenotype", + "target": "AP-1_complex", + "sign": true + }, + { + "id": "t17", + "source": "AP-1_complex", + "target": "3b", + "sign": true + }, + { + "id": "t18", + "source": "MAP2K4_phosphorylated", + "target": "MEKK1/4_complex", + "sign": true + }, + { + "id": "t19", + "source": "Apoptosis_phenotype", + "target": "BCL2_phosphorylated", + "sign": false + }, + { + "id": "t20", + "source": "Autophagy_phenotype", + "target": "BCL2_phosphorylated", + "sign": true + }, + { + "id": "t21", + "source": "TP53_signalling_phenotype", + "target": "TP53_phosphorylated", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Kynurenine_pathway.json b/scripts/covid19_diseasemaps/regnet_amr/Kynurenine_pathway.json new file mode 100644 index 000000000..85e7bcb07 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Kynurenine_pathway.json @@ -0,0 +1,3050 @@ +{ + "header": { + "name": "Kynurenine_pathway", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Kynurenine_pathway", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "AHR/L-KYN_complex", + "name": "AHR/L-KYN_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Regulatory_T-cell_generation_phenotype", + "name": "Regulatory_T-cell_generation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Kynurenine_simple_molecule", + "name": "L-Kynurenine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_cell", + "name": "H2O_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP-DOBu_simple_molecule", + "name": "AP-DOBu_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADP+_simple_molecule_cell", + "name": "NADP+_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Ala_simple_molecule", + "name": "L-Ala_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "3HKYN_simple_molecule", + "name": "3HKYN_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "T-cell_apoptosis_phenotype", + "name": "T-cell_apoptosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AHR", + "name": "AHR", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nf-KB_Complex_complex", + "name": "Nf-KB_Complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "iNOS_rna", + "name": "iNOS_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO_simple_molecule", + "name": "CO_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IDO1_complex", + "name": "IDO1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NFK_simple_molecule", + "name": "NFK_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Heme_simple_molecule", + "name": "Heme_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion", + "name": "Fe2+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Biliverdin_simple_molecule", + "name": "Biliverdin_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "apo-IDO1", + "name": "apo-IDO1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Tryptophan_simple_molecule_cell", + "name": "L-Tryptophan_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Tryptophan_simple_molecule_human_host", + "name": "L-Tryptophan_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Effector_T-cell_apoptosis_phenotype", + "name": "Effector_T-cell_apoptosis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC36A4", + "name": "SLC36A4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IDO1_rna", + "name": "IDO1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HCOOH_simple_molecule", + "name": "HCOOH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_cell", + "name": "H+_ion_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "3HAA_simple_molecule", + "name": "3HAA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADH_simple_molecule_cell", + "name": "NADH_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAD+_simple_molecule_cell", + "name": "NAD+_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "2AM_simple_molecule", + "name": "2AM_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPi_simple_molecule", + "name": "PPi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Glu_simple_molecule", + "name": "L-Glu_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AMP_simple_molecule_cell", + "name": "AMP_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADPH_simple_molecule_cell", + "name": "NADPH_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NO_simple_molecule", + "name": "NO_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Citrulline_simple_molecule", + "name": "Citrulline_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO2_simple_molecule", + "name": "CO2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAMN_simple_molecule_cell", + "name": "NAMN_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_simple_molecule", + "name": "O2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACS_simple_molecule", + "name": "ACS_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "KMO", + "name": "KMO", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "KYNA_simple_molecule", + "name": "KYNA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "QUIN_simple_molecule", + "name": "QUIN_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "2AMA_simple_molecule", + "name": "2AMA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRPP_simple_molecule", + "name": "PRPP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "QPRT", + "name": "QPRT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMOX1_cell", + "name": "HMOX1_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "IDO2", + "name": "IDO2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Epacadostat_drug", + "name": "Epacadostat_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PYR_simple_molecule", + "name": "PYR_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PXLP-KYAT1_complex", + "name": "PXLP-KYAT1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "I3PROPA", + "name": "I3PROPA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Phe_simple_molecule", + "name": "L-Phe_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "I3LACT", + "name": "I3LACT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AFMID", + "name": "AFMID", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP_simple_molecule_cell", + "name": "ADP_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAM_simple_molecule_cell", + "name": "NAM_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "(ADP-D-ribosyl)(n+1)-acceptor_simple_molecule", + "name": "(ADP-D-ribosyl)(n+1)-acceptor_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule_cell", + "name": "ATP_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPi(3-)_simple_molecule_cell", + "name": "PPi(3-)_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMN_simple_molecule_cell", + "name": "NMN_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADK:Zn2+_tetramer_complex", + "name": "NADK:Zn2+_tetramer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Arginine_simple_molecule", + "name": "L-Arginine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "iNOS", + "name": "iNOS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAR_simple_molecule", + "name": "NAR_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMRK1", + "name": "NMRK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMRK2", + "name": "NMRK2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NR_simple_molecule", + "name": "NR_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CCBL2", + "name": "CCBL2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Dendritic_cell_maturation_phenotype", + "name": "Dendritic_cell_maturation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "KYNU", + "name": "KYNU", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMOX1_rna", + "name": "HMOX1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CA_simple_molecule", + "name": "CA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Th1_cell_cytokine_production_phenotype", + "name": "Th1_cell_cytokine_production_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HAAO", + "name": "HAAO", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACMSD", + "name": "ACMSD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAAD_simple_molecule_cell", + "name": "NAAD_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Gln_simple_molecule", + "name": "L-Gln_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADSYN1_hexamer", + "name": "NADSYN1_hexamer", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNAT2:Mg2+_complex", + "name": "NMNAT2:Mg2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFN-G", + "name": "IFN-G", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAMN_simple_molecule_mitochondrial_matrix", + "name": "NAMN_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPi_(3-)_simple_molecule", + "name": "PPi_(3-)_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAAD_simple_molecule_mitochondrial_matrix", + "name": "NAAD_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule_mitochondrial_matrix", + "name": "ATP_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_mitochondrial_matrix", + "name": "H+_ion_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP_simple_molecule_mitochondrial_matrix", + "name": "ADP_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADPH_simple_molecule_mitochondrial_matrix", + "name": "NADPH_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADP+_simple_molecule_mitochondrial_matrix", + "name": "NADP+_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pi_simple_molecule", + "name": "Pi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNAT3:Mg2+_complex", + "name": "NMNAT3:Mg2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S-NADPHX_simple_molecule", + "name": "S-NADPHX_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CARKD", + "name": "CARKD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAD+_simple_molecule_mitochondrial_matrix", + "name": "NAD+_simple_molecule_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADK2", + "name": "NADK2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "R-NADPHX_simple_molecule", + "name": "R-NADPHX_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "APOA1BP", + "name": "APOA1BP", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NCA_simple_molecule", + "name": "NCA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC22A13", + "name": "SLC22A13", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAPRT1", + "name": "NAPRT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mg2+_ion", + "name": "Mg2+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MNA_simple_molecule", + "name": "MNA_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AdoHcy_simple_molecule", + "name": "AdoHcy_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAMPT", + "name": "NAMPT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PGH2_simple_molecule", + "name": "PGH2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_endoplasmic_reticulum", + "name": "H2O_simple_molecule_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AdoMet_simple_molecule", + "name": "AdoMet_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NNMT", + "name": "NNMT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "(ADP-D-ribosyl)(n)-acceptor_simple_molecule", + "name": "(ADP-D-ribosyl)(n)-acceptor_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PARPs", + "name": "PARPs", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_human_host", + "name": "H+_ion_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O2_simple_molecule", + "name": "H2O2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAD+_simple_molecule_human_host", + "name": "NAD+_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAM_simple_molecule_human_host", + "name": "NAM_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP-ribose_simple_molecule", + "name": "ADP-ribose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pi_ion", + "name": "Pi_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMN_simple_molecule_human_host", + "name": "NMN_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_human_host", + "name": "H2O_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NRNAM_simple_molecule", + "name": "NRNAM_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BST1", + "name": "BST1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CD38", + "name": "CD38", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dh-beta-NAD_simple_molecule", + "name": "dh-beta-NAD_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_ion", + "name": "O2_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RNLS:FAD_complex", + "name": "RNLS:FAD_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NT5E:Zn2+_complex", + "name": "NT5E:Zn2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADH_simple_molecule_peroxisome", + "name": "NADH_simple_molecule_peroxisome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNH_simple_molecule", + "name": "NMNH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_peroxisome", + "name": "H+_ion_peroxisome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AMP_simple_molecule_peroxisome", + "name": "AMP_simple_molecule_peroxisome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_peroxisome", + "name": "H2O_simple_molecule_peroxisome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUDT12", + "name": "NUDT12", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAMN_simple_molecule_nucleus", + "name": "NAMN_simple_molecule_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAAD_simple_molecule_nucleus", + "name": "NAAD_simple_molecule_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPi(3-)_simple_molecule_nucleus", + "name": "PPi(3-)_simple_molecule_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule_nucleus", + "name": "ATP_simple_molecule_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNAT1:Zn2+_complex", + "name": "NMNAT1:Zn2+_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PGI2_simple_molecule", + "name": "PGI2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PTGIS", + "name": "PTGIS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PGG2_simple_molecule", + "name": "PGG2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "e-_ion", + "name": "e-_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion_endoplasmic_reticulum", + "name": "H+_ion_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PTGS2", + "name": "PTGS2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PTCS2:celecoxib_complex", + "name": "PTCS2:celecoxib_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "monocarboxylates_transported_by_SLC5A8_simple_molecule_human_host", + "name": "monocarboxylates_transported_by_SLC5A8_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "monocarboxylates_transported_by_SLC5A8_simple_molecule_cell", + "name": "monocarboxylates_transported_by_SLC5A8_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Na+_ion_cell", + "name": "Na+_ion_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Na+_ion_human_host", + "name": "Na+_ion_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC5A8", + "name": "SLC5A8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a", + "name": "Orf3a", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "Regulatory_T-cell_generation_phenotype", + "target": "AHR/L-KYN_complex", + "sign": true + }, + { + "id": "t2", + "source": "AHR/L-KYN_complex", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t3", + "source": "H2O_simple_molecule_cell", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t4", + "source": "AP-DOBu_simple_molecule", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t5", + "source": "NADP+_simple_molecule_cell", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t6", + "source": "L-Ala_simple_molecule", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t7", + "source": "3HKYN_simple_molecule", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t8", + "source": "T-cell_apoptosis_phenotype", + "target": "L-Kynurenine_simple_molecule", + "sign": true + }, + { + "id": "t9", + "source": "AHR/L-KYN_complex", + "target": "AHR", + "sign": true + }, + { + "id": "t10", + "source": "iNOS_rna", + "target": "Nf-KB_Complex_complex", + "sign": true + }, + { + "id": "t11", + "source": "Nf-KB_Complex_complex", + "target": "CO_simple_molecule", + "sign": false + }, + { + "id": "t12", + "source": "iNOS_rna", + "target": "CO_simple_molecule", + "sign": false + }, + { + "id": "t13", + "source": "NFK_simple_molecule", + "target": "IDO1_complex", + "sign": true + }, + { + "id": "t14", + "source": "IDO1_complex", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t15", + "source": "H2O_simple_molecule_cell", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t16", + "source": "NADP+_simple_molecule_cell", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t17", + "source": "Fe2+_ion", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t18", + "source": "Biliverdin_simple_molecule", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t19", + "source": "CO_simple_molecule", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t20", + "source": "IDO1_complex", + "target": "apo-IDO1", + "sign": true + }, + { + "id": "t21", + "source": "NFK_simple_molecule", + "target": "L-Tryptophan_simple_molecule_cell", + "sign": true + }, + { + "id": "t22", + "source": "L-Tryptophan_simple_molecule_cell", + "target": "L-Tryptophan_simple_molecule_human_host", + "sign": true + }, + { + "id": "t23", + "source": "Effector_T-cell_apoptosis_phenotype", + "target": "L-Tryptophan_simple_molecule_human_host", + "sign": false + }, + { + "id": "t24", + "source": "L-Tryptophan_simple_molecule_cell", + "target": "SLC36A4", + "sign": true + }, + { + "id": "t25", + "source": "apo-IDO1", + "target": "IDO1_rna", + "sign": true + }, + { + "id": "t26", + "source": "HCOOH_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t27", + "source": "L-Kynurenine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t28", + "source": "H+_ion_cell", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t29", + "source": "L-Ala_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t30", + "source": "3HAA_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t31", + "source": "NADH_simple_molecule_cell", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t32", + "source": "NAD+_simple_molecule_cell", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t33", + "source": "2AM_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t34", + "source": "PPi_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t35", + "source": "L-Glu_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t36", + "source": "AMP_simple_molecule_cell", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t37", + "source": "H2O_simple_molecule_cell", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t38", + "source": "NADP+_simple_molecule_cell", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t39", + "source": "H+_ion_cell", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t40", + "source": "3HKYN_simple_molecule", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t41", + "source": "NO_simple_molecule", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t42", + "source": "Fe2+_ion", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t43", + "source": "Biliverdin_simple_molecule", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t44", + "source": "CO_simple_molecule", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t45", + "source": "Citrulline_simple_molecule", + "target": "NADPH_simple_molecule_cell", + "sign": true + }, + { + "id": "t46", + "source": "H2O_simple_molecule_cell", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t47", + "source": "NADP+_simple_molecule_cell", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t48", + "source": "3HKYN_simple_molecule", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t49", + "source": "CO2_simple_molecule", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t50", + "source": "PPi_simple_molecule", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t51", + "source": "NAMN_simple_molecule_cell", + "target": "H+_ion_cell", + "sign": true + }, + { + "id": "t52", + "source": "H2O_simple_molecule_cell", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t53", + "source": "NFK_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t54", + "source": "NADP+_simple_molecule_cell", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t55", + "source": "H+_ion_cell", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t56", + "source": "3HKYN_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t57", + "source": "ACS_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t58", + "source": "NO_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t59", + "source": "Fe2+_ion", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t60", + "source": "Biliverdin_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t61", + "source": "CO_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t62", + "source": "Citrulline_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t63", + "source": "H2O_simple_molecule_cell", + "target": "KMO", + "sign": true + }, + { + "id": "t64", + "source": "NADP+_simple_molecule_cell", + "target": "KMO", + "sign": true + }, + { + "id": "t65", + "source": "3HKYN_simple_molecule", + "target": "KMO", + "sign": true + }, + { + "id": "t66", + "source": "H2O_simple_molecule_cell", + "target": "AP-DOBu_simple_molecule", + "sign": true + }, + { + "id": "t67", + "source": "KYNA_simple_molecule", + "target": "AP-DOBu_simple_molecule", + "sign": true + }, + { + "id": "t68", + "source": "H2O_simple_molecule_cell", + "target": "ACS_simple_molecule", + "sign": true + }, + { + "id": "t69", + "source": "CO2_simple_molecule", + "target": "ACS_simple_molecule", + "sign": true + }, + { + "id": "t70", + "source": "QUIN_simple_molecule", + "target": "ACS_simple_molecule", + "sign": true + }, + { + "id": "t71", + "source": "2AMA_simple_molecule", + "target": "ACS_simple_molecule", + "sign": true + }, + { + "id": "t72", + "source": "H2O_simple_molecule_cell", + "target": "QUIN_simple_molecule", + "sign": true + }, + { + "id": "t73", + "source": "CO2_simple_molecule", + "target": "QUIN_simple_molecule", + "sign": true + }, + { + "id": "t74", + "source": "NAMN_simple_molecule_cell", + "target": "QUIN_simple_molecule", + "sign": true + }, + { + "id": "t75", + "source": "H2O_simple_molecule_cell", + "target": "PRPP_simple_molecule", + "sign": true + }, + { + "id": "t76", + "source": "CO2_simple_molecule", + "target": "PRPP_simple_molecule", + "sign": true + }, + { + "id": "t77", + "source": "PPi_simple_molecule", + "target": "PRPP_simple_molecule", + "sign": true + }, + { + "id": "t78", + "source": "NAMN_simple_molecule_cell", + "target": "PRPP_simple_molecule", + "sign": true + }, + { + "id": "t79", + "source": "H2O_simple_molecule_cell", + "target": "QPRT", + "sign": true + }, + { + "id": "t80", + "source": "CO2_simple_molecule", + "target": "QPRT", + "sign": true + }, + { + "id": "t81", + "source": "NAMN_simple_molecule_cell", + "target": "QPRT", + "sign": true + }, + { + "id": "t82", + "source": "H2O_simple_molecule_cell", + "target": "HMOX1_cell", + "sign": true + }, + { + "id": "t83", + "source": "NADP+_simple_molecule_cell", + "target": "HMOX1_cell", + "sign": true + }, + { + "id": "t84", + "source": "Fe2+_ion", + "target": "HMOX1_cell", + "sign": true + }, + { + "id": "t85", + "source": "Biliverdin_simple_molecule", + "target": "HMOX1_cell", + "sign": true + }, + { + "id": "t86", + "source": "CO_simple_molecule", + "target": "HMOX1_cell", + "sign": true + }, + { + "id": "t87", + "source": "HCOOH_simple_molecule", + "target": "NFK_simple_molecule", + "sign": true + }, + { + "id": "t88", + "source": "L-Kynurenine_simple_molecule", + "target": "NFK_simple_molecule", + "sign": true + }, + { + "id": "t89", + "source": "NFK_simple_molecule", + "target": "IDO2", + "sign": true + }, + { + "id": "t90", + "source": "NFK_simple_molecule", + "target": "Epacadostat_drug", + "sign": false + }, + { + "id": "t91", + "source": "AP-DOBu_simple_molecule", + "target": "PYR_simple_molecule", + "sign": true + }, + { + "id": "t92", + "source": "L-Ala_simple_molecule", + "target": "PYR_simple_molecule", + "sign": true + }, + { + "id": "t93", + "source": "AP-DOBu_simple_molecule", + "target": "PXLP-KYAT1_complex", + "sign": true + }, + { + "id": "t94", + "source": "L-Ala_simple_molecule", + "target": "PXLP-KYAT1_complex", + "sign": true + }, + { + "id": "t95", + "source": "AP-DOBu_simple_molecule", + "target": "I3PROPA", + "sign": false + }, + { + "id": "t96", + "source": "L-Ala_simple_molecule", + "target": "I3PROPA", + "sign": false + }, + { + "id": "t97", + "source": "AP-DOBu_simple_molecule", + "target": "L-Phe_simple_molecule", + "sign": false + }, + { + "id": "t98", + "source": "L-Ala_simple_molecule", + "target": "L-Phe_simple_molecule", + "sign": false + }, + { + "id": "t99", + "source": "AP-DOBu_simple_molecule", + "target": "I3LACT", + "sign": false + }, + { + "id": "t100", + "source": "L-Ala_simple_molecule", + "target": "I3LACT", + "sign": false + }, + { + "id": "t101", + "source": "HCOOH_simple_molecule", + "target": "AFMID", + "sign": true + }, + { + "id": "t102", + "source": "L-Kynurenine_simple_molecule", + "target": "AFMID", + "sign": true + }, + { + "id": "t103", + "source": "NADP+_simple_molecule_cell", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t104", + "source": "H+_ion_cell", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t105", + "source": "NADH_simple_molecule_cell", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t106", + "source": "2AM_simple_molecule", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t107", + "source": "ADP_simple_molecule_cell", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t108", + "source": "NAM_simple_molecule_cell", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t109", + "source": "(ADP-D-ribosyl)(n+1)-acceptor_simple_molecule", + "target": "NAD+_simple_molecule_cell", + "sign": true + }, + { + "id": "t110", + "source": "NADP+_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t111", + "source": "H+_ion_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t112", + "source": "NAD+_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t113", + "source": "PPi_simple_molecule", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t114", + "source": "NAMN_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t115", + "source": "PPi(3-)_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t116", + "source": "L-Glu_simple_molecule", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t117", + "source": "AMP_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t118", + "source": "ADP_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t119", + "source": "NMN_simple_molecule_cell", + "target": "ATP_simple_molecule_cell", + "sign": true + }, + { + "id": "t120", + "source": "NADP+_simple_molecule_cell", + "target": "NADK:Zn2+_tetramer_complex", + "sign": true + }, + { + "id": "t121", + "source": "ADP_simple_molecule_cell", + "target": "NADK:Zn2+_tetramer_complex", + "sign": true + }, + { + "id": "t122", + "source": "NADP+_simple_molecule_cell", + "target": "L-Arginine_simple_molecule", + "sign": true + }, + { + "id": "t123", + "source": "H+_ion_cell", + "target": "L-Arginine_simple_molecule", + "sign": true + }, + { + "id": "t124", + "source": "NO_simple_molecule", + "target": "L-Arginine_simple_molecule", + "sign": true + }, + { + "id": "t125", + "source": "Citrulline_simple_molecule", + "target": "L-Arginine_simple_molecule", + "sign": true + }, + { + "id": "t126", + "source": "NADP+_simple_molecule_cell", + "target": "iNOS", + "sign": true + }, + { + "id": "t127", + "source": "H+_ion_cell", + "target": "iNOS", + "sign": true + }, + { + "id": "t128", + "source": "NO_simple_molecule", + "target": "iNOS", + "sign": true + }, + { + "id": "t129", + "source": "Citrulline_simple_molecule", + "target": "iNOS", + "sign": true + }, + { + "id": "t130", + "source": "H+_ion_cell", + "target": "2AMA_simple_molecule", + "sign": true + }, + { + "id": "t131", + "source": "NADH_simple_molecule_cell", + "target": "2AMA_simple_molecule", + "sign": true + }, + { + "id": "t132", + "source": "2AM_simple_molecule", + "target": "2AMA_simple_molecule", + "sign": true + }, + { + "id": "t133", + "source": "H+_ion_cell", + "target": "NAR_simple_molecule", + "sign": true + }, + { + "id": "t134", + "source": "NAMN_simple_molecule_cell", + "target": "NAR_simple_molecule", + "sign": true + }, + { + "id": "t135", + "source": "ADP_simple_molecule_cell", + "target": "NAR_simple_molecule", + "sign": true + }, + { + "id": "t136", + "source": "H+_ion_cell", + "target": "NMRK1", + "sign": true + }, + { + "id": "t137", + "source": "NAMN_simple_molecule_cell", + "target": "NMRK1", + "sign": true + }, + { + "id": "t138", + "source": "ADP_simple_molecule_cell", + "target": "NMRK1", + "sign": true + }, + { + "id": "t139", + "source": "NMN_simple_molecule_cell", + "target": "NMRK1", + "sign": true + }, + { + "id": "t140", + "source": "H+_ion_cell", + "target": "NMRK2", + "sign": true + }, + { + "id": "t141", + "source": "NAMN_simple_molecule_cell", + "target": "NMRK2", + "sign": true + }, + { + "id": "t142", + "source": "ADP_simple_molecule_cell", + "target": "NMRK2", + "sign": true + }, + { + "id": "t143", + "source": "NMN_simple_molecule_cell", + "target": "NMRK2", + "sign": true + }, + { + "id": "t144", + "source": "H+_ion_cell", + "target": "NR_simple_molecule", + "sign": true + }, + { + "id": "t145", + "source": "ADP_simple_molecule_cell", + "target": "NR_simple_molecule", + "sign": true + }, + { + "id": "t146", + "source": "NMN_simple_molecule_cell", + "target": "NR_simple_molecule", + "sign": true + }, + { + "id": "t147", + "source": "L-Ala_simple_molecule", + "target": "CCBL2", + "sign": true + }, + { + "id": "t148", + "source": "L-Ala_simple_molecule", + "target": "3HKYN_simple_molecule", + "sign": true + }, + { + "id": "t149", + "source": "3HAA_simple_molecule", + "target": "3HKYN_simple_molecule", + "sign": true + }, + { + "id": "t150", + "source": "T-cell_apoptosis_phenotype", + "target": "3HKYN_simple_molecule", + "sign": true + }, + { + "id": "t151", + "source": "Dendritic_cell_maturation_phenotype", + "target": "3HKYN_simple_molecule", + "sign": true + }, + { + "id": "t152", + "source": "L-Ala_simple_molecule", + "target": "KYNU", + "sign": true + }, + { + "id": "t153", + "source": "3HAA_simple_molecule", + "target": "KYNU", + "sign": true + }, + { + "id": "t154", + "source": "Regulatory_T-cell_generation_phenotype", + "target": "3HAA_simple_molecule", + "sign": true + }, + { + "id": "t155", + "source": "ACS_simple_molecule", + "target": "3HAA_simple_molecule", + "sign": true + }, + { + "id": "t156", + "source": "HMOX1_rna", + "target": "3HAA_simple_molecule", + "sign": true + }, + { + "id": "t157", + "source": "CA_simple_molecule", + "target": "3HAA_simple_molecule", + "sign": true + }, + { + "id": "t158", + "source": "Th1_cell_cytokine_production_phenotype", + "target": "3HAA_simple_molecule", + "sign": false + }, + { + "id": "t159", + "source": "T-cell_apoptosis_phenotype", + "target": "3HAA_simple_molecule", + "sign": true + }, + { + "id": "t160", + "source": "Dendritic_cell_maturation_phenotype", + "target": "3HAA_simple_molecule", + "sign": true + }, + { + "id": "t161", + "source": "ACS_simple_molecule", + "target": "HAAO", + "sign": true + }, + { + "id": "t162", + "source": "CO2_simple_molecule", + "target": "ACMSD", + "sign": true + }, + { + "id": "t163", + "source": "2AMA_simple_molecule", + "target": "ACMSD", + "sign": true + }, + { + "id": "t164", + "source": "NAD+_simple_molecule_cell", + "target": "NAAD_simple_molecule_cell", + "sign": true + }, + { + "id": "t165", + "source": "PPi_simple_molecule", + "target": "NAAD_simple_molecule_cell", + "sign": true + }, + { + "id": "t166", + "source": "L-Glu_simple_molecule", + "target": "NAAD_simple_molecule_cell", + "sign": true + }, + { + "id": "t167", + "source": "AMP_simple_molecule_cell", + "target": "NAAD_simple_molecule_cell", + "sign": true + }, + { + "id": "t168", + "source": "NAD+_simple_molecule_cell", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t169", + "source": "PPi_simple_molecule", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t170", + "source": "L-Glu_simple_molecule", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t171", + "source": "AMP_simple_molecule_cell", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t172", + "source": "NAD+_simple_molecule_cell", + "target": "NADSYN1_hexamer", + "sign": true + }, + { + "id": "t173", + "source": "PPi_simple_molecule", + "target": "NADSYN1_hexamer", + "sign": true + }, + { + "id": "t174", + "source": "L-Glu_simple_molecule", + "target": "NADSYN1_hexamer", + "sign": true + }, + { + "id": "t175", + "source": "AMP_simple_molecule_cell", + "target": "NADSYN1_hexamer", + "sign": true + }, + { + "id": "t176", + "source": "NAD+_simple_molecule_cell", + "target": "NMN_simple_molecule_cell", + "sign": true + }, + { + "id": "t177", + "source": "PPi(3-)_simple_molecule_cell", + "target": "NMN_simple_molecule_cell", + "sign": true + }, + { + "id": "t178", + "source": "NAD+_simple_molecule_cell", + "target": "NMNAT2:Mg2+_complex", + "sign": true + }, + { + "id": "t179", + "source": "NAAD_simple_molecule_cell", + "target": "NMNAT2:Mg2+_complex", + "sign": true + }, + { + "id": "t180", + "source": "PPi(3-)_simple_molecule_cell", + "target": "NMNAT2:Mg2+_complex", + "sign": true + }, + { + "id": "t181", + "source": "iNOS", + "target": "iNOS_rna", + "sign": true + }, + { + "id": "t182", + "source": "iNOS_rna", + "target": "IFN-G", + "sign": true + }, + { + "id": "t183", + "source": "IDO1_rna", + "target": "IFN-G", + "sign": true + }, + { + "id": "t184", + "source": "HMOX1_rna", + "target": "IFN-G", + "sign": true + }, + { + "id": "t185", + "source": "IDO1_rna", + "target": "NO_simple_molecule", + "sign": false + }, + { + "id": "t186", + "source": "HMOX1_rna", + "target": "NO_simple_molecule", + "sign": true + }, + { + "id": "t187", + "source": "PPi_(3-)_simple_molecule", + "target": "NAMN_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t188", + "source": "NAAD_simple_molecule_mitochondrial_matrix", + "target": "NAMN_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t189", + "source": "PPi_(3-)_simple_molecule", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t190", + "source": "NAAD_simple_molecule_mitochondrial_matrix", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t191", + "source": "H+_ion_mitochondrial_matrix", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t192", + "source": "ADP_simple_molecule_mitochondrial_matrix", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t193", + "source": "NADPH_simple_molecule_mitochondrial_matrix", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t194", + "source": "NADP+_simple_molecule_mitochondrial_matrix", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t195", + "source": "Pi_simple_molecule", + "target": "ATP_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t196", + "source": "PPi_(3-)_simple_molecule", + "target": "NMNAT3:Mg2+_complex", + "sign": true + }, + { + "id": "t197", + "source": "NAAD_simple_molecule_mitochondrial_matrix", + "target": "NMNAT3:Mg2+_complex", + "sign": true + }, + { + "id": "t198", + "source": "H+_ion_mitochondrial_matrix", + "target": "S-NADPHX_simple_molecule", + "sign": true + }, + { + "id": "t199", + "source": "ADP_simple_molecule_mitochondrial_matrix", + "target": "S-NADPHX_simple_molecule", + "sign": true + }, + { + "id": "t200", + "source": "NADPH_simple_molecule_mitochondrial_matrix", + "target": "S-NADPHX_simple_molecule", + "sign": true + }, + { + "id": "t201", + "source": "Pi_simple_molecule", + "target": "S-NADPHX_simple_molecule", + "sign": true + }, + { + "id": "t202", + "source": "H+_ion_mitochondrial_matrix", + "target": "CARKD", + "sign": true + }, + { + "id": "t203", + "source": "ADP_simple_molecule_mitochondrial_matrix", + "target": "CARKD", + "sign": true + }, + { + "id": "t204", + "source": "NADPH_simple_molecule_mitochondrial_matrix", + "target": "CARKD", + "sign": true + }, + { + "id": "t205", + "source": "Pi_simple_molecule", + "target": "CARKD", + "sign": true + }, + { + "id": "t206", + "source": "H+_ion_mitochondrial_matrix", + "target": "NAD+_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t207", + "source": "ADP_simple_molecule_mitochondrial_matrix", + "target": "NAD+_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t208", + "source": "NADP+_simple_molecule_mitochondrial_matrix", + "target": "NAD+_simple_molecule_mitochondrial_matrix", + "sign": true + }, + { + "id": "t209", + "source": "H+_ion_mitochondrial_matrix", + "target": "NADK2", + "sign": true + }, + { + "id": "t210", + "source": "ADP_simple_molecule_mitochondrial_matrix", + "target": "NADK2", + "sign": true + }, + { + "id": "t211", + "source": "NADP+_simple_molecule_mitochondrial_matrix", + "target": "NADK2", + "sign": true + }, + { + "id": "t212", + "source": "S-NADPHX_simple_molecule", + "target": "R-NADPHX_simple_molecule", + "sign": true + }, + { + "id": "t213", + "source": "S-NADPHX_simple_molecule", + "target": "APOA1BP", + "sign": true + }, + { + "id": "t214", + "source": "PPi_simple_molecule", + "target": "NCA_simple_molecule", + "sign": true + }, + { + "id": "t215", + "source": "NAMN_simple_molecule_cell", + "target": "NCA_simple_molecule", + "sign": true + }, + { + "id": "t216", + "source": "NCA_simple_molecule", + "target": "SLC22A13", + "sign": true + }, + { + "id": "t217", + "source": "PPi_simple_molecule", + "target": "NAPRT1", + "sign": true + }, + { + "id": "t218", + "source": "NAMN_simple_molecule_cell", + "target": "NAPRT1", + "sign": true + }, + { + "id": "t219", + "source": "PPi_simple_molecule", + "target": "Mg2+_ion", + "sign": true + }, + { + "id": "t220", + "source": "NAMN_simple_molecule_cell", + "target": "Mg2+_ion", + "sign": true + }, + { + "id": "t221", + "source": "PPi_simple_molecule", + "target": 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"target": "H2O_simple_molecule_human_host", + "sign": true + }, + { + "id": "t247", + "source": "NAM_simple_molecule_human_host", + "target": "H2O_simple_molecule_human_host", + "sign": true + }, + { + "id": "t248", + "source": "ADP-ribose_simple_molecule", + "target": "H2O_simple_molecule_human_host", + "sign": true + }, + { + "id": "t249", + "source": "Pi_ion", + "target": "H2O_simple_molecule_human_host", + "sign": true + }, + { + "id": "t250", + "source": "NMN_simple_molecule_human_host", + "target": "H2O_simple_molecule_human_host", + "sign": true + }, + { + "id": "t251", + "source": "NRNAM_simple_molecule", + "target": "H2O_simple_molecule_human_host", + "sign": true + }, + { + "id": "t252", + "source": "H+_ion_human_host", + "target": "BST1", + "sign": true + }, + { + "id": "t253", + "source": "NAM_simple_molecule_human_host", + "target": "BST1", + "sign": true + }, + { + "id": "t254", + "source": "ADP-ribose_simple_molecule", + "target": "BST1", + "sign": true + }, + { + "id": "t255", + "source": "H+_ion_human_host", + "target": "CD38", + "sign": true + }, + { + "id": "t256", + "source": "NAM_simple_molecule_human_host", + "target": "CD38", + "sign": true + }, + { + "id": "t257", + "source": "ADP-ribose_simple_molecule", + "target": "CD38", + "sign": true + }, + { + "id": "t258", + "source": "H2O2_simple_molecule", + "target": "dh-beta-NAD_simple_molecule", + "sign": true + }, + { + "id": "t259", + "source": "NAD+_simple_molecule_human_host", + "target": "dh-beta-NAD_simple_molecule", + "sign": true + }, + { + "id": "t260", + "source": "H2O2_simple_molecule", + "target": "O2_ion", + "sign": true + }, + { + "id": "t261", + "source": "NAD+_simple_molecule_human_host", + "target": "O2_ion", + "sign": true + }, + { + "id": "t262", + "source": "H2O2_simple_molecule", + "target": "RNLS:FAD_complex", + "sign": true + }, + { + "id": "t263", + "source": "NAD+_simple_molecule_human_host", + "target": "RNLS:FAD_complex", + "sign": true + }, + { + "id": "t264", + "source": "Pi_ion", + "target": "NT5E:Zn2+_complex", + "sign": true + }, + { + "id": "t265", + "source": "NMN_simple_molecule_human_host", + "target": "NT5E:Zn2+_complex", + "sign": true + }, + { + "id": "t266", + "source": "NRNAM_simple_molecule", + "target": "NT5E:Zn2+_complex", + "sign": true + }, + { + "id": "t267", + "source": "Pi_ion", + "target": "NMN_simple_molecule_human_host", + "sign": true + }, + { + "id": "t268", + "source": "NRNAM_simple_molecule", + "target": "NMN_simple_molecule_human_host", + "sign": true + }, + { + "id": "t269", + "source": "NMNH_simple_molecule", + "target": "NADH_simple_molecule_peroxisome", + "sign": true + }, + { + "id": "t270", + "source": "H+_ion_peroxisome", + "target": "NADH_simple_molecule_peroxisome", + "sign": true + }, + { + "id": "t271", + "source": "NMNH_simple_molecule", + "target": "AMP_simple_molecule_peroxisome", + "sign": true + }, + { + "id": "t272", + "source": "H+_ion_peroxisome", + "target": "AMP_simple_molecule_peroxisome", + "sign": true + }, + { + "id": "t273", + "source": "NMNH_simple_molecule", + "target": "H2O_simple_molecule_peroxisome", + "sign": true + }, + { + "id": "t274", + "source": "H+_ion_peroxisome", + "target": "H2O_simple_molecule_peroxisome", + "sign": true + }, + { + "id": "t275", + "source": "NMNH_simple_molecule", + "target": "NUDT12", + "sign": true + }, + { + "id": "t276", + "source": "H+_ion_peroxisome", + "target": "NUDT12", + "sign": true + }, + { + "id": "t277", + "source": "NAAD_simple_molecule_nucleus", + "target": "NAMN_simple_molecule_nucleus", + "sign": true + }, + { + "id": "t278", + "source": "PPi(3-)_simple_molecule_nucleus", + "target": "NAMN_simple_molecule_nucleus", + "sign": true + }, + { + "id": "t279", + "source": "NAAD_simple_molecule_nucleus", + "target": "ATP_simple_molecule_nucleus", + "sign": true + }, + { + "id": "t280", + "source": "PPi(3-)_simple_molecule_nucleus", + "target": "ATP_simple_molecule_nucleus", + "sign": true + }, + { + "id": "t281", + "source": "NAAD_simple_molecule_nucleus", + "target": "NMNAT1:Zn2+_complex", + "sign": true + }, + { + "id": "t282", + "source": "PPi(3-)_simple_molecule_nucleus", + "target": "NMNAT1:Zn2+_complex", + "sign": true + }, + { + "id": "t283", + "source": "PGI2_simple_molecule", + "target": "PGH2_simple_molecule", + "sign": true + }, + { + "id": "t284", + "source": "PGI2_simple_molecule", + "target": "PTGIS", + "sign": true + }, + { + "id": "t285", + "source": "PGH2_simple_molecule", + "target": "PGG2_simple_molecule", + "sign": true + }, + { + "id": "t286", + "source": "H2O_simple_molecule_endoplasmic_reticulum", + "target": "PGG2_simple_molecule", + "sign": true + }, + { + "id": "t287", + "source": "PGH2_simple_molecule", + "target": "e-_ion", + "sign": true + }, + { + "id": "t288", + "source": "H2O_simple_molecule_endoplasmic_reticulum", + "target": "e-_ion", + "sign": true + }, + { + "id": "t289", + "source": "PGH2_simple_molecule", + "target": "H+_ion_endoplasmic_reticulum", + "sign": true + }, 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"monocarboxylates_transported_by_SLC5A8_simple_molecule_cell", + "target": "Na+_ion_human_host", + "sign": true + }, + { + "id": "t298", + "source": "Na+_ion_cell", + "target": "Na+_ion_human_host", + "sign": true + }, + { + "id": "t299", + "source": "monocarboxylates_transported_by_SLC5A8_simple_molecule_cell", + "target": "SLC5A8", + "sign": true + }, + { + "id": "t300", + "source": "Na+_ion_cell", + "target": "SLC5A8", + "sign": true + }, + { + "id": "t301", + "source": "HMOX1_cell", + "target": "HMOX1_rna", + "sign": true + }, + { + "id": "t303", + "source": "HMOX1_cell", + "target": "Orf3a", + "sign": true + }, + { + "id": "t304", + "source": "T-cell_apoptosis_phenotype", + "target": "CA_simple_molecule", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/NLRP3_Activation.json b/scripts/covid19_diseasemaps/regnet_amr/NLRP3_Activation.json new file mode 100644 index 000000000..09b6aa880 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/NLRP3_Activation.json @@ -0,0 +1,995 @@ +{ + "header": { + "name": "NLRP3_Activation", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on NLRP3_Activation", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "ASC:MAVS:TRAF3_complex_cell", + "name": "ASC:MAVS:TRAF3_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "ASC:MAVS_complex", + "name": "ASC:MAVS_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRAF3", + "name": "TRAF3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRAF3:SARS_Orf3a_complex_cell", + "name": "TRAF3:SARS_Orf3a_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3:SUGT1:HSP90_complex", + "name": "NLRP3:SUGT1:HSP90_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SUGT1:HSP90AB1_complex", + "name": "SUGT1:HSP90AB1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_cell", + "name": "NLRP3_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXNIP:NLRP3_complex", + "name": "TXNIP:NLRP3_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "p105_ubiquitinated", + "name": "p105_ubiquitinated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_oligomer:ASC:proCaspase1_complex", + "name": "NLRP3_oligomer:ASC:proCaspase1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_oligomer:ASC_complex", + "name": "NLRP3_oligomer:ASC_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CASP1_cell", + "name": "CASP1_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTSG", + "name": "CTSG", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ASC_ubiquitinated", + "name": "ASC_ubiquitinated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Caspase-1_Tetramer_complex", + "name": "Caspase-1_Tetramer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-18_cell", + "name": "IL-18_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-1B_cell", + "name": "IL-1B_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "proIL-18_cell", + "name": "proIL-18_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "proIL-1B_cell", + "name": "proIL-1B_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "CASP1(120-197):CASP1(317-404)_complex", + "name": "CASP1(120-197):CASP1(317-404)_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXNIP", + "name": "TXNIP", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thioredoxin:TXNIP_complex", + "name": "Thioredoxin:TXNIP_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAVS", + "name": "MAVS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nf-KB_Complex_complex_nucleus", + "name": "Nf-KB_Complex_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NF-KB_COMPLEX:IKBA_complex", + "name": "NF-KB_COMPLEX:IKBA_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IKBA_phosphorylated_phosphorylated", + "name": "IKBA_phosphorylated_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nf-KB_Complex_complex_cell", + "name": "Nf-KB_Complex_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "p50", + "name": "p50", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "p65", + "name": "p65", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "proIL-18_rna", + "name": "proIL-18_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "proIL-1B_rna", + "name": "proIL-1B_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TXN_cell", + "name": "TXN_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "ASC", + "name": "ASC", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a", + "name": "Orf3a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DAMPs_phenotype", + "name": "DAMPs_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PAMPs_phenotype", + "name": "PAMPs_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_Elicitor_Small_Molecules_simple_molecule", + "name": "NLRP3_Elicitor_Small_Molecules_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NLRP3_Elicitor_Proteins", + "name": "NLRP3_Elicitor_Proteins", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Reactive_Oxygen_Species_simple_molecule", + "name": "Reactive_Oxygen_Species_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ca2+_ion", + "name": "Ca2+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO_simple_molecule", + "name": "CO_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-18_default_compartment", + "name": "IL-18_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IL-1B_default_compartment", + "name": "IL-1B_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_Golgi_apparatus", + "name": "E_Golgi_apparatus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_endoplasmic_reticulum-Golgi_intermediate_compartment", + "name": "E_endoplasmic_reticulum-Golgi_intermediate_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Heme_simple_molecule", + "name": "Heme_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADP+_simple_molecule", + "name": "NADP+_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Biliverdin_simple_molecule", + "name": "Biliverdin_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule", + "name": "H2O_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fe2+_ion", + "name": "Fe2+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O2_simple_molecule", + "name": "O2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADPH_simple_molecule", + "name": "NADPH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HMOX1", + "name": "HMOX1", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t2", + "source": "ASC:MAVS:TRAF3_complex_cell", + "target": "ASC:MAVS_complex", + "sign": true + }, + { + "id": "t3", + "source": "ASC:MAVS:TRAF3_complex_cell", + "target": "TRAF3", + "sign": true + }, + { + "id": "t4", + "source": "TRAF3:SARS_Orf3a_complex_cell", + "target": "TRAF3", + "sign": true + }, + { + "id": "t5", + "source": "SUGT1:HSP90AB1_complex", + "target": "NLRP3:SUGT1:HSP90_complex", + "sign": true + }, + { + "id": "t6", + "source": "NLRP3_cell", + "target": "NLRP3:SUGT1:HSP90_complex", + "sign": true + }, + { + "id": "t7", + "source": "NLRP3:SUGT1:HSP90_complex", + "target": "NLRP3_cell", + "sign": true + }, + { + "id": "t8", + "source": "TXNIP:NLRP3_complex", + "target": "NLRP3_cell", + "sign": true + }, + { + "id": "t9", + "source": "NLRP3:SUGT1:HSP90_complex", + "target": "SUGT1:HSP90AB1_complex", + "sign": true + }, + { + "id": "t10", + "source": "p105_ubiquitinated", + "target": "TRAF3:SARS_Orf3a_complex_cell", + "sign": true + }, + { + "id": "t11", + "source": "NLRP3_oligomer:ASC_complex", + "target": "NLRP3_oligomer:ASC:proCaspase1_complex", + "sign": true + }, + { + "id": "t12", + "source": "CASP1_cell", + "target": "NLRP3_oligomer:ASC:proCaspase1_complex", + "sign": true + }, + { + "id": "t13", + "source": "NLRP3_oligomer:ASC:proCaspase1_complex", + "target": "CASP1_cell", + "sign": true + }, + { + "id": "t14", + "source": "NLRP3_oligomer:ASC:proCaspase1_complex", + "target": "NLRP3_oligomer:ASC_complex", + "sign": true + }, + { + "id": "t15", + "source": "NLRP3_oligomer:ASC_complex", + "target": "CTSG", + "sign": true + }, + { + "id": "t16", + "source": "CASP1_cell", + "target": "CTSG", + "sign": true + }, + { + "id": "t17", + "source": "NLRP3_oligomer:ASC_complex", + "target": "ASC_ubiquitinated", + "sign": true + }, + { + "id": "t18", + "source": "NLRP3_oligomer:ASC_complex", + "target": "NLRP3_cell", + "sign": true + }, + { + "id": "t19", + "source": "IL-18_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t20", + "source": "IL-1B_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t21", + "source": "proIL-18_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t22", + "source": "proIL-1B_cell", + "target": "Caspase-1_Tetramer_complex", + "sign": true + }, + { + "id": "t23", + "source": "Caspase-1_Tetramer_complex", + "target": "CASP1(120-197):CASP1(317-404)_complex", + "sign": true + }, + { + "id": "t24", + "source": "SUGT1:HSP90AB1_complex", + "target": "TXNIP:NLRP3_complex", + "sign": true + }, + { + "id": "t25", + "source": "NLRP3_cell", + "target": "TXNIP:NLRP3_complex", + "sign": true + }, + { + "id": "t26", + "source": "TXNIP:NLRP3_complex", + "target": "TXNIP", + "sign": true + }, + { + "id": "t27", + "source": "Thioredoxin:TXNIP_complex", + "target": "TXNIP", + "sign": true + }, + { + "id": "t28", + "source": "CASP1(120-197):CASP1(317-404)_complex", + "target": "CASP1_cell", + "sign": true + }, + { + "id": "t29", + "source": "TRAF3", + "target": "ASC:MAVS:TRAF3_complex_cell", + "sign": true + }, + { + "id": "t30", + "source": "MAVS", + "target": "ASC:MAVS:TRAF3_complex_cell", + "sign": true + }, + { + "id": "t31", + "source": "ASC_ubiquitinated", + "target": "ASC:MAVS:TRAF3_complex_cell", + "sign": true + }, + { + "id": "t32", + "source": "ASC:MAVS:TRAF3_complex_cell", + "target": "TRAF3:SARS_Orf3a_complex_cell", + "sign": true + }, + { + "id": "t33", + "source": "Nf-KB_Complex_complex_nucleus", + "target": "NF-KB_COMPLEX:IKBA_complex", + "sign": false + }, + { + "id": "t34", + "source": "NF-KB_COMPLEX:IKBA_complex", + "target": "IKBA_phosphorylated_phosphorylated", + "sign": true + }, + { + "id": "t35", + "source": "NF-KB_COMPLEX:IKBA_complex", + "target": "Nf-KB_Complex_complex_cell", + "sign": true + }, + { + "id": "t36", + "source": "Nf-KB_Complex_complex_nucleus", + "target": "Nf-KB_Complex_complex_cell", + "sign": true + }, + { + "id": "t37", + "source": "Nf-KB_Complex_complex_cell", + "target": "p50", + "sign": true + }, + { + "id": "t38", + "source": "Nf-KB_Complex_complex_cell", + "target": "p65", + "sign": true + }, + { + "id": "t39", + "source": "proIL-18_rna", + "target": "Nf-KB_Complex_complex_nucleus", + "sign": true + }, + { + "id": "t40", + "source": "proIL-1B_rna", + "target": "Nf-KB_Complex_complex_nucleus", + "sign": true + }, + { + "id": "t41", + "source": "TXNIP", + "target": "Thioredoxin:TXNIP_complex", + "sign": true + }, + { + "id": "t42", + "source": "TXN_cell", + "target": "Thioredoxin:TXNIP_complex", + "sign": true + }, + { + "id": "t43", + "source": "Thioredoxin:TXNIP_complex", + "target": "TXN_cell", + "sign": true + }, + { + "id": "t45", + "source": "ASC:MAVS_complex", + "target": "ASC", + "sign": true + }, + { + "id": "t46", + "source": "ASC:MAVS_complex", + "target": "MAVS", + "sign": true + }, + { + "id": "t47", + "source": "TRAF3:SARS_Orf3a_complex_cell", + "target": "Orf3a", + "sign": true + }, + { + "id": "t48", + "source": "SUGT1:HSP90AB1_complex", + "target": "DAMPs_phenotype", + "sign": true + }, + { + "id": "t49", + "source": "NLRP3_cell", + "target": "DAMPs_phenotype", + "sign": true + }, + { + "id": "t50", + "source": "SUGT1:HSP90AB1_complex", + "target": "PAMPs_phenotype", + "sign": true + }, + { + "id": "t51", + "source": "NLRP3_cell", + "target": "PAMPs_phenotype", + "sign": true + }, + { + "id": "t52", + "source": "SUGT1:HSP90AB1_complex", + "target": "NLRP3_Elicitor_Small_Molecules_simple_molecule", + "sign": true + }, + { + "id": "t53", + "source": "NLRP3_cell", + "target": "NLRP3_Elicitor_Small_Molecules_simple_molecule", + "sign": true + }, + { + "id": "t54", + "source": "SUGT1:HSP90AB1_complex", + "target": "NLRP3_Elicitor_Proteins", + "sign": true + }, + { + "id": "t55", + "source": "NLRP3_cell", + "target": "NLRP3_Elicitor_Proteins", + "sign": true + }, + { + "id": "t56", + "source": "SUGT1:HSP90AB1_complex", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t57", + "source": "NLRP3_cell", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t58", + "source": "TXN_cell", + "target": "Reactive_Oxygen_Species_simple_molecule", + "sign": true + }, + { + "id": "t59", + "source": "SUGT1:HSP90AB1_complex", + "target": "Ca2+_ion", + "sign": true + }, + { + "id": "t60", + "source": "NLRP3_cell", + "target": "Ca2+_ion", + "sign": true + }, + { + "id": "t61", + "source": "Reactive_Oxygen_Species_simple_molecule", + "target": "CO_simple_molecule", + "sign": false + }, + { + "id": "t62", + "source": "IL-18_cell", + "target": "proIL-18_cell", + "sign": true + }, + { + "id": "t64", + "source": "proIL-18_cell", + "target": "proIL-18_rna", + "sign": true + }, + { + "id": "t65", + "source": "IL-1B_cell", + "target": "proIL-1B_cell", + "sign": true + }, + { + "id": "t67", + "source": "proIL-1B_cell", + "target": "proIL-1B_rna", + "sign": true + }, + { + "id": "t68", + "source": "IL-18_default_compartment", + "target": "IL-18_cell", + "sign": true + }, + { + "id": "t69", + "source": "IL-1B_default_compartment", + "target": "IL-1B_cell", + "sign": true + }, + { + "id": "t70", + "source": "p50", + "target": "p105_ubiquitinated", + "sign": true + }, + { + "id": "t71", + "source": "Ca2+_ion", + "target": "E_Golgi_apparatus", + "sign": true + }, + { + "id": "t72", + "source": "Ca2+_ion", + "target": "E_endoplasmic_reticulum-Golgi_intermediate_compartment", + "sign": true + }, + { + "id": "t73", + "source": "NADP+_simple_molecule", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t74", + "source": "Biliverdin_simple_molecule", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t75", + "source": "H2O_simple_molecule", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t76", + "source": "CO_simple_molecule", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t77", + "source": "Fe2+_ion", + "target": "Heme_simple_molecule", + "sign": true + }, + { + "id": "t78", + "source": "NADP+_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t79", + "source": "Biliverdin_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t80", + "source": "H2O_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t81", + "source": "CO_simple_molecule", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t82", + "source": "Fe2+_ion", + "target": "O2_simple_molecule", + "sign": true + }, + { + "id": "t83", + "source": "NADP+_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t84", + "source": "Biliverdin_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t85", + "source": "H2O_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t86", + "source": "CO_simple_molecule", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t87", + "source": "Fe2+_ion", + "target": "NADPH_simple_molecule", + "sign": true + }, + { + "id": "t88", + "source": "NADP+_simple_molecule", + "target": "HMOX1", + "sign": true + }, + { + "id": "t89", + "source": "Biliverdin_simple_molecule", + "target": "HMOX1", + "sign": true + }, + { + "id": "t90", + "source": "H2O_simple_molecule", + "target": "HMOX1", + "sign": true + }, + { + "id": "t91", + "source": "CO_simple_molecule", + "target": "HMOX1", + "sign": true + }, + { + "id": "t92", + "source": "Fe2+_ion", + "target": "HMOX1", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Nsp14.json b/scripts/covid19_diseasemaps/regnet_amr/Nsp14.json new file mode 100644 index 000000000..88df3d3ac --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Nsp14.json @@ -0,0 +1,4697 @@ +{ + "header": { + "name": "Nsp14", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Nsp14", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "SIRT5:Nsp14_complex", + "name": "SIRT5:Nsp14_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nicotinamide_simple_molecule", + "name": "Nicotinamide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Histone-L-lysine_simple_molecule", + "name": "Histone-L-lysine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "O-Acetyl-ADP-ribose_simple_molecule", + "name": "O-Acetyl-ADP-ribose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SIRT5", + "name": "SIRT5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Urea_cycle_phenotype", + "name": "Urea_cycle_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp14_mitochondrion", + "name": "Nsp14_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GLA:Nsp14_complex", + "name": "GLA:Nsp14_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "D-Galactose_simple_molecule", + "name": "D-Galactose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "_alpha_-D-Glucose_simple_molecule", + "name": "_alpha_-D-Glucose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Raffinose_simple_molecule", + "name": "Raffinose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Sucrose_simple_molecule", + "name": "Sucrose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GLA", + "name": "GLA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp14_cell", + "name": "Nsp14_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IMPDH2:Nsp14_complex", + "name": "IMPDH2:Nsp14_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H_simple_molecule", + "name": "H_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADH_simple_molecule", + "name": "NADH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "XMP_simple_molecule", + "name": "XMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IMPDH2", + "name": "IMPDH2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Guanine_nucleotide_synthesis_phenotype", + "name": "Guanine_nucleotide_synthesis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "_alpha_-D-Galactose_simple_molecule", + "name": "_alpha_-D-Galactose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Lactose_simple_molecule", + "name": "Lactose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_cell", + "name": "H2O_simple_molecule_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP_simple_molecule", + "name": "ADP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPi_simple_molecule", + "name": "PPi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "N-Ribosyl-nicotinamide_simple_molecule", + "name": "N-Ribosyl-nicotinamide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nicotinamide_D-ribonucleotide_simple_molecule", + "name": "Nicotinamide_D-ribonucleotide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAD_simple_molecule", + "name": "NAD_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nicotinate_D-ribonucleotide_simple_molecule", + "name": "Nicotinate_D-ribonucleotide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Glutamate_simple_molecule", + "name": "L-Glutamate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AMP_simple_molecule", + "name": "AMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pi_simple_molecule", + "name": "Pi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP-D-ribose_simple_molecule", + "name": "ADP-D-ribose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "5-phospho-beta-D-ribosylamine_simple_molecule", + "name": "5-phospho-beta-D-ribosylamine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "name": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IMP_simple_molecule", + "name": "IMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GMP_simple_molecule", + "name": "GMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GDP_simple_molecule", + "name": "GDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dGMP_simple_molecule", + "name": "dGMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Guanosine_simple_molecule", + "name": "Guanosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ammonium_simple_molecule", + "name": "Ammonium_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Xanthosine_simple_molecule", + "name": "Xanthosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Xanthine_simple_molecule", + "name": "Xanthine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Inosine_simple_molecule", + "name": "Inosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Adenosine_simple_molecule", + "name": "Adenosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Deoxyinosine_simple_molecule", + "name": "Deoxyinosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GLB1", + "name": "GLB1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "LCT", + "name": "LCT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Galacitol_simple_molecule", + "name": "Galacitol_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADPH_simple_molecule", + "name": "NADPH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADP_simple_molecule", + "name": "NADP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "nicotinate-adenine_dinucleotide_phosphate_simple_molecule", + "name": "nicotinate-adenine_dinucleotide_phosphate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AKR1B1", + "name": "AKR1B1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Melibiose_simple_molecule", + "name": "Melibiose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Migalastat_drug", + "name": "Migalastat_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Stachyose_simple_molecule", + "name": "Stachyose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "_alpha_-D-Galactose-1P_simple_molecule", + "name": "_alpha_-D-Galactose-1P_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GALM", + "name": "GALM", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UDP-_alpha_-D-Galactose_simple_molecule", + "name": "UDP-_alpha_-D-Galactose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "_alpha_-D-Glucose-1-P_simple_molecule", + "name": "_alpha_-D-Glucose-1-P_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule", + "name": "ATP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Deamino-NAD_simple_molecule", + "name": "Deamino-NAD_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "name": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "name": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Aminoimidazole_ribotide_simple_molecule", + "name": "Aminoimidazole_ribotide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "name": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GTP_simple_molecule", + "name": "GTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dGDP_simple_molecule", + "name": "dGDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dGTP_simple_molecule", + "name": "dGTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dAMP_simple_molecule", + "name": "dAMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dADP_simple_molecule", + "name": "dADP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dATP_simple_molecule", + "name": "dATP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GALK1", + "name": "GALK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thioredoxin_disulfide_simple_molecule", + "name": "Thioredoxin_disulfide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADK", + "name": "NADK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Glutamine_simple_molecule", + "name": "L-Glutamine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADSYN1", + "name": "NADSYN1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "name": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NRK1", + "name": "NRK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nicotinate_simple_molecule", + "name": "Nicotinate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO2_simple_molecule", + "name": "CO2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAPRT1", + "name": "NAPRT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Glycine_simple_molecule", + "name": "Glycine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GART", + "name": "GART", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "name": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Tetrahydrofolate_simple_molecule", + "name": "Tetrahydrofolate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PFAS", + "name": "PFAS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "name": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Aspartate_simple_molecule", + "name": "L-Aspartate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PAICS", + "name": "PAICS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GUK1", + "name": "GUK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NME3", + "name": "NME3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nucleoside_diphosphate_kinase_complex_cell", + "name": "Nucleoside_diphosphate_kinase_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NME5", + "name": "NME5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NME6", + "name": "NME6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NME7", + "name": "NME7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Deoxyguanosine_simple_molecule", + "name": "Deoxyguanosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Guanine_simple_molecule", + "name": "Guanine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "name": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DCK", + "name": "DCK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Adenine_simple_molecule", + "name": "Adenine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADK", + "name": "ADK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AK7", + "name": "AK7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AK1", + "name": "AK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AK8", + "name": "AK8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AK5", + "name": "AK5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Deoxyadenosine_simple_molecule", + "name": "Deoxyadenosine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UDP_simple_molecule", + "name": "UDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UDP-_alpha_-D-Glucose_simple_molecule", + "name": "UDP-_alpha_-D-Glucose_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UTP_simple_molecule", + "name": "UTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GALT", + "name": "GALT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GALE", + "name": "GALE", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UGP2", + "name": "UGP2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNAT2", + "name": "NMNAT2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNAT1", + "name": "NMNAT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NMNAT3", + "name": "NMNAT3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NAMPT", + "name": "NAMPT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Quinolinate_simple_molecule", + "name": "Quinolinate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "QPRT", + "name": "QPRT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPAT", + "name": "PPAT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GMPS", + "name": "GMPS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ITPA", + "name": "ITPA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENPP1", + "name": "ENPP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENPP3", + "name": "ENPP3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HPRT1", + "name": "HPRT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Hypoxanthine_simple_molecule", + "name": "Hypoxanthine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "APRT", + "name": "APRT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "lactose_synthetase_complex", + "name": "lactose_synthetase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", + "name": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATIC", + "name": "ATIC", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Thioredoxin_simple_molecule", + "name": "Thioredoxin_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ribonucleoside_reductase_complex_cell", + "name": "ribonucleoside_reductase_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NNT", + "name": "NNT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GMPR", + "name": "GMPR", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GMPR2", + "name": "GMPR2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CD38", + "name": "CD38", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "10-Formyltetrahydrofolate_simple_molecule", + "name": "10-Formyltetrahydrofolate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IMPDH1", + "name": "IMPDH1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Mycophenolic_acid_drug", + "name": "Mycophenolic_acid_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Merimepodib_drug", + "name": "Merimepodib_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ribavirin_drug", + "name": "Ribavirin_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENTPD2", + "name": "ENTPD2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NTPCR", + "name": "NTPCR", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENTPD4", + "name": "ENTPD4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENTPD5", + "name": "ENTPD5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENTPD6", + "name": "ENTPD6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CANT1", + "name": "CANT1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "XDH", + "name": "XDH", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PNP", + "name": "PNP", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Histone_N6-acetyl-L-lysine_simple_molecule", + "name": "Histone_N6-acetyl-L-lysine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H2O_simple_molecule_mitochondrion", + "name": "H2O_simple_molecule_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NT5E", + "name": "NT5E", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "D-Ribose_5P_simple_molecule", + "name": "D-Ribose_5P_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRPS1", + "name": "PRPS1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRPS2", + "name": "PRPS2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRPS1L1", + "name": "PRPS1L1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "_alpha_D-Ribose_1P_simple_molecule", + "name": "_alpha_D-Ribose_1P_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PGM2", + "name": "PGM2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "name": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fumarate_simple_molecule", + "name": "Fumarate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADSL", + "name": "ADSL", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AMDP2", + "name": "AMDP2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AMPD1", + "name": "AMPD1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AMPD3", + "name": "AMPD3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GDA", + "name": "GDA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADA", + "name": "ADA", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "Nicotinamide_simple_molecule", + "target": "SIRT5:Nsp14_complex", + "sign": true + }, + { + "id": "t2", + "source": "Histone-L-lysine_simple_molecule", + "target": "SIRT5:Nsp14_complex", + "sign": true + }, + { + "id": "t3", + "source": "O-Acetyl-ADP-ribose_simple_molecule", + "target": "SIRT5:Nsp14_complex", + "sign": true + }, + { + "id": "t4", + "source": "SIRT5:Nsp14_complex", + "target": "SIRT5", + "sign": true + }, + { + "id": "t5", + "source": "Nicotinamide_simple_molecule", + "target": "SIRT5", + "sign": true + }, + { + "id": "t6", + "source": "Histone-L-lysine_simple_molecule", + "target": "SIRT5", + "sign": true + }, + { + "id": "t7", + "source": "O-Acetyl-ADP-ribose_simple_molecule", + "target": "SIRT5", + "sign": true + }, + { + "id": "t8", + "source": "Urea_cycle_phenotype", + "target": "SIRT5", + "sign": true + }, + { + "id": "t9", + "source": "SIRT5:Nsp14_complex", + "target": "Nsp14_mitochondrion", + "sign": true + }, + { + "id": "t10", + "source": "D-Galactose_simple_molecule", + "target": "GLA:Nsp14_complex", + "sign": true + }, + { + "id": "t11", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "GLA:Nsp14_complex", + "sign": true + }, + { + "id": "t12", + "source": "Raffinose_simple_molecule", + "target": "GLA:Nsp14_complex", + "sign": true + }, + { + "id": "t13", + "source": "Sucrose_simple_molecule", + "target": "GLA:Nsp14_complex", + "sign": true + }, + { + "id": "t14", + "source": "GLA:Nsp14_complex", + "target": "GLA", + "sign": true + }, + { + "id": "t15", + "source": "D-Galactose_simple_molecule", + "target": "GLA", + "sign": true + }, + { + "id": "t16", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "GLA", + "sign": true + }, + { + "id": "t17", + "source": "Raffinose_simple_molecule", + "target": "GLA", + "sign": true + }, + { + "id": "t18", + "source": "Sucrose_simple_molecule", + "target": "GLA", + "sign": true + }, + { + "id": "t19", + "source": "GLA:Nsp14_complex", + "target": "Nsp14_cell", + "sign": true + }, + { + "id": "t20", + "source": "IMPDH2:Nsp14_complex", + "target": "Nsp14_cell", + "sign": true + }, + { + "id": "t21", + "source": "H_simple_molecule", + "target": "IMPDH2:Nsp14_complex", + "sign": true + }, + { + "id": "t22", + "source": "NADH_simple_molecule", + "target": "IMPDH2:Nsp14_complex", + "sign": true + }, + { + "id": "t23", + "source": "XMP_simple_molecule", + "target": "IMPDH2:Nsp14_complex", + "sign": true + }, + { + "id": "t24", + "source": "IMPDH2:Nsp14_complex", + "target": "IMPDH2", + "sign": true + }, + { + "id": "t25", + "source": "H_simple_molecule", + "target": "IMPDH2", + "sign": true + }, + { + "id": "t26", + "source": "NADH_simple_molecule", + "target": "IMPDH2", + "sign": true + }, + { + "id": "t27", + "source": "XMP_simple_molecule", + "target": "IMPDH2", + "sign": true + }, + { + "id": "t28", + "source": "Guanine_nucleotide_synthesis_phenotype", + "target": "IMPDH2", + "sign": true + }, + { + "id": "t29", + "source": "_alpha_-D-Galactose_simple_molecule", + "target": "D-Galactose_simple_molecule", + "sign": true + }, + { + "id": "t30", + "source": "D-Galactose_simple_molecule", + "target": "Lactose_simple_molecule", + "sign": true + }, + { + "id": "t31", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "Lactose_simple_molecule", + "sign": true + }, + { + "id": "t32", + "source": "D-Galactose_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t33", + "source": "ADP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t34", + "source": "PPi_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t35", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t36", + "source": "H_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t37", + "source": "Raffinose_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t38", + "source": "Sucrose_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t39", + "source": "Nicotinamide_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t40", + "source": "N-Ribosyl-nicotinamide_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t41", + "source": "Nicotinamide_D-ribonucleotide_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t42", + "source": "NAD_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t43", + "source": "Nicotinate_D-ribonucleotide_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t44", + "source": "NADH_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t45", + "source": "L-Glutamate_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t46", + "source": "AMP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t47", + "source": "Pi_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t48", + "source": "ADP-D-ribose_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t49", + "source": "5-phospho-beta-D-ribosylamine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t50", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t51", + "source": "IMP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t52", + "source": "XMP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t53", + "source": "GMP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t54", + "source": "GDP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t55", + "source": "dGMP_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t56", + "source": "Guanosine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t57", + "source": "Ammonium_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t58", + "source": "Xanthosine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t59", + "source": "Xanthine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t60", + "source": "Inosine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t61", + "source": "Adenosine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t62", + "source": "Deoxyinosine_simple_molecule", + "target": "H2O_simple_molecule_cell", + "sign": true + }, + { + "id": "t63", + "source": "D-Galactose_simple_molecule", + "target": "GLB1", + "sign": true + }, + { + "id": "t64", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "GLB1", + "sign": true + }, + { + "id": "t65", + "source": "D-Galactose_simple_molecule", + "target": "LCT", + "sign": true + }, + { + "id": "t66", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "LCT", + "sign": true + }, + { + "id": "t67", + "source": "D-Galactose_simple_molecule", + "target": "Galacitol_simple_molecule", + "sign": true + }, + { + "id": "t68", + "source": "NADPH_simple_molecule", + "target": "Galacitol_simple_molecule", + "sign": true + }, + { + "id": "t69", + "source": "H_simple_molecule", + "target": "Galacitol_simple_molecule", + "sign": true + }, + { + "id": "t70", + "source": "D-Galactose_simple_molecule", + "target": "NADP_simple_molecule", + "sign": true + }, + { + "id": "t71", + "source": "NADPH_simple_molecule", + "target": "NADP_simple_molecule", + "sign": true + }, + { + "id": "t72", + "source": "H_simple_molecule", + "target": "NADP_simple_molecule", + "sign": true + }, + { + "id": "t73", + "source": "Nicotinamide_simple_molecule", + "target": "NADP_simple_molecule", + "sign": true + }, + { + "id": "t74", + "source": "nicotinate-adenine_dinucleotide_phosphate_simple_molecule", + "target": "NADP_simple_molecule", + "sign": true + }, + { + "id": "t75", + "source": "GMP_simple_molecule", + "target": "NADP_simple_molecule", + "sign": true + }, + { + "id": "t76", + "source": "D-Galactose_simple_molecule", + "target": "AKR1B1", + "sign": true + }, + { + "id": "t77", + "source": "NADPH_simple_molecule", + "target": "AKR1B1", + "sign": true + }, + { + "id": "t78", + "source": "H_simple_molecule", + "target": "AKR1B1", + "sign": true + }, + { + "id": "t79", + "source": "D-Galactose_simple_molecule", + "target": "Melibiose_simple_molecule", + "sign": true + }, + { + "id": "t80", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "Melibiose_simple_molecule", + "sign": true + }, + { + "id": "t81", + "source": "D-Galactose_simple_molecule", + "target": "Migalastat_drug", + "sign": false + }, + { + "id": "t82", + "source": "_alpha_-D-Glucose_simple_molecule", + "target": "Migalastat_drug", + "sign": false + }, + { + "id": "t83", + "source": "Raffinose_simple_molecule", + "target": "Migalastat_drug", + "sign": false + }, + { + "id": "t84", + "source": "Sucrose_simple_molecule", + "target": "Migalastat_drug", + "sign": false + }, + { + "id": "t85", + "source": "D-Galactose_simple_molecule", + "target": "Raffinose_simple_molecule", + "sign": true + }, + { + "id": "t86", + "source": "Sucrose_simple_molecule", + "target": "Raffinose_simple_molecule", + "sign": true + }, + { + "id": "t87", + "source": "D-Galactose_simple_molecule", + "target": "Stachyose_simple_molecule", + "sign": true + }, + { + "id": "t88", + "source": "Raffinose_simple_molecule", + "target": "Stachyose_simple_molecule", + "sign": true + }, + { + "id": "t89", + "source": "_alpha_-D-Galactose-1P_simple_molecule", + "target": "_alpha_-D-Galactose_simple_molecule", + "sign": true + }, + { + "id": "t90", + "source": "ADP_simple_molecule", + "target": "_alpha_-D-Galactose_simple_molecule", + "sign": true + }, + { + "id": "t91", + "source": "_alpha_-D-Galactose_simple_molecule", + "target": "GALM", + "sign": true + }, + { + "id": "t92", + "source": "UDP-_alpha_-D-Galactose_simple_molecule", + "target": "_alpha_-D-Galactose-1P_simple_molecule", + "sign": true + }, + { + "id": "t93", + "source": "_alpha_-D-Glucose-1-P_simple_molecule", + "target": "_alpha_-D-Galactose-1P_simple_molecule", + "sign": true + }, + { + "id": "t94", + "source": "_alpha_-D-Galactose-1P_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t95", + "source": "ADP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t96", + "source": "PPi_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t97", + "source": "NADP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t98", + "source": "H_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t99", + "source": "Nicotinamide_D-ribonucleotide_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t100", + "source": "NAD_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t101", + "source": "Deamino-NAD_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t102", + "source": "Nicotinate_D-ribonucleotide_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t103", + "source": "L-Glutamate_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t104", + "source": "AMP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t105", + "source": "Pi_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t106", + "source": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t107", + "source": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t108", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t109", + "source": "Aminoimidazole_ribotide_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t110", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t111", + "source": "GMP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t112", + "source": "GDP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t113", + "source": "GTP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t114", + "source": "dGDP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t115", + "source": "dGTP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t116", + "source": "dGMP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t117", + "source": "dAMP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t118", + "source": "dADP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t119", + "source": "dATP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t120", + "source": "_alpha_-D-Galactose-1P_simple_molecule", + "target": "GALK1", + "sign": true + }, + { + "id": "t121", + "source": "ADP_simple_molecule", + "target": "GALK1", + "sign": true + }, + { + "id": "t122", + "source": "H2O_simple_molecule_cell", + "target": "ADP_simple_molecule", + "sign": true + }, + { + "id": "t123", + "source": "Thioredoxin_disulfide_simple_molecule", + "target": "ADP_simple_molecule", + "sign": true + }, + { + "id": "t124", + "source": "dADP_simple_molecule", + "target": "ADP_simple_molecule", + "sign": true + }, + { + "id": "t125", + "source": "ADP_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t126", + "source": "NADP_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t127", + "source": "H_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t128", + "source": "Nicotinamide_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t129", + "source": "Nicotinamide_D-ribonucleotide_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t130", + "source": "NADH_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t131", + "source": "AMP_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t132", + "source": "Histone-L-lysine_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t133", + "source": "O-Acetyl-ADP-ribose_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t134", + "source": "ADP-D-ribose_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t135", + "source": "XMP_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t136", + "source": "Xanthine_simple_molecule", + "target": "NAD_simple_molecule", + "sign": true + }, + { + "id": "t137", + "source": "ADP_simple_molecule", + "target": "NADK", + "sign": true + }, + { + "id": "t138", + "source": "NADP_simple_molecule", + "target": "NADK", + "sign": true + }, + { + "id": "t139", + "source": "H_simple_molecule", + "target": "NADK", + "sign": true + }, + { + "id": "t140", + "source": 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"sign": true + }, + { + "id": "t179", + "source": "CO2_simple_molecule", + "target": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "sign": true + }, + { + "id": "t180", + "source": "5-phospho-beta-D-ribosylamine_simple_molecule", + "target": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "sign": true + }, + { + "id": "t181", + "source": "IMP_simple_molecule", + "target": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "sign": true + }, + { + "id": "t182", + "source": "GMP_simple_molecule", + "target": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "sign": true + }, + { + "id": "t183", + "source": "ADP_simple_molecule", + "target": "NAPRT1", + "sign": true + }, + { + "id": "t184", + "source": "PPi_simple_molecule", + "target": "NAPRT1", + "sign": true + }, + { + "id": "t185", + "source": "Nicotinate_D-ribonucleotide_simple_molecule", + "target": "NAPRT1", + "sign": true + }, + { + "id": "t186", + "source": "Pi_simple_molecule", 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"sign": true + }, + { + "id": "t203", + "source": "H_simple_molecule", + "target": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t204", + "source": "L-Glutamate_simple_molecule", + "target": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t205", + "source": "Pi_simple_molecule", + "target": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t206", + "source": "2-(Formamido)-N1-(5'-phosphoribosyl)acetamidine_simple_molecule", + "target": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t207", + "source": "ADP_simple_molecule", + "target": "PFAS", + "sign": true + }, + { + "id": "t208", + "source": "H_simple_molecule", + "target": "PFAS", + "sign": true + }, + { + "id": "t209", + "source": "L-Glutamate_simple_molecule", + "target": "PFAS", + "sign": true + }, + { + "id": "t210", + "source": "Pi_simple_molecule", + "target": 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+ "sign": true + }, + { + "id": "t270", + "source": "Guanine_simple_molecule", + "target": "Deoxyguanosine_simple_molecule", + "sign": true + }, + { + "id": "t271", + "source": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "target": "Deoxyguanosine_simple_molecule", + "sign": true + }, + { + "id": "t272", + "source": "ADP_simple_molecule", + "target": "DCK", + "sign": true + }, + { + "id": "t273", + "source": "H_simple_molecule", + "target": "DCK", + "sign": true + }, + { + "id": "t274", + "source": "dGMP_simple_molecule", + "target": "DCK", + "sign": true + }, + { + "id": "t275", + "source": "dAMP_simple_molecule", + "target": "DCK", + "sign": true + }, + { + "id": "t276", + "source": "ADP_simple_molecule", + "target": "Adenosine_simple_molecule", + "sign": true + }, + { + "id": "t277", + "source": "H_simple_molecule", + "target": "Adenosine_simple_molecule", + "sign": true + }, + { + "id": "t278", + "source": "AMP_simple_molecule", + "target": "Adenosine_simple_molecule", 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+ "sign": true + }, + { + "id": "t288", + "source": "IMP_simple_molecule", + "target": "AMP_simple_molecule", + "sign": true + }, + { + "id": "t289", + "source": "Ammonium_simple_molecule", + "target": "AMP_simple_molecule", + "sign": true + }, + { + "id": "t290", + "source": "Adenosine_simple_molecule", + "target": "AMP_simple_molecule", + "sign": true + }, + { + "id": "t291", + "source": "ADP_simple_molecule", + "target": "AK7", + "sign": true + }, + { + "id": "t292", + "source": "ADP_simple_molecule", + "target": "AK1", + "sign": true + }, + { + "id": "t293", + "source": "ADP_simple_molecule", + "target": "AK8", + "sign": true + }, + { + "id": "t294", + "source": "ADP_simple_molecule", + "target": "AK5", + "sign": true + }, + { + "id": "t295", + "source": "dADP_simple_molecule", + "target": "AK5", + "sign": true + }, + { + "id": "t296", + "source": "ADP_simple_molecule", + "target": "Deoxyadenosine_simple_molecule", + "sign": true + }, + { + "id": "t297", + "source": "H_simple_molecule", + "target": "Deoxyadenosine_simple_molecule", + "sign": true + }, + { + "id": "t298", + "source": "Ammonium_simple_molecule", + "target": "Deoxyadenosine_simple_molecule", + "sign": true + }, + { + "id": "t299", + "source": "Deoxyinosine_simple_molecule", + "target": "Deoxyadenosine_simple_molecule", + "sign": true + }, + { + "id": "t300", + "source": "dAMP_simple_molecule", + "target": "Deoxyadenosine_simple_molecule", + "sign": true + }, + { + "id": "t301", + "source": "ADP_simple_molecule", + "target": "dAMP_simple_molecule", + "sign": true + }, + { + "id": "t302", + "source": "dADP_simple_molecule", + "target": "dAMP_simple_molecule", + "sign": true + }, + { + "id": "t303", + "source": "ADP_simple_molecule", + "target": "dADP_simple_molecule", + "sign": true + }, + { + "id": "t304", + "source": "dATP_simple_molecule", + "target": "dADP_simple_molecule", + "sign": true + }, + { + "id": "t305", + "source": "dATP_simple_molecule", + "target": "Nucleoside_diphosphate_kinase_complex_cell", + "sign": true + }, + { + "id": "t306", + "source": "Lactose_simple_molecule", + "target": "UDP-_alpha_-D-Galactose_simple_molecule", + "sign": true + }, + { + "id": "t307", + "source": "UDP_simple_molecule", + "target": "UDP-_alpha_-D-Galactose_simple_molecule", + "sign": true + }, + { + "id": "t308", + "source": "UDP-_alpha_-D-Galactose_simple_molecule", + "target": "UDP-_alpha_-D-Glucose_simple_molecule", + "sign": true + }, + { + "id": "t309", + "source": "_alpha_-D-Glucose-1-P_simple_molecule", + "target": "UDP-_alpha_-D-Glucose_simple_molecule", + "sign": true + }, + { + "id": "t310", + "source": "UTP_simple_molecule", + "target": "UDP-_alpha_-D-Glucose_simple_molecule", + "sign": true + }, + { + "id": "t311", + "source": "UDP-_alpha_-D-Galactose_simple_molecule", + "target": "GALT", + "sign": true + }, + { + "id": "t312", + "source": "_alpha_-D-Glucose-1-P_simple_molecule", + "target": "GALT", + "sign": true + }, + { + "id": "t313", 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"NADPH_simple_molecule", + "target": "GMPR2", + "sign": true + }, + { + "id": "t438", + "source": "H_simple_molecule", + "target": "GMPR2", + "sign": true + }, + { + "id": "t439", + "source": "GMP_simple_molecule", + "target": "GMPR2", + "sign": true + }, + { + "id": "t440", + "source": "H_simple_molecule", + "target": "CD38", + "sign": true + }, + { + "id": "t441", + "source": "Nicotinamide_simple_molecule", + "target": "CD38", + "sign": true + }, + { + "id": "t442", + "source": "nicotinate-adenine_dinucleotide_phosphate_simple_molecule", + "target": "CD38", + "sign": true + }, + { + "id": "t443", + "source": "ADP-D-ribose_simple_molecule", + "target": "CD38", + "sign": true + }, + { + "id": "t444", + "source": "H_simple_molecule", + "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t445", + "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t446", + "source": "Tetrahydrofolate_simple_molecule", + "target": "5-phospho-beta-D-ribosylglycinamide_simple_molecule", + "sign": true + }, + { + "id": "t447", + "source": "H_simple_molecule", + "target": "10-Formyltetrahydrofolate_simple_molecule", + "sign": true + }, + { + "id": "t448", + "source": "5-phosphoribosyl-N-formylglycinamide_simple_molecule", + "target": "10-Formyltetrahydrofolate_simple_molecule", + "sign": true + }, + { + "id": "t449", + "source": "Tetrahydrofolate_simple_molecule", + "target": "10-Formyltetrahydrofolate_simple_molecule", + "sign": true + }, + { + "id": "t450", + "source": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", + "target": "10-Formyltetrahydrofolate_simple_molecule", + "sign": true + }, + { + "id": "t451", + "source": "H_simple_molecule", + "target": "Aminoimidazole_ribotide_simple_molecule", + "sign": true + }, + { + "id": "t452", + "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "target": "Aminoimidazole_ribotide_simple_molecule", + "sign": true + }, + { + "id": "t453", + "source": "H_simple_molecule", + "target": "CO2_simple_molecule", + "sign": true + }, + { + "id": "t454", + "source": "1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate_simple_molecule", + "target": "CO2_simple_molecule", + "sign": true + }, + { + "id": "t455", + "source": "H_simple_molecule", + "target": "IMPDH1", + "sign": true + }, + { + "id": "t456", + "source": "NADH_simple_molecule", + "target": "IMPDH1", + "sign": true + }, + { + "id": "t457", + "source": "XMP_simple_molecule", + "target": "IMPDH1", + "sign": true + }, + { + "id": "t458", + "source": "H_simple_molecule", + "target": "Mycophenolic_acid_drug", + "sign": false + }, + { + "id": "t459", + "source": "NADH_simple_molecule", + "target": "Mycophenolic_acid_drug", + "sign": false + }, + { + "id": "t460", + "source": "XMP_simple_molecule", + "target": "Mycophenolic_acid_drug", + "sign": false + }, + { + "id": "t461", + "source": "H_simple_molecule", + "target": "Merimepodib_drug", + "sign": false + }, + { + "id": "t462", + "source": "NADH_simple_molecule", + "target": "Merimepodib_drug", + "sign": false + }, + { + "id": "t463", + "source": "XMP_simple_molecule", + "target": "Merimepodib_drug", + "sign": false + }, + { + "id": "t464", + "source": "H_simple_molecule", + "target": "Ribavirin_drug", + "sign": false + }, + { + "id": "t465", + "source": "NADH_simple_molecule", + "target": "Ribavirin_drug", + "sign": false + }, + { + "id": "t466", + "source": "XMP_simple_molecule", + "target": "Ribavirin_drug", + "sign": false + }, + { + "id": "t467", + "source": "H_simple_molecule", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t468", + "source": "Pi_simple_molecule", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t469", + "source": "GMP_simple_molecule", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t470", + "source": "GDP_simple_molecule", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t471", + "source": "H_simple_molecule", + "target": "ENTPD2", + "sign": true + }, + { + "id": "t472", + "source": "Pi_simple_molecule", + "target": "ENTPD2", + "sign": true + }, + { + "id": "t473", + "source": "GMP_simple_molecule", + "target": "ENTPD2", + "sign": true + }, + { + "id": "t474", + "source": "GDP_simple_molecule", + "target": "ENTPD2", + "sign": true + }, + { + "id": "t475", + "source": "H_simple_molecule", + "target": "NTPCR", + "sign": true + }, + { + "id": "t476", + "source": "Pi_simple_molecule", + "target": "NTPCR", + "sign": true + }, + { + "id": "t477", + "source": "GDP_simple_molecule", + "target": "NTPCR", + "sign": true + }, + { + "id": "t478", + "source": "H_simple_molecule", + "target": "ENTPD4", + "sign": true + }, + { + "id": "t479", + "source": "Pi_simple_molecule", + "target": "ENTPD4", + "sign": true + }, + { + "id": "t480", + "source": "GMP_simple_molecule", + "target": "ENTPD4", + "sign": true + }, + { + "id": "t481", + "source": "H_simple_molecule", + "target": "ENTPD5", + "sign": true + }, + { + "id": "t482", + "source": "Pi_simple_molecule", + "target": "ENTPD5", + "sign": true + }, + { + "id": "t483", + "source": "GMP_simple_molecule", + "target": "ENTPD5", + "sign": true + }, + { + "id": "t484", + "source": "H_simple_molecule", + "target": "ENTPD6", + "sign": true + }, + { + "id": "t485", + "source": "Pi_simple_molecule", + "target": "ENTPD6", + "sign": true + }, + { + "id": "t486", + "source": "GMP_simple_molecule", + "target": "ENTPD6", + "sign": true + }, + { + "id": "t487", + "source": "H_simple_molecule", + "target": "CANT1", + "sign": true + }, + { + "id": "t488", + "source": "Pi_simple_molecule", + "target": "CANT1", + "sign": true + }, + { + "id": "t489", + "source": "GMP_simple_molecule", + "target": "CANT1", + "sign": true + }, + { + "id": "t490", + "source": "H_simple_molecule", + "target": "XDH", + "sign": true + }, + { + "id": "t491", + "source": "NADH_simple_molecule", + "target": "XDH", + "sign": true + }, + { + "id": "t492", + "source": "Xanthine_simple_molecule", + "target": "XDH", + "sign": true + }, + { + "id": "t493", + "source": "Nicotinamide_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t494", + "source": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t495", + "source": "Guanine_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t496", + "source": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t497", + "source": "Xanthine_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t498", + "source": "Hypoxanthine_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t499", + "source": "Adenine_simple_molecule", + "target": "Pi_simple_molecule", + "sign": true + }, + { + "id": "t500", + "source": "Nicotinamide_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t501", + "source": "Pi_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t502", + "source": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t503", + "source": "Guanine_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t504", + "source": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t505", + "source": "Xanthine_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t506", + "source": "Hypoxanthine_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t507", + "source": "Adenine_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t508", + "source": "Deoxyinosine_simple_molecule", + "target": "PNP", + "sign": true + }, + { + "id": "t509", + "source": "Nicotinamide_simple_molecule", + "target": "Histone_N6-acetyl-L-lysine_simple_molecule", + "sign": true + }, + { + "id": "t510", + "source": "Histone-L-lysine_simple_molecule", + "target": "Histone_N6-acetyl-L-lysine_simple_molecule", + "sign": true + }, + { + "id": "t511", + "source": "O-Acetyl-ADP-ribose_simple_molecule", + "target": "Histone_N6-acetyl-L-lysine_simple_molecule", + "sign": true + }, + { + "id": "t512", + "source": "Nicotinamide_simple_molecule", + "target": "H2O_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t513", + "source": "Histone-L-lysine_simple_molecule", + "target": "H2O_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t514", + "source": "O-Acetyl-ADP-ribose_simple_molecule", + "target": "H2O_simple_molecule_mitochondrion", + "sign": true + }, + { + "id": "t515", + "source": "N-Ribosyl-nicotinamide_simple_molecule", + "target": "NT5E", + "sign": true + }, + { + "id": "t516", + "source": "Pi_simple_molecule", + "target": "NT5E", + "sign": true + }, + { + "id": "t517", + "source": "Guanosine_simple_molecule", + "target": "NT5E", + "sign": true + }, + { + "id": "t518", + "source": "Xanthosine_simple_molecule", + "target": "NT5E", + "sign": true + }, + { + "id": "t519", + "source": "Inosine_simple_molecule", + "target": "NT5E", + "sign": true + }, + { + "id": "t520", + "source": "Adenosine_simple_molecule", + "target": "NT5E", + "sign": true + }, + { + "id": "t521", + "source": "AMP_simple_molecule", + "target": "D-Ribose_5P_simple_molecule", + "sign": true + }, + { + "id": "t522", + "source": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "target": "D-Ribose_5P_simple_molecule", + "sign": true + }, + { + "id": "t523", + "source": "AMP_simple_molecule", + "target": "PRPS1", + "sign": true + }, + { + "id": "t524", + "source": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "target": "PRPS1", + "sign": true + }, + { + "id": "t525", + "source": "AMP_simple_molecule", + "target": "PRPS2", + "sign": true + }, + { + "id": "t526", + "source": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "target": "PRPS2", + "sign": true + }, + { + "id": "t527", + "source": "AMP_simple_molecule", + "target": "PRPS1L1", + "sign": true + }, + { + "id": "t528", + "source": "5-phospho-_alpha_-D-ribose_1-diphosphate_simple_molecule", + "target": "PRPS1L1", + "sign": true + }, + { + "id": "t529", + "source": "Pi_simple_molecule", + "target": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "sign": true + }, + { + "id": "t530", + "source": "Deoxyinosine_simple_molecule", + "target": "2-deoxy-_alpha_-D-ribose_1-phosphate_simple_molecule", + "sign": true + }, + { + "id": "t531", + "source": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "target": "Guanosine_simple_molecule", + "sign": true + }, + { + "id": "t532", + "source": "Guanine_simple_molecule", + "target": "Guanosine_simple_molecule", + "sign": true + }, + { + "id": "t533", + "source": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "target": "Xanthosine_simple_molecule", + "sign": true + }, + { + "id": "t534", + "source": "Xanthine_simple_molecule", + "target": "Xanthosine_simple_molecule", + "sign": true + }, + { + "id": "t535", + "source": "_alpha_-D-Ribose_1-phosphate_simple_molecule", + "target": "Inosine_simple_molecule", + "sign": true + }, + { + "id": "t536", + "source": "Hypoxanthine_simple_molecule", + "target": "Inosine_simple_molecule", + "sign": true + }, + { + "id": "t537", + "source": "D-Ribose_5P_simple_molecule", + "target": "_alpha_D-Ribose_1P_simple_molecule", + "sign": true + }, + { + "id": "t538", + "source": "D-Ribose_5P_simple_molecule", + "target": "PGM2", + "sign": true + }, + { + "id": "t539", + "source": "Tetrahydrofolate_simple_molecule", + "target": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "sign": true + }, + { + "id": "t540", + "source": "1-(5'-Phosphoribosyl)-5-formamido-4-imidazolecarboxamide_simple_molecule", + "target": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "sign": true + }, + { + "id": "t541", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "target": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "sign": true + }, + { + "id": "t542", + "source": "Fumarate_simple_molecule", + "target": "1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole_simple_molecule", + "sign": true + }, + { + "id": "t543", + "source": "1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide_simple_molecule", + "target": "ADSL", + "sign": true + }, + { + "id": "t544", + "source": "Fumarate_simple_molecule", + "target": "ADSL", + "sign": true + }, + { + "id": "t545", + "source": "IMP_simple_molecule", + "target": "AMDP2", + "sign": true + }, + { + "id": "t546", + "source": "Ammonium_simple_molecule", + "target": "AMDP2", + "sign": true + }, + { + "id": "t547", + "source": "IMP_simple_molecule", + "target": "AMPD1", + "sign": true + }, + { + "id": "t548", + "source": "Ammonium_simple_molecule", + "target": "AMPD1", + "sign": true + }, + { + "id": "t549", + "source": "IMP_simple_molecule", + "target": "AMPD3", + "sign": true + }, + { + "id": "t550", + "source": "Ammonium_simple_molecule", + "target": "AMPD3", + "sign": true + }, + { + "id": "t551", + "source": "Ammonium_simple_molecule", + "target": "GDA", + "sign": true + }, + { + "id": "t552", + "source": "Xanthine_simple_molecule", + "target": "GDA", + "sign": true + }, + { + "id": "t553", + "source": "Ammonium_simple_molecule", + "target": "ADA", + "sign": true + }, + { + "id": "t554", + "source": "Inosine_simple_molecule", + "target": "ADA", + "sign": true + }, + { + "id": "t555", + "source": "Deoxyinosine_simple_molecule", + "target": "ADA", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Nsp4_Nsp6.json b/scripts/covid19_diseasemaps/regnet_amr/Nsp4_Nsp6.json new file mode 100644 index 000000000..2c1f7705c --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Nsp4_Nsp6.json @@ -0,0 +1,897 @@ +{ + "header": { + "name": "Nsp4_Nsp6", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Nsp4_Nsp6", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "Nsp3:Nsp4:Nsp6_complex", + "name": "Nsp3:Nsp4:Nsp6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Plasma_membrane_organization_phenotype", + "name": "Plasma_membrane_organization_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp3", + "name": "Nsp3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6", + "name": "Nsp6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F-ATPase:Nsp6_complex", + "name": "F-ATPase:Nsp6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "name": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "P-ATPase:Nsp6_complex", + "name": "P-ATPase:Nsp6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC6A15:Nsp6_complex", + "name": "SLC6A15:Nsp6_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "name": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_cell", + "name": "Nsp4_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "name": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nsp4:DNAJC11_complex", + "name": "Nsp4:DNAJC11_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "name": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4:IDE_complex_cell", + "name": "Nsp4:IDE_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nsp4_mitochondrion", + "name": "Nsp4_mitochondrion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ALG11_endoplasmic_reticulum", + "name": "ALG11_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nsp4_IDE_complex", + "name": "Nsp4_IDE_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DNAJC11", + "name": "DNAJC11", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "F-ATPase_complex_mitochondrial_matrix", + "name": "F-ATPase_complex_mitochondrial_matrix", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nsp4:NUP210_complex_nucleus", + "name": "Nsp4:NUP210_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP210_endoplasmic_reticulum", + "name": "NUP210_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, 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"Nsp6:SIGMAR1_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6:SIGMAR1_complex_cell", + "name": "Nsp6:SIGMAR1_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase:Nsp6_complex_endosome", + "name": "V-ATPase:Nsp6_complex_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TIM_complex:Nsp4_complex", + "name": "TIM_complex:Nsp4_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TIM_complex_complex", + "name": "TIM_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase_complex_endoplasmic_reticulum", + "name": "V-ATPase_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase_complex_endosome", + "name": "V-ATPase_complex_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP5MG", + "name": "ATP5MG", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-type_space_proton_space_ATPase_complex", + "name": "V-type_space_proton_space_ATPase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion", + "name": "H+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP6AP1", + "name": "ATP6AP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP6AP1:Bafilomycin_A1_complex", + "name": "ATP6AP1:Bafilomycin_A1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Selinexor_drug", + "name": "Selinexor_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "P-ATPase_complex_cell", + "name": "P-ATPase_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "ATP13A3", + "name": "ATP13A3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC6A15", + "name": "SLC6A15", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC6A15:Orf9c_complex", + "name": "SLC6A15:Orf9c_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC6A15:M_complex", + "name": "SLC6A15:M_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SLC6A15:Loratadine_complex", + "name": "SLC6A15:Loratadine_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9c", + "name": "Orf9c", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M", + "name": "M", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Loratadine_drug", + "name": "Loratadine_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Bafilomycin_A1_drug", + "name": "Bafilomycin_A1_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IDE_cell", + "name": "IDE_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "IDE_human_host", + "name": "IDE_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_(+)_rna", + "name": "Nsp4_(+)_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_(-)_rna", + "name": "Nsp4_(-)_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6_(+)_rna", + "name": "Nsp6_(+)_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6_(-)_rna", + "name": "Nsp6_(-)_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp3_(+)_rna", + "name": "Nsp3_(+)_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp3_(-)_rna", + "name": "Nsp3_(-)_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TOM_complex_complex", + "name": "TOM_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "Plasma_membrane_organization_phenotype", + "target": "Nsp3:Nsp4:Nsp6_complex", + "sign": true + }, + { + "id": "t2", + "source": "Nsp3:Nsp4:Nsp6_complex", + "target": "Nsp3", + "sign": true + }, + { + "id": "t3", + "source": "Nsp3:Nsp4:Nsp6_complex", + "target": "Nsp6", + "sign": true + }, + { + "id": "t4", + "source": "F-ATPase:Nsp6_complex", + "target": "Nsp6", + "sign": true + }, + { + "id": "t5", + "source": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "target": "Nsp6", + "sign": true + }, + { + "id": "t6", + "source": "P-ATPase:Nsp6_complex", + "target": "Nsp6", + "sign": true + }, + { + "id": "t7", + "source": "SLC6A15:Nsp6_complex", + "target": "Nsp6", + "sign": true + }, + { + "id": "t8", + "source": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "target": "Nsp6", + "sign": true + }, + { + "id": "t9", + "source": "Nsp3:Nsp4:Nsp6_complex", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t10", + "source": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t11", + "source": "Nsp4:DNAJC11_complex", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t12", + "source": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t13", + "source": "Nsp4:IDE_complex_cell", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t14", + "source": "Nsp4_mitochondrion", + "target": "Nsp4_cell", + "sign": true + }, + { + "id": "t16", + "source": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "target": "ALG11_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t18", + "source": "Nsp4_IDE_complex", + "target": "Nsp4:IDE_complex_cell", + "sign": true + }, + { + "id": "t20", + "source": "Nsp4:DNAJC11_complex", + "target": "DNAJC11", + "sign": true + }, + { + "id": "t21", + "source": "F-ATPase:Nsp6_complex", + "target": "F-ATPase_complex_mitochondrial_matrix", + "sign": true + }, + { + "id": "t22", + "source": "Nsp4:NUP210_complex_nucleus", + "target": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t23", + "source": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "target": "NUP210_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t24", + "source": "NUP210:Selinexor_complex", + "target": "NUP210_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t25", + "source": "NUP210_nucleus", + "target": "NUP210_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t26", + "source": "SIGMAR1:Drugs_complex", + "target": "Several_drugs_drug", + "sign": true + }, + { + "id": "t27", + "source": "SIGMAR1:Drugs_complex", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t28", + "source": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t29", + "source": "SIGMAR1_nucleus", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t30", + "source": "SIGMAR1_cell", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t31", + "source": "Nsp6:SIGMAR1_complex_nucleus", + "target": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t32", + "source": "Nsp6:SIGMAR1_complex_cell", + "target": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t33", + "source": "V-ATPase:Nsp6_complex_endosome", + "target": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t34", + "source": "TIM_complex:Nsp4_complex", + "target": "Nsp4_mitochondrion", + "sign": true + }, + { + "id": "t35", + "source": "TIM_complex:Nsp4_complex", + "target": "TIM_complex_complex", + "sign": true + }, + { + "id": "t36", + "source": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "target": "V-ATPase_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t37", + "source": "V-ATPase_complex_endosome", + "target": "V-ATPase_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t38", + "source": "F-ATPase_complex_mitochondrial_matrix", + "target": "ATP5MG", + "sign": true + }, + { + "id": "t40", + "source": "V-ATPase_complex_endoplasmic_reticulum", + "target": "V-type_space_proton_space_ATPase_complex", + "sign": true + }, + { + "id": "t41", + "source": "H+_ion", + "target": "V-type_space_proton_space_ATPase_complex", + "sign": true + }, + { + "id": "t42", + "source": "V-ATPase_complex_endoplasmic_reticulum", + "target": "ATP6AP1", + "sign": true + }, + { + "id": "t43", + "source": "ATP6AP1:Bafilomycin_A1_complex", + "target": "ATP6AP1", + "sign": true + }, + { + "id": "t44", + "source": "NUP210:Selinexor_complex", + "target": "Selinexor_drug", + "sign": true + }, + { + "id": "t45", + "source": "P-ATPase:Nsp6_complex", + "target": "P-ATPase_complex_cell", + "sign": true + }, + { + "id": "t46", + "source": "P-ATPase_complex_cell", + "target": "ATP13A3", + "sign": true + }, + { + "id": "t48", + "source": "SLC6A15:Nsp6_complex", + "target": "SLC6A15", + "sign": true + }, + { + "id": "t49", + "source": "SLC6A15:Orf9c_complex", + "target": "SLC6A15", + "sign": true + }, + { + "id": "t50", + "source": "SLC6A15:M_complex", + "target": "SLC6A15", + "sign": true + }, + { + "id": "t51", + "source": "SLC6A15:Loratadine_complex", + "target": "SLC6A15", + "sign": true + }, + { + "id": "t52", + "source": "SLC6A15:Orf9c_complex", + "target": "Orf9c", + "sign": true + }, + { + "id": "t53", + "source": "SLC6A15:M_complex", + "target": "M", + "sign": true + }, + { + "id": "t54", + "source": "SLC6A15:Loratadine_complex", + "target": "Loratadine_drug", + "sign": true + }, + { + "id": "t55", + "source": "ATP6AP1:Bafilomycin_A1_complex", + "target": "Bafilomycin_A1_drug", + "sign": true + }, + { + "id": "t56", + "source": "Nsp4:IDE_complex_cell", + "target": "IDE_cell", + "sign": true + }, + { + "id": "t57", + "source": "IDE_human_host", + "target": "IDE_cell", + "sign": true + }, + { + "id": "t59", + "source": "Nsp4_cell", + "target": "Nsp4_(+)_rna", + "sign": true + }, + { + "id": "t60", + "source": "Nsp4_(-)_rna", + "target": "Nsp4_(+)_rna", + "sign": true + }, + { + "id": "t61", + "source": "Nsp4_(+)_rna", + "target": "Nsp4_(-)_rna", + "sign": true + }, + { + "id": "t62", + "source": "Nsp6", + "target": "Nsp6_(+)_rna", + "sign": true + }, + { + "id": "t63", + "source": "Nsp6_(-)_rna", + "target": "Nsp6_(+)_rna", + "sign": true + }, + { + "id": "t64", + "source": "Nsp6_(+)_rna", + "target": "Nsp6_(-)_rna", + "sign": true + }, + { + "id": "t65", + "source": "Nsp3", + "target": "Nsp3_(+)_rna", + "sign": true + }, + { + "id": "t66", + "source": "Nsp3_(-)_rna", + "target": "Nsp3_(+)_rna", + "sign": true + }, + { + "id": "t67", + "source": "Nsp3_(+)_rna", + "target": "Nsp3_(-)_rna", + "sign": true + }, + { + "id": "t68", + "source": "Nsp4_mitochondrion", + "target": "TOM_complex_complex", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Nsp9_protein.json b/scripts/covid19_diseasemaps/regnet_amr/Nsp9_protein.json new file mode 100644 index 000000000..826908491 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Nsp9_protein.json @@ -0,0 +1,3484 @@ +{ + "header": { + "name": "Nsp9_protein", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Nsp9_protein", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "Nsp9_cell", + "name": "Nsp9_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fibrillincomp_complex", + "name": "Fibrillincomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nuclear_Pore_comp_complex", + "name": "Nuclear_Pore_comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mibcomp_complex", + "name": "mibcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "pathogen_complex", + "name": "pathogen_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "spartcomp_complex", + "name": "spartcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "mat2bcomp_complex", + "name": "mat2bcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NspComp_complex", + "name": "NspComp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "homodimer_complex", + "name": "homodimer_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Fibrillin_complex_human_host", + "name": "Fibrillin_complex_human_host", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "FBLN5", + "name": "FBLN5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "LOXcomp_complex", + "name": "LOXcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PLG", + "name": "PLG", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nuclear_Pore_complex", + "name": "Nuclear_Pore_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MIB1", + "name": "MIB1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MIBcomp_complex", + "name": "MIBcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DLL1", + "name": "DLL1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Vpr", + "name": "Vpr", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS_complex_nucleus", + "name": "COPS_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "SCARB1", + "name": "SCARB1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "lipidcomp_complex", + "name": "lipidcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SCARB1_complex", + "name": "SCARB1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Phosphatidyl_serine_simple_molecule", + "name": "Phosphatidyl_serine_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAT1A", + "name": "MAT1A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SAdComp_complex", + "name": 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{}, + "context": {} + } + }, + { + "id": "Nsp7812_complex_cell", + "name": "Nsp7812_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "FOCADcomp_complex", + "name": "FOCADcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SRP54comp_complex", + "name": "SRP54comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MPHOSPHcomp_complex", + "name": "MPHOSPHcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MRPScomp_complex", + "name": "MRPScomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SEPSECScomp_complex", + "name": "SEPSECScomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NOL10comp_complex", + "name": "NOL10comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AATFcomp_complex", + "name": "AATFcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DDX10comp_complex", + "name": "DDX10comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NGDNcomp_complex", + "name": "NGDNcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CCDCcomp_complex", + "name": "CCDCcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MEPCEcomp_complex", + "name": "MEPCEcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NARS2comp_complex", + "name": "NARS2comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EXOSC3", + "name": "EXOSC3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EXOSC5", + "name": "EXOSC5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EXOSC8", + "name": "EXOSC8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp9_nucleus", + "name": "Nsp9_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "gtf2f2comp_complex", + "name": "gtf2f2comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "znfcomp_complex", + "name": "znfcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "eifcomp_complex", + "name": "eifcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dcafcomp_complex", + "name": "dcafcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "nek9comp_complex", + "name": "nek9comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GTF2F2", + "name": "GTF2F2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "gtfrnapoly_complex", + "name": "gtfrnapoly_complex", + "grounding": { + "identifiers": {}, + "context": {} + } 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+ "identifiers": {}, + "context": {} + } + }, + { + "id": "EDN1-homo_complex_nucleus", + "name": "EDN1-homo_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "EDN1-homo_complex_endoplasmic_reticulum", + "name": "EDN1-homo_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ZNF503", + "name": "ZNF503", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dcafznf_complex", + "name": "dcafznf_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp7", + "name": "Nsp7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RHOA7comp_complex", + "name": "RHOA7comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CA12comp_complex", + "name": "CA12comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CYB5R3comp_complex", + "name": "CYB5R3comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COMT_complex", + "name": "COMT_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RALAcomp_complex", + "name": "RALAcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RAB7comp_complex", + "name": "RAB7comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACSLcomp_complex", + "name": "ACSLcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SRP72comp_complex", + "name": "SRP72comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp12", + "name": "Nsp12", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MYCBPcomp_complex", + "name": "MYCBPcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SBNOcomp_complex", + "name": "SBNOcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "s389_complex", + "name": "s389_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RBMcomp_complex", + "name": "RBMcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ZNFcomp_complex", + "name": "ZNFcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "LARPcomp_complex", + "name": "LARPcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ZC3H7Acomp_complex", + "name": "ZC3H7Acomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TCFcomp_complex", + "name": "TCFcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "virus_replication_phenotype", + "name": "virus_replication_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RdRpassembled_rna", + "name": "RdRpassembled_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "remdesivir__drug", + "name": "remdesivir__drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "favipiravir_drug", + "name": "favipiravir_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP54", + "name": "NUP54", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP58", + "name": "NUP58", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP62", + "name": "NUP62", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP214", + "name": "NUP214", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP88", + "name": "NUP88", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BAG6", + "name": "BAG6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NEK9", + "name": "NEK9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NEKs_complex", + "name": "NEKs_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NEK7", + "name": "NEK7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NEK6", + "name": "NEK6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GTF2B", + "name": "GTF2B", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "POLR2A", + "name": "POLR2A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "POLR2B", + "name": "POLR2B", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "POLR2E", + "name": "POLR2E", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "POLR2G", + "name": "POLR2G", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EDN1", + "name": "EDN1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EIF4H", + "name": "EIF4H", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS2", + "name": "COPS2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS4", + "name": "COPS4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS5", + "name": "COPS5", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS6", + "name": "COPS6", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS7A", + "name": "COPS7A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COPS8", + "name": "COPS8", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UBQLN4", + "name": "UBQLN4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TAT", + "name": "TAT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DCAF7", + "name": "DCAF7", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EDN1_rna", + "name": "EDN1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SPART", + "name": "SPART", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SPARTcomp_complex", + "name": "SPARTcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AIFM1", + "name": "AIFM1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AIFMFlaComp_complex", + "name": "AIFMFlaComp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Neutrophil_activation_phenotype", + "name": "Neutrophil_activation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp10_cell", + "name": "Nsp10_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP2A2comp_complex", + "name": "AP2A2comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GFERcomp_complex", + "name": "GFERcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP2M1comp_complex", + "name": "AP2M1comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp16", + "name": "Nsp16", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NEMF", + "name": "NEMF", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp14_cell", + "name": "Nsp14_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SIRT5comp_complex", + "name": "SIRT5comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PEG10comp_complex", + "name": "PEG10comp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CA12", + "name": "CA12", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HCTcomp_complex", + "name": "HCTcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ZonisamideComp_complex", + "name": "ZonisamideComp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "EAcomp_complex", + "name": "EAcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HFTcomp_complex", + "name": "HFTcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BZcomp_complex", + "name": "BZcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Hydrochlorothiazide_drug", + "name": "Hydrochlorothiazide_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FOCAD", + "name": "FOCAD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RNArecognition_complex", + "name": "RNArecognition_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ssRNAoligo_rna", + "name": "ssRNAoligo_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAT2B", + "name": "MAT2B", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NEC1_complex", + "name": "NEC1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MAT2A", + "name": "MAT2A", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PTGS2", + "name": "PTGS2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PTGScomp_complex", + "name": "PTGScomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Rofecoxib_drug", + "name": "Rofecoxib_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RofecoxibComp_complex", + "name": "RofecoxibComp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RHOA", + "name": "RHOA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RGcomp_complex_cell", + "name": "RGcomp_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PCSK1", + "name": "PCSK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NECINsComp_complex", + "name": "NECINsComp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NECENVComp_complex", + "name": "NECENVComp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Flavin_adenine_dinucleotide_drug", + "name": "Flavin_adenine_dinucleotide_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Sitaxentan_drug", + "name": "Sitaxentan_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ambrisentan_drug", + "name": "Ambrisentan_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Acetylsalicylic_acid_drug", + "name": "Acetylsalicylic_acid_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Macitentan_drug", + "name": "Macitentan_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SEPSECS", + "name": "SEPSECS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SPcomp_complex", + "name": "SPcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Pyridoxal_phosphate_simple_molecule", + "name": "Pyridoxal_phosphate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MYCBP2", + "name": "MYCBP2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SBNO1", + "name": "SBNO1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BCKDK", + "name": "BCKDK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADPcomp_complex", + "name": "ADPcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADP_simple_molecule", + "name": "ADP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RBM41", + "name": "RBM41", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ZNF318", + "name": "ZNF318", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "LARP4B_", + "name": "LARP4B_", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SRP54", + "name": "SRP54", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SRP19", + "name": "SRP19", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ZC3H7A_", + "name": "ZC3H7A_", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Insulin", + "name": "Insulin", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Zonisamide_drug", + "name": "Zonisamide_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Ellagic_Acid_drug", + "name": "Ellagic_Acid_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Hydroflumethiazide_drug", + "name": "Hydroflumethiazide_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Benzthiazide_drug", + "name": "Benzthiazide_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AP2A2", + "name": "AP2A2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ELN", + "name": "ELN", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENV", + "name": "ENV", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CYB5R3", + "name": "CYB5R3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADHcomp_complex", + "name": "NADHcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FADcomp_complex", + "name": "FADcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NADH_simple_molecule", + "name": "NADH_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FAD_simple_molecule", + "name": "FAD_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "FGCOMP_complex", + "name": "FGCOMP_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "COMT", + "name": "COMT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TCcomp_complex", + "name": "TCcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NCcomp_complex", + "name": "NCcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DCcomp_complex", + "name": "DCcomp_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACcomp_complex", + "name": "ACcomp_complex", + "grounding": { + "identifiers": {}, + 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+ { + "id": "t251", + "source": "Mycophenolic_acid_drug", + "target": "Mycophenolate_mofetil_drug", + "sign": true + }, + { + "id": "t252", + "source": "PLG", + "target": "PLAT", + "sign": true + }, + { + "id": "t253", + "source": "PLG", + "target": "Nafamostat_drug", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Orf10_Cul2_pathway.json b/scripts/covid19_diseasemaps/regnet_amr/Orf10_Cul2_pathway.json new file mode 100644 index 000000000..e855659d6 --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Orf10_Cul2_pathway.json @@ -0,0 +1,1116 @@ +{ + "header": { + "name": "Orf10_Cul2_pathway", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Orf10_Cul2_pathway", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "Cul2_ubiquitin_ligase_complex", + "name": "Cul2_ubiquitin_ligase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Zyg11B:EloBC_complex", + "name": "Zyg11B:EloBC_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Cul2_ubiquitin_ligase:Orf10_complex", + "name": "Cul2_ubiquitin_ligase:Orf10_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Cul2_ubiquitin_ligase:substrate_complex_cell", + "name": "Cul2_ubiquitin_ligase:substrate_complex_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Rbx1:Cul2_complex", + "name": "Rbx1:Cul2_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UBE2M", + "name": "UBE2M", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ubit_traget", + "name": "ubit_traget", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Cul2_ubiquitin_ligase:Orf10:substrate_complex", + "name": "Cul2_ubiquitin_ligase:Orf10:substrate_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf10", + "name": "Orf10", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Cul2_ubiquitin_ligase:N8_complex", + "name": "Cul2_ubiquitin_ligase:N8_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CSN5_complex", + "name": "CSN5_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ELOB:ELOC_complex", + "name": "ELOB:ELOC_complex", + "grounding": { + "identifiers": {}, + 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"source": "UBA3", + "target": "UBA3_rna", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Orf3a.json b/scripts/covid19_diseasemaps/regnet_amr/Orf3a.json new file mode 100644 index 000000000..891eee57d --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Orf3a.json @@ -0,0 +1,662 @@ +{ + "header": { + "name": "Orf3a", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Orf3a", + "model_version": 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"context": {} + }, + "sign": true + }, + { + "id": "ORF8b", + "name": "ORF8b", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TICAM1", + "name": "TICAM1", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "TRIM23", + "name": "TRIM23", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIM38", + "name": "TRIM38", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TLR3", + "name": "TLR3", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "BTRC", + "name": "BTRC", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "TRIM9", + "name": "TRIM9", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TRIM39", + "name": "TRIM39", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "IFNB1", + "name": "IFNB1", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "double-stranded_RNA_rna", + "name": "double-stranded_RNA_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "Hops_Complex_complex", + "target": "Orf3a", + "sign": true + }, + { + "id": "t2", + "source": "P65/P015_complex", + "target": "Orf3a", + "sign": true + }, + { + "id": "t3", + "source": "TRIM59", + "target": "Orf3a", + "sign": true + }, + { + "id": "t4", + "source": "PYCARD_ubiquitinated_ubiquitinated_ubiquitinated", + "target": "Orf3a", + "sign": true + }, + { + "id": "t5", + "source": "S", + "target": "Orf3a", + "sign": true + }, + { + "id": "t6", + "source": "P65/P015_complex", + "target": "IKBKG/IKBKB/CHUK_complex", + "sign": true + }, + { + "id": "t7", + "source": "IKBKG/IKBKB/CHUK_complex", + "target": "LPS/TNF_\u03b1/IL-1_complex", + "sign": true + }, + { + "id": "t8", + "source": "TRAF6", + "target": "LPS/TLR4/MYD88_complex", + "sign": true + }, + { + "id": 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true + }, + { + "id": "t46", + "source": "TRAF6", + "target": "TRIM38", + "sign": false + }, + { + "id": "t47", + "source": "TICAM1", + "target": "TRIM38", + "sign": false + }, + { + "id": "t48", + "source": "TICAM1", + "target": "TLR3", + "sign": true + }, + { + "id": "t49", + "source": "NFKBIA_phosphorylated_ubiquitinated_ubiquitinated_ubiquitinated", + "target": "BTRC", + "sign": true + }, + { + "id": "t51", + "source": "BTRC", + "target": "TRIM9", + "sign": false + }, + { + "id": "t53", + "source": "CACTIN", + "target": "TRIM39", + "sign": true + }, + { + "id": "t54", + "source": "IFNB1", + "target": "SERPINF2", + "sign": true + }, + { + "id": "t57", + "source": "TLR3", + "target": "double-stranded_RNA_rna", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/PAMP_signaling.json b/scripts/covid19_diseasemaps/regnet_amr/PAMP_signaling.json new file mode 100644 index 000000000..85554c32e --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/PAMP_signaling.json @@ -0,0 +1,1201 @@ +{ + "header": { + "name": "PAMP_signaling", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on PAMP_signaling", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "MYD88:IRAK:TRAF_complex", + "name": "MYD88:IRAK:TRAF_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IRF7_phosphorylated", + "name": "IRF7_phosphorylated", + "grounding": { 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"source": "IFIH1:dsRNA_complex", + "target": "IFIH1", + "sign": true + }, + { + "id": "t64", + "source": "IFIH1:dsRNA_complex", + "target": "Nsp15", + "sign": false + }, + { + "id": "t65", + "source": "EIF2AK2:dsRNA_complex", + "target": "Nsp15", + "sign": false + }, + { + "id": "t66", + "source": "AP1_complex", + "target": "JNK_complex", + "sign": true + }, + { + "id": "t67", + "source": "JNK_complex", + "target": "MAP2K7_phosphorylated", + "sign": true + }, + { + "id": "t68", + "source": "JNK_complex", + "target": "MAP2K4_phosphorylated", + "sign": true + }, + { + "id": "t69", + "source": "transcription_of_proinflammatory_proteins_phenotype", + "target": "NFKB_complex", + "sign": true + }, + { + "id": "t70", + "source": "NFKB_complex", + "target": "NFKB:NFKBIA_complex_cell", + "sign": true + }, + { + "id": "t71", + "source": "NFKBIA_phosphorylated", + "target": "NFKB:NFKBIA_complex_cell", + "sign": true + }, + { + "id": "t72", + "source": "NFKB_complex", + "target": "N", + "sign": true + }, + { + "id": "t73", + "source": "DDX58_ubiquitinated", + "target": "N", + "sign": false + }, + { + "id": "t74", + "source": "NFKBIA_phosphorylated", + "target": "N", + "sign": true + }, + { + "id": "t75", + "source": "MAP2K6_phosphorylated", + "target": "EIF2AK2:dsRNA_complex", + "sign": true + }, + { + "id": "t76", + "source": "EIF2AK2:dsRNA_complex", + "target": "EIF2AK2", + "sign": true + }, + { + "id": "t77", + "source": "NFKB:NFKBIA_complex_cell", + "target": "IKK_Complex_complex_cell", + "sign": true + }, + { + "id": "t78", + "source": "IKK_Complex_complex_cell", + "target": "TRAF6_ubiquitinated", + "sign": true + }, + { + "id": "t79", + "source": "TRAF6", + "target": "TRAF6_ubiquitinated", + "sign": true + }, + { + "id": "t80", + "source": "MAP3K7", + "target": "TRAF6_ubiquitinated", + "sign": true + }, + { + "id": "t81", + "source": "IKK_Complex_complex_cell", + "target": "CASP8", + "sign": true + }, + { + "id": "t82", + "source": "IKK_Complex_complex_cell", + "target": "CASP10", + "sign": true + }, + { + "id": "t83", + "source": "transcription_of_proinflammatory_proteins_phenotype", + "target": "AP1_complex", + "sign": true + }, + { + "id": "t84", + "source": "AP1_complex", + "target": "MAPK14_phosphorylated", + "sign": true + }, + { + "id": "t85", + "source": "IRF3_phosphorylated_cell", + "target": "TBK1_cell", + "sign": true + }, + { + "id": "t87", + "source": "IRF7_phosphorylated", + "target": "IKBKE_cell", + "sign": true + }, + { + "id": "t88", + "source": "IRF3_phosphorylated_nucleus", + "target": "IRF3_phosphorylated_cell", + "sign": true + }, + { + "id": "t89", + "source": "IRF3_phosphorylated_cell", + "target": "IRF3", + "sign": true + }, + { + "id": "t90", + "source": "IRF3_phosphorylated_cell", + "target": "Orf3b", + "sign": false + }, + { + "id": "t91", + "source": "IRF3_phosphorylated_cell", + "target": "Orf8", + "sign": false + }, + { + "id": "t92", + "source": "MAVS", + "target": "DDX58_ubiquitinated", + "sign": true + }, + { + "id": "t93", + "source": "DDX58_ubiquitinated", + "target": "RNF135", + "sign": true + }, + { + "id": "t94", + "source": "DDX58_ubiquitinated", + "target": "TRIM25", + "sign": true + }, + { + "id": "t95", + "source": "transcription_of_proinflammatory_proteins_phenotype", + "target": "IRF3_phosphorylated_nucleus", + "sign": true + }, + { + "id": "t96", + "source": "transcription_of_proinflammatory_proteins_phenotype", + "target": "IRF7_phosphorylated", + "sign": true + }, + { + "id": "t97", + "source": "TRAF6_ubiquitinated", + "target": "UBE2N", + "sign": true + }, + { + "id": "t98", + "source": "MAP2K6_phosphorylated", + "target": "MAP3K7", + "sign": true + }, + { + "id": "t99", + "source": "MAP2K3_phosphorylated", + "target": "MAP3K7", + "sign": true + }, + { + "id": "t100", + "source": "MAP2K4_phosphorylated", + "target": "MAP3K7", + "sign": true + }, + { + "id": "t101", + "source": "MAP2K7_phosphorylated", + "target": "MAP3K7", + "sign": true + }, + { + "id": "t102", + "source": "MAPK14_phosphorylated", + "target": "MAP2K6_phosphorylated", + "sign": true + }, + { + "id": "t103", + "source": "MAPK14_phosphorylated", + "target": "MAP2K3_phosphorylated", + "sign": true + }, + { + "id": "t104", + "source": "ITCH", + "target": "Orf9", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file diff --git a/scripts/covid19_diseasemaps/regnet_amr/Pyrimidine_deprivation.json b/scripts/covid19_diseasemaps/regnet_amr/Pyrimidine_deprivation.json new file mode 100644 index 000000000..ce217de0d --- /dev/null +++ b/scripts/covid19_diseasemaps/regnet_amr/Pyrimidine_deprivation.json @@ -0,0 +1,1601 @@ +{ + "header": { + "name": "Pyrimidine_deprivation", + "schema": "https://raw.githubusercontent.com/DARPA-ASKEM/Model-Representations/regnet_v0.2/regnet/regnet_schema.json", + "schema_name": "regnet", + "description": "A submodel of the COVID-10 Disease Map focusing on Pyrimidine_deprivation", + "model_version": "0.1" + }, + "model": { + "vertices": [ + { + "id": "IFNB1_space_expression_space_complex_complex", + "name": "IFNB1_space_expression_space_complex_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNA1_rna", + "name": "IFNA1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNB1_rna", + "name": "IFNB1_rna", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NF-kB_complex", + "name": "NF-kB_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IRF3_phosphorylated", + "name": "IRF3_phosphorylated", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cGAMP:STING_complex_Golgi_apparatus", + "name": "cGAMP:STING_complex_Golgi_apparatus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "STING:TBK1_complex_Golgi_apparatus", + "name": "STING:TBK1_complex_Golgi_apparatus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cGAMP:STING_complex_endoplasmic_reticulum", + "name": "cGAMP:STING_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cGAMP-STING_complex_COPII-coated_vesicle", + "name": "cGAMP-STING_complex_COPII-coated_vesicle", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "cGAMP_simple_molecule", + "name": "cGAMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "STING_endoplasmic_reticulum", + "name": "STING_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "STING_Golgi_apparatus", + "name": 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}, + { + "id": "UMP_simple_molecule", + "name": "UMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UDP_simple_molecule", + "name": "UDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UCK2", + "name": "UCK2", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "orotidine_space_5'-monophosphate_simple_molecule", + "name": "orotidine_space_5'-monophosphate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CO2_simple_molecule", + "name": "CO2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UMPS", + "name": "UMPS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PPi_simple_molecule", + "name": "PPi_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP_simple_molecule", + "name": "ATP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "GTP_simple_molecule", + "name": "GTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RTC_and_transcription_pw_phenotype", + "name": "RTC_and_transcription_pw_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "RNA_space_biosynthesis_phenotype", + "name": "RNA_space_biosynthesis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dCDP_simple_molecule", + "name": "dCDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dCTP_simple_molecule", + "name": "dCTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CDP_simple_molecule", + "name": "CDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTP_simple_molecule", + "name": "CTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ribonucleoside-diphosphate_reductase_complex", + "name": "ribonucleoside-diphosphate_reductase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dUDP_simple_molecule", + "name": "dUDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "UTP_simple_molecule", + "name": "UTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CMPK", + "name": "CMPK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dTMP_simple_molecule", + "name": "dTMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dTDP_simple_molecule", + "name": "dTDP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dUMP_simple_molecule", + "name": "dUMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "TYMS", + "name": "TYMS", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNA1_pulmonary_endothelial_cell", + "name": "IFNA1_pulmonary_endothelial_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNA1_human_host", + "name": "IFNA1_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Gln_simple_molecule", + "name": "L-Gln_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HCO3-simple_molecule", + "name": "HCO3-simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "L-Asp_simple_molecule", + "name": "L-Asp_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "QH2_simple_molecule", + "name": "QH2_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "orotate_simple_molecule", + "name": "orotate_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dUTP_simple_molecule", + "name": "dUTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DUT", + "name": "DUT", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dCMP_simple_molecule", + "name": "dCMP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DCTD", + "name": "DCTD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNB1_human_host", + "name": "IFNB1_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HCoVs_Type_I_Ifn_signalling(WP4868)_phenotype", + "name": "HCoVs_Type_I_Ifn_signalling(WP4868)_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Interferon_1_pathway_phenotype", + "name": "Interferon_1_pathway_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "HCoVs_IFN_induction_WP4880_phenotype", + "name": "HCoVs_IFN_induction_WP4880_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "IFNB1_pulmonary_endothelial_cell", + "name": "IFNB1_pulmonary_endothelial_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dTTP_simple_molecule", + "name": "dTTP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DNA_space_biosynthesis_phenotype", + "name": "DNA_space_biosynthesis_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "virus_space_replication_phenotype", + "name": "virus_space_replication_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dTYMK", + "name": "dTYMK", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DNA_damage_phenotype", + "name": "DNA_damage_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NME1", + "name": "NME1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRPP_simple_molecule", + "name": "PRPP_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CDA", + "name": "CDA", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DCTPP1", + "name": "DCTPP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CoQ_simple_molecule", + "name": "CoQ_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "dihydroorotate_space_dehydrogenase_space_holoenzyme_simple_molecule", + "name": "dihydroorotate_space_dehydrogenase_space_holoenzyme_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "P1788_simple_molecule", + "name": "P1788_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Teriflunomide_drug", + "name": "Teriflunomide_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTPS1", + "name": "CTPS1", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "IFNA1_rna", + "target": "IFNB1_space_expression_space_complex_complex", + "sign": true + }, + { + "id": "t2", + "source": "IFNB1_rna", + "target": "IFNB1_space_expression_space_complex_complex", + "sign": true + }, + { + "id": "t3", + "source": "IFNB1_space_expression_space_complex_complex", + "target": "NF-kB_complex", + "sign": true + }, + { + "id": "t4", + "source": "IFNB1_space_expression_space_complex_complex", + "target": "IRF3_phosphorylated", + "sign": true + }, + { + "id": "t5", + "source": "STING:TBK1_complex_Golgi_apparatus", + "target": "cGAMP:STING_complex_Golgi_apparatus", + "sign": true + }, + { + "id": "t6", + "source": "cGAMP:STING_complex_Golgi_apparatus", + "target": "cGAMP:STING_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t7", + "source": "cGAMP-STING_complex_COPII-coated_vesicle", + "target": "cGAMP:STING_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t8", + "source": "cGAMP:STING_complex_endoplasmic_reticulum", + "target": "cGAMP_simple_molecule", + "sign": true + }, + { + "id": "t9", + "source": "cGAMP:STING_complex_endoplasmic_reticulum", + "target": "STING_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t10", + "source": "STING_Golgi_apparatus", + "target": "STING_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t11", + "source": "cGAMP:STING:LC3_complex", + "target": "cGAMP-STING_complex_endoplasmic_reticulum-Golgi_intermediate_compartment", + "sign": true + }, + { + "id": "t12", + "source": "cGAMP-STING_complex_endoplasmic_reticulum-Golgi_intermediate_compartment", + "target": "cGAMP-STING_complex_COPII-coated_vesicle", + "sign": true + }, + { + "id": "t13", + "source": "HCoVs_autophagy_(WP4863)_phenotype", + "target": "cGAMP:STING:LC3_complex", + "sign": true + }, + { + "id": "t14", + "source": "cGAMP:STING:LC3_complex", + "target": "LC3", + "sign": true + }, + { + "id": "t15", + "source": "cGAMP:STING:LC3_complex", + "target": "WIPI2", + "sign": true + }, + { + "id": "t16", + "source": "cGAMP_simple_molecule", + "target": "cGAS:dsDNA_complex", + "sign": true + }, + { + "id": "t17", + "source": "cGAS:dsDNA_complex", + "target": "dsDNA_simple_molecule", + "sign": true + }, + { + "id": "t18", + "source": "MRE11:dsDNA_complex", + "target": "dsDNA_simple_molecule", + "sign": true + }, + { + "id": "t19", + "source": "DNA_gene", + "target": "dsDNA_simple_molecule", + "sign": true + }, + { + "id": "t20", + "source": "cGAS:dsDNA_complex", + "target": "cGAS", + "sign": true + }, + { + "id": "t21", + "source": "MRE11:RAD50:DNA_complex_pulmonary_endothelial_cell", + "target": "MRE11:dsDNA_complex", + "sign": true + }, + { + "id": "t22", + "source": "MRE11:dsDNA_complex", + "target": "MRE11", + "sign": true + }, + { + "id": "t23", + "source": "STING:TBK1_complex_endolysosome", + "target": "STING:TBK1_complex_Golgi_apparatus", + "sign": true + }, + { + "id": "t24", + "source": "STING:TBK1_complex_Golgi_apparatus", + "target": "TBK1", + "sign": true + }, + { + "id": "t25", + "source": "STING:TBK1_complex_Golgi_apparatus", + "target": "STING_Golgi_apparatus", + "sign": true + }, + { + "id": "t26", + "source": "cGAMP-STING_complex_COPII-coated_vesicle", + "target": "SAR1A", + "sign": true + }, + { + "id": "t27", + "source": "IRF3_phosphorylated", + "target": "STING:TBK1_complex_endolysosome", + "sign": true + }, + { + "id": "t28", + "source": "STING_Golgi_apparatus", + "target": "MRE11:RAD50:DNA_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t29", + "source": "MRE11:RAD50:DNA_complex_endoplasmic_reticulum", + "target": "MRE11:RAD50:DNA_complex_pulmonary_endothelial_cell", + "sign": true + }, + { + "id": "t30", + "source": "MRE11:RAD50:DNA_complex_pulmonary_endothelial_cell", + "target": "RAD50", + "sign": true + }, + { + "id": "t31", + "source": "CMP_simple_molecule", + "target": "cytidine_simple_molecule", + "sign": true + }, + { + "id": "t32", + "source": "uridine_simple_molecule", + "target": "cytidine_simple_molecule", + "sign": true + }, + { + "id": "t33", + "source": "Pi_simple_molecule", + "target": "H2O_simple_molecule", + "sign": true + }, + { + "id": "t34", + "source": "ADP_simple_molecule", + "target": "H2O_simple_molecule", + "sign": true + }, + { + "id": "t35", + "source": "L-Glu_simple_molecule", + "target": "H2O_simple_molecule", + "sign": true + }, + { + "id": "t36", + "source": "CAP_simple_molecule", + "target": "H2O_simple_molecule", + "sign": true + }, + { + "id": "t37", + "source": "H2O_simple_molecule", + "target": "N-carbamoyl-L-aspartate_simple_molecule", + "sign": true + }, + { + "id": "t38", + "source": "(S)-dihydroorotate_simple_molecule", + "target": "N-carbamoyl-L-aspartate_simple_molecule", + "sign": true + }, + { + "id": "t39", + "source": "H2O_simple_molecule", + "target": "H+simple_molecule", + "sign": true + }, + { + "id": "t40", + "source": "(S)-dihydroorotate_simple_molecule", + "target": "H+simple_molecule", + "sign": true + }, + { + "id": "t41", + "source": "H2O_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t42", + "source": "Pi_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t43", + "source": "(S)-dihydroorotate_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t44", + "source": "ADP_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t45", + "source": "N-carbamoyl-L-aspartate_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t46", + "source": "L-Glu_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t47", + "source": "CAP_simple_molecule", + "target": "CAD", + "sign": true + }, + { + "id": "t48", + "source": "UDP_simple_molecule", + "target": "UMP_simple_molecule", + "sign": true + }, + { + "id": "t49", + "source": "UMP_simple_molecule", + "target": "uridine_simple_molecule", + "sign": true + }, + { + "id": "t50", + "source": "UMP_simple_molecule", + "target": "UCK2", + "sign": true + }, + { + "id": "t51", + "source": "CMP_simple_molecule", + "target": "UCK2", + "sign": true + }, + { + "id": "t52", + "source": "UMP_simple_molecule", + "target": "orotidine_space_5'-monophosphate_simple_molecule", + "sign": true + }, + { + "id": "t53", + "source": "CO2_simple_molecule", + "target": "orotidine_space_5'-monophosphate_simple_molecule", + "sign": true + }, + { + "id": "t54", + "source": "UMP_simple_molecule", + "target": "UMPS", + "sign": true + }, + { + "id": "t55", + "source": "PPi_simple_molecule", + "target": "UMPS", + "sign": true + }, + { + "id": "t56", + "source": "orotidine_space_5'-monophosphate_simple_molecule", + "target": "UMPS", + "sign": true + }, + { + "id": "t57", + "source": "CO2_simple_molecule", + "target": "UMPS", + "sign": true + }, + { + "id": "t58", + "source": "cGAMP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t59", + "source": "Pi_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t60", + "source": "ADP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t61", + "source": "L-Glu_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t62", + "source": "CAP_simple_molecule", + "target": "ATP_simple_molecule", + "sign": true + }, + { + "id": "t63", + "source": "cGAMP_simple_molecule", + "target": "GTP_simple_molecule", + "sign": true + }, + { + "id": "t64", + "source": "RNA_space_biosynthesis_phenotype", + "target": "RTC_and_transcription_pw_phenotype", + "sign": true + }, + { + "id": "t65", + "source": "dCTP_simple_molecule", + "target": "dCDP_simple_molecule", + "sign": true + }, + { + "id": "t66", + "source": "dCDP_simple_molecule", + "target": "CDP_simple_molecule", + "sign": true + }, + { + "id": "t67", + "source": "CTP_simple_molecule", + "target": "CDP_simple_molecule", + "sign": true + }, + { + "id": "t68", + "source": "dCDP_simple_molecule", + "target": "ribonucleoside-diphosphate_reductase_complex", + "sign": true + }, + { + "id": "t69", + "source": "dUDP_simple_molecule", + "target": "ribonucleoside-diphosphate_reductase_complex", + "sign": true + }, + { + "id": "t70", + "source": "UTP_simple_molecule", + "target": "UDP_simple_molecule", + "sign": true + }, + { + "id": "t71", + "source": "dUDP_simple_molecule", + "target": "UDP_simple_molecule", + "sign": true + }, + { + "id": "t72", + "source": "UDP_simple_molecule", + "target": "CMPK", + "sign": true + }, + { + "id": "t73", + "source": "CDP_simple_molecule", + "target": "CMPK", + "sign": true + }, + { + "id": "t74", + "source": "dTDP_simple_molecule", + "target": "dTMP_simple_molecule", + "sign": true + }, + { + "id": "t75", + "source": "dTMP_simple_molecule", + "target": "dUMP_simple_molecule", + "sign": true + }, + { + "id": "t76", + "source": "dTMP_simple_molecule", + "target": "TYMS", + "sign": true + }, + { + "id": "t77", + "source": "IFNA1_human_host", + "target": "IFNA1_pulmonary_endothelial_cell", + "sign": true + }, + { + "id": "t78", + "source": "IFNA1_pulmonary_endothelial_cell", + "target": "IFNA1_rna", + "sign": true + }, + { + "id": "t79", + "source": "Pi_simple_molecule", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t80", + "source": "ADP_simple_molecule", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t81", + "source": "L-Glu_simple_molecule", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t82", + "source": "CAP_simple_molecule", + "target": "L-Gln_simple_molecule", + "sign": true + }, + { + "id": "t83", + "source": "Pi_simple_molecule", + "target": "HCO3-simple_molecule", + "sign": true + }, + { + "id": "t84", + "source": "ADP_simple_molecule", + "target": "HCO3-simple_molecule", + "sign": true + }, + { + "id": "t85", + "source": "L-Glu_simple_molecule", + "target": "HCO3-simple_molecule", + "sign": true + }, + { + "id": "t86", + "source": "CAP_simple_molecule", + "target": "HCO3-simple_molecule", + "sign": true + }, + { + "id": "t87", + "source": "Pi_simple_molecule", + "target": "CAP_simple_molecule", + "sign": true + }, + { + "id": "t88", + "source": "N-carbamoyl-L-aspartate_simple_molecule", + "target": "CAP_simple_molecule", + "sign": true + }, + { + "id": "t89", + "source": "Pi_simple_molecule", + "target": "L-Asp_simple_molecule", + "sign": true + }, + { + "id": "t90", + "source": "N-carbamoyl-L-aspartate_simple_molecule", + "target": "L-Asp_simple_molecule", + "sign": true + }, + { + "id": "t91", + "source": "QH2_simple_molecule", + "target": "(S)-dihydroorotate_simple_molecule", + "sign": true + }, + { + "id": "t92", + "source": "orotate_simple_molecule", + "target": "(S)-dihydroorotate_simple_molecule", + "sign": true + }, + { + "id": "t93", + "source": "dUMP_simple_molecule", + "target": "dUTP_simple_molecule", + "sign": true + }, + { + "id": "t94", + "source": "dUMP_simple_molecule", + "target": "DUT", + "sign": true + }, + { + "id": "t95", + "source": "dUMP_simple_molecule", + "target": "dCMP_simple_molecule", + "sign": true + }, + { + "id": "t96", + "source": "dUMP_simple_molecule", + "target": "DCTD", + "sign": true + }, + { + "id": "t97", + "source": "CDP_simple_molecule", + "target": "CMP_simple_molecule", + "sign": true + }, + { + "id": "t98", + "source": "HCoVs_Type_I_Ifn_signalling(WP4868)_phenotype", + "target": "IFNB1_human_host", + "sign": true + }, + { + "id": "t99", + "source": "Interferon_1_pathway_phenotype", + "target": "IFNB1_human_host", + "sign": true + }, + { + "id": "t100", + "source": "HCoVs_IFN_induction_WP4880_phenotype", + "target": "IFNB1_human_host", + "sign": true + }, + { + "id": "t101", + "source": "IFNB1_human_host", + "target": "IFNB1_pulmonary_endothelial_cell", + "sign": true + }, + { + "id": "t102", + "source": "DNA_gene", 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"identifiers": {}, + "context": {} + } + }, + { + "id": "ACE_cell", + "name": "ACE_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE_cell_active", + "name": "ACE_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTSD", + "name": "CTSD", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTSG", + "name": "CTSG", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CMA1", + "name": "CMA1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "KLK1", + "name": "KLK1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "angiotensin_1-5_simple_molecule", + "name": "angiotensin_1-5_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MRGPRD_cell_active", + "name": "MRGPRD_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MME_cell", + "name": "MME_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MME_cell_active", + "name": "MME_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PRCP", + "name": "PRCP", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "THOP1", + "name": "THOP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "PREP", + "name": "PREP", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AGTR2_cell", + "name": "AGTR2_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CGP42112A_drug", + "name": "CGP42112A_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "AR234960_drug", + "name": "AR234960_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Calcitriol_simple_molecule", + "name": "Calcitriol_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, 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+ } + }, + { + "id": "ethynylestradiol_simple_molecule", + "name": "ethynylestradiol_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "androgen_simple_molecule", + "name": "androgen_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "MRGPRD_cell", + "name": "MRGPRD_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "LNPEP_cell_active", + "name": "LNPEP_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "neurodegeneration_phenotype", + "name": "neurodegeneration_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "angiotensin_IV_simple_molecule", + "name": "angiotensin_IV_simple_molecule", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENPEP_cell_active", + "name": "ENPEP_cell_active", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ANPEP_", + "name": "ANPEP_", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ENPEP_cell", + "name": "ENPEP_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "QGC001_drug", + "name": "QGC001_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "sex,_male_phenotype", + "name": "sex,_male_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "angiotensin_1-7_simple_molecule_human_host", + "name": "angiotensin_1-7_simple_molecule_human_host", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ADAM17", + "name": "ADAM17", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Lisinopril_drug", + "name": "Lisinopril_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ABO_blood_group_system_phenotype", + "name": "ABO_blood_group_system_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Losartan_drug", + "name": "Losartan_drug", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "LNPEP_cell", + "name": "LNPEP_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "ACE2:AGTR1_complex", + "target": "AGTR1_cell", + "sign": true + }, + { + "id": "t2", + "source": "AGTR1_cell_active", + "target": "AGTR1_cell", + "sign": true + }, + { + "id": "t3", + "source": "ACE2:AGTR1_complex", + "target": "ACE2_cell", + "sign": true + }, + { + "id": "t4", + "source": "ACE2-Spike_complex_complex", + "target": "ACE2_cell", + "sign": true + }, + { + "id": "t5", + "source": "angiotensin_1-9_simple_molecule", + "target": "ACE2_cell", + "sign": true + }, + { + "id": "t6", + "source": "angiotensin_1-7_simple_molecule_cell", + "target": "ACE2_cell", + "sign": true + }, + { + "id": "t7", + "source": "alamandine_simple_molecule", + "target": "ACE2_cell", + "sign": true + }, + { + "id": "t8", + 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"identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_epithelial_space_cell", + "name": "Nsp4_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "name": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "name": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "IDE_epithelial_space_cell", + "name": "IDE_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "IDE_default_compartment", + "name": "IDE_default_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "SARS-CoV2_candidate_drugs_complex", + "name": "SARS-CoV2_candidate_drugs_complex", + "grounding": { + "identifiers": {}, + "context": {} 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"grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP210_endoplasmic_reticulum", + "name": "NUP210_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP210:Selinexor_complex", + "name": "NUP210:Selinexor_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "NUP210_nucleus", + "name": "NUP210_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "name": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase:Nsp6_complex_endosome", + "name": "V-ATPase:Nsp6_complex_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6_epithelial_space_cell", + "name": "Nsp6_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase_complex_endoplasmic_reticulum", + "name": "V-ATPase_complex_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-ATPase_complex_endosome", + "name": "V-ATPase_complex_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "V-type_space_proton_space_ATPase_complex", + "name": "V-type_space_proton_space_ATPase_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "H+_ion", + "name": "H+_ion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP6AP1", + "name": "ATP6AP1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ATP6AP1:Bafilomycin_space_A1_complex", + "name": "ATP6AP1:Bafilomycin_space_A1_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp6:SIGMAR1_complex_nucleus", + "name": "Nsp6:SIGMAR1_complex_nucleus", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + 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"(-)ss_space_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "(-)ss_space_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "(+)ss_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "(+)ss_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Host_space_translation_phenotype", + "name": "Host_space_translation_phenotype", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp1", + "name": "Nsp1", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "S_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S_rough_space_endoplasmic_space_reticulum", + "name": "S_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "E_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "E_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "Orf9b_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "Orf9b_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "M_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "M_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b_rough_space_endoplasmic_space_reticulum", + "name": "Orf9b_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "Orf9b_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "pp1ab_space_nsp6-16", + "name": "pp1ab_space_nsp6-16", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "pp1ab_space_Nsp3-16_endoplasmic_reticulum", + "name": "pp1ab_space_Nsp3-16_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "Nsp5_epithelial_space_cell", + "name": "Nsp5_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Nsp3-4", + "name": "Nsp3-4", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_rough_space_endoplasmic_space_reticulum", + "name": "E_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "E_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "E_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "E_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "name": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a_rough_space_endoplasmic_space_reticulum", + "name": "Orf3a_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf6_rough_space_endoplasmic_space_reticulum", + "name": "Orf6_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a_rough_space_endoplasmic_space_reticulum", + "name": "Orf7a_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf14_rough_space_endoplasmic_space_reticulum", + "name": "Orf14_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7b_rough_space_endoplasmic_space_reticulum", + "name": "Orf7b_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M_rough_space_endoplasmic_space_reticulum", + "name": "M_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf8_rough_space_endoplasmic_space_reticulum", + "name": "Orf8_rough_space_endoplasmic_space_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf14_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "Orf14_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "pp1a", + "name": "pp1a", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "pp1a_space_Nsp3-11_endoplasmic_reticulum", + "name": "pp1a_space_Nsp3-11_endoplasmic_reticulum", + "grounding": { + "identifiers": {}, + "context": {} + }, + "sign": true + }, + { + "id": "pp1ab", + "name": "pp1ab", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Host_space_translation_space_complex_complex_epithelial_space_cell", + "name": "Host_space_translation_space_complex_complex_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf14_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": 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"Orf3a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf3a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf9b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf9b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf6_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "Orf6_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf6__(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf6__(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "Orf7a_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf7a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "Orf7a_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "Orf7a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "M_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "N_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "N_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "S_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "S_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf14_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf14_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "S_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", + "name": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "S1_endosome", + "name": "S1_endosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTSB", + "name": "CTSB", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "CTSL", + "name": "CTSL", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf8_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "name": "Orf8_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf7b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf7b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "Orf3a_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "name": "Orf3a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "M_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "M_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf3a_lysosome", + "name": "Orf3a_lysosome", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "Orf8_(+)ss_sgmRNA_rna_epithelial_space_cell", + "name": "Orf8_(+)ss_sgmRNA_rna_epithelial_space_cell", + "grounding": { + "identifiers": {}, + "context": {} + } + }, + { + "id": "DMV_molecular_pore_complex", + "name": "DMV_molecular_pore_complex", + "grounding": { + "identifiers": {}, + "context": {} + } + } + ], + "edges": [ + { + "id": "t1", + "source": "Replication_space_transcription_space_complex:N_space_oligomer_complex", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t2", + "source": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t3", + "source": "Orf9b_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t4", + "source": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t5", + "source": "M_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t6", + "source": "Orf14_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t7", + "source": "E_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t8", + "source": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t9", + "source": "ds_space_gRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t10", + "source": "M_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t11", + "source": "Orf7b_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t12", + "source": "N_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t13", + "source": "N_space_space_(-)ss_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t14", + "source": "Orf6_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t15", + "source": "Orf8_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t16", + "source": "S_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t17", + "source": "Orf8_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t18", + "source": "Orf6_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t19", + "source": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t20", + "source": "Orf14_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t21", + "source": "Orf7a_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t22", + "source": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t23", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t24", + "source": "S_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t25", + "source": "Orf3a_space_ds_space_sgmRNA_rna", + "target": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t26", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp16", + "sign": true + }, + { + "id": "t27", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp15", + "sign": true + }, + { + "id": "t28", + "source": "cellular_space_response_space_to_space_exogenous_space_dsRNA_phenotype", + "target": "Nsp15", + "sign": false + }, + { + "id": "t29", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp14", + "sign": true + }, + { + "id": "t30", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp13", + "sign": true + }, + { + "id": "t31", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp12", + "sign": true + }, + { + "id": "t32", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp9", + "sign": true + }, + { + "id": "t33", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp8", + "sign": true + }, + { + "id": "t34", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp6_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t35", + "source": "double_membrane_vesicle_viral_factory_assembly_phenotype", + "target": "Nsp6_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t36", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp3", + "sign": true + }, + { + "id": "t37", + "source": "double_membrane_vesicle_viral_factory_assembly_phenotype", + "target": "Nsp3", + "sign": true + }, + { + "id": "t38", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp4_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t39", + "source": "double_membrane_vesicle_viral_factory_assembly_phenotype", + "target": "Nsp4_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t40", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp7", + "sign": true + }, + { + "id": "t41", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp10", + "sign": true + }, + { + "id": "t42", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Nsp2", + "sign": true + }, + { + "id": "t44", + "source": "S2_epithelial_space_cell", + "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t45", + "source": "ACE2_epithelial_space_cell", + "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t46", + "source": "ACE2_default_compartment", + "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t47", + "source": "S1_default_compartment", + "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t48", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "target": "ACE2_epithelial_space_cell", + "sign": true + }, + { + "id": "t49", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "target": "S_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t50", + "source": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "target": "Heparan_space_sulfate_simple_molecule", + "sign": true + }, + { + "id": "t51", + "source": "(+)ss_space_gRNA_rna", + "target": "Nucleocapsid_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t52", + "source": "N_epithelial_space_cell", + "target": "Nucleocapsid_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t53", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t54", + "source": "Orf7a_epithelial_space_cell", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t55", + "source": "M_epithelial_space_cell", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t56", + "source": "E_epithelial_space_cell", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t57", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t58", + "source": "Orf7a_epithelial_space_cell", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t59", + "source": "M_epithelial_space_cell", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t60", + "source": "E_epithelial_space_cell", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t61", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t62", + "source": "Orf7a_epithelial_space_cell", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t63", + "source": "M_epithelial_space_cell", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t64", + "source": "E_epithelial_space_cell", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t65", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t66", + "source": "Orf7a_epithelial_space_cell", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t67", + "source": "M_epithelial_space_cell", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t68", + "source": "E_epithelial_space_cell", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t69", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "S2_epithelial_space_cell", + "sign": true + }, + { + "id": "t70", + "source": "Orf7a_epithelial_space_cell", + "target": "S2_epithelial_space_cell", + "sign": true + }, + { + "id": "t71", + "source": "M_epithelial_space_cell", + "target": "S2_epithelial_space_cell", + "sign": true + }, + { + "id": "t72", + "source": "E_epithelial_space_cell", + "target": "S2_epithelial_space_cell", + "sign": true + }, + { + "id": "t73", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "cholesterol_simple_molecule", + "sign": true + }, + { + "id": "t74", + "source": "Orf7a_epithelial_space_cell", + "target": "cholesterol_simple_molecule", + "sign": true + }, + { + "id": "t75", + "source": "M_epithelial_space_cell", + "target": "cholesterol_simple_molecule", + "sign": true + }, + { + "id": "t76", + "source": "E_epithelial_space_cell", + "target": "cholesterol_simple_molecule", + "sign": true + }, + { + "id": "t77", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "S1:NRP1_space_complex_complex", + "sign": true + }, + { + "id": "t78", + "source": "Orf7a_epithelial_space_cell", + "target": "S1:NRP1_space_complex_complex", + "sign": true + }, + { + "id": "t79", + "source": "M_epithelial_space_cell", + "target": "S1:NRP1_space_complex_complex", + "sign": true + }, + { + "id": "t80", + "source": "E_epithelial_space_cell", + "target": "S1:NRP1_space_complex_complex", + "sign": true + }, + { + "id": "t81", + "source": "Orf7a_endosome", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t82", + "source": "E_endosome", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t83", + "source": "M_endosome", + "target": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t84", + "source": "Orf7a_endosome", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t85", + "source": "E_endosome", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t86", + "source": "M_endosome", + "target": "E_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t87", + "source": "Orf7a_endosome", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t88", + "source": "E_endosome", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t89", + "source": "M_endosome", + "target": "M_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t90", + "source": "Orf7a_endosome", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t91", + "source": "E_endosome", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t92", + "source": "M_endosome", + "target": "Orf7a_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t93", + "source": "Nucleocapsid_complex_epithelial_space_cell", + "target": "S2_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t94", + "source": "Orf7a_endosome", + "target": "S2_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t95", + "source": "E_endosome", + "target": "S2_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t96", + "source": "M_endosome", + "target": "S2_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t97", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "target": "ACE2:SPIKE_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t98", + "source": "S1:NRP1_space_complex_complex", + "target": "S1_default_compartment", + "sign": true + }, + { + "id": "t99", + "source": "S1:NRP1_space_complex_complex", + "target": "NRP1", + "sign": true + }, + { + "id": "t100", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Replication_space_transcription_space_complex:N_space_oligomer_complex", + "sign": true + }, + { + "id": "t101", + "source": "Nucleocapsid_complex_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "Replication_space_transcription_space_complex:N_space_oligomer_complex", + "sign": true + }, + { + "id": "t102", + "source": "Replication_space_transcription_space_complex:N_space_oligomer_complex", + "target": "N_epithelial_space_cell", + "sign": true + }, + { + "id": "t104", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "target": "Nucleocapsid_complex_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "sign": true + }, + { + "id": "t105", + "source": "Replication_space_transcription_space_complex_complex_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "(+)ss_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t106", + "source": "Nucleocapsid_complex_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "(+)ss_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t107", + "source": "Nsp4_IDE_complex", + "target": "Nsp4:IDE_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t109", + "source": "Nsp4:IDE_complex_epithelial_space_cell", + "target": "Nsp4_epithelial_space_cell", + "sign": true + }, + { + "id": "t110", + "source": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "target": "Nsp4_epithelial_space_cell", + "sign": true + }, + { + "id": "t111", + "source": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "target": "Nsp4_epithelial_space_cell", + "sign": true + }, + { + "id": "t112", + "source": "Nsp4:IDE_complex_epithelial_space_cell", + "target": "IDE_epithelial_space_cell", + "sign": true + }, + { + "id": "t113", + "source": "IDE_default_compartment", + "target": "IDE_epithelial_space_cell", + "sign": true + }, + { + "id": "t115", + "source": "SIGMAR1:_drug_complex_complex", + "target": "SARS-CoV2_candidate_drugs_complex", + "sign": true + }, + { + "id": "t116", + "source": "viral_life_cycle_phenotype", + "target": "SARS-CoV2_candidate_drugs_complex", + "sign": false + }, + { + "id": "t117", + "source": "SIGMAR1:_drug_complex_complex", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t118", + "source": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t119", + "source": "SIGMAR1_epithelial_space_cell", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t120", + "source": "SIGMAR1_nucleus", + "target": "SIGMAR1_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t121", + "source": "Nsp4:NUP210_complex_nucleus", + "target": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t122", + "source": "Nsp4:NUP210_complex_endoplasmic_reticulum", + "target": "NUP210_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t123", + "source": "NUP210:Selinexor_complex", + "target": "NUP210_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t124", + "source": "NUP210_nucleus", + "target": "NUP210_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t125", + "source": "V-ATPase:Nsp6_complex_endosome", + "target": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t126", + "source": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "target": "Nsp6_epithelial_space_cell", + "sign": true + }, + { + "id": "t127", + "source": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "target": "Nsp6_epithelial_space_cell", + "sign": true + }, + { + "id": "t128", + "source": "V-ATPase:Nsp6_complex_endoplasmic_reticulum", + "target": "V-ATPase_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t129", + "source": "V-ATPase_complex_endosome", + "target": "V-ATPase_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t130", + "source": "V-ATPase_complex_endoplasmic_reticulum", + "target": "V-type_space_proton_space_ATPase_complex", + "sign": true + }, + { + "id": "t131", + "source": "H+_ion", + "target": "V-type_space_proton_space_ATPase_complex", + "sign": true + }, + { + "id": "t132", + "source": "V-ATPase_complex_endoplasmic_reticulum", + "target": "ATP6AP1", + "sign": true + }, + { + "id": "t133", + "source": "ATP6AP1:Bafilomycin_space_A1_complex", + "target": "ATP6AP1", + "sign": true + }, + { + "id": "t134", + "source": "Nsp6:SIGMAR1_complex_nucleus", + "target": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t135", + "source": "Nsp6:SIGMAR1_complex_epithelial_space_cell", + "target": "Nsp6:SIGMAR1_complex_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t136", + "source": "NUP210:Selinexor_complex", + "target": "Selinexor_drug", + "sign": true + }, + { + "id": "t137", + "source": "ATP6AP1:Bafilomycin_space_A1_complex", + "target": "bafilomycin_space_A1_drug", + "sign": true + }, + { + "id": "t138", + "source": "viral_life_cycle_phenotype", + "target": "bafilomycin_space_A1_drug", + "sign": false + }, + { + "id": "t140", + "source": "Nsp4_ALG11_complex_endoplasmic_reticulum", + "target": "ALG11_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t142", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "target": "RAB7A", + "sign": true + }, + { + "id": "t143", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "target": "ARL8B", + "sign": true + }, + { + "id": "t144", + "source": "Nucleocapsid_complex_SARS-CoV-2_space_virion", + "target": "Ca+2_simple_molecule", + "sign": true + }, + { + "id": "t145", + "source": "(-)ss_space_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "ds_space_gRNA_rna", + "sign": true + }, + { + "id": "t146", + "source": "(+)ss_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "ds_space_gRNA_rna", + "sign": true + }, + { + "id": "t147", + "source": "Host_space_translation_phenotype", + "target": "Nsp1", + "sign": false + }, + { + "id": "t148", + "source": "S_SARS-CoV-2_space_virion", + "target": "S_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "sign": true + }, + { + "id": "t149", + "source": "S_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "S_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t150", + "source": "Orf9b_space_ds_space_sgmRNA_rna", + "target": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t151", + "source": "Orf9b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t152", + "source": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t153", + "source": "M_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t154", + "source": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t155", + "source": "ds_space_gRNA_rna", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t156", + "source": "N_space_space_(-)ss_space_sgmRNA_rna", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t157", + "source": "S_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t158", + "source": "Orf8_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t159", + "source": "Orf6_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t160", + "source": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t161", + "source": "Orf14_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t162", + "source": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "target": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t163", + "source": "E_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "E_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t164", + "source": "E_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "E_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t165", + "source": "Orf9b_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf9b_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t166", + "source": "Orf9b_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf9b_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t167", + "source": "M_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "M_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t168", + "source": "M_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "M_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t169", + "source": "Orf9b_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "Orf9b_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t170", + "source": "Orf3a_space_ds_space_sgmRNA_rna", + "target": "Orf3a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t171", + "source": "Nsp13", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t172", + "source": "Nsp7", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t173", + "source": "Nsp16", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t174", + "source": "Nsp12", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t175", + "source": "Nsp14", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t176", + "source": "Nsp10", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t177", + "source": "Nsp9", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t178", + "source": "Nsp8", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t179", + "source": "Nsp6_endoplasmic_reticulum", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t180", + "source": "Nsp15", + "target": "pp1ab_space_nsp6-16", + "sign": true + }, + { + "id": "t181", + "source": "pp1ab_space_nsp6-16", + "target": "pp1ab_space_Nsp3-16_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t182", + "source": "Nsp5_epithelial_space_cell", + "target": "pp1ab_space_Nsp3-16_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t183", + "source": "Nsp3-4", + "target": "pp1ab_space_Nsp3-16_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t185", + "source": "E_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "E_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t186", + "source": "E_rough_space_endoplasmic_space_reticulum", + "target": "E_(+)ss_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t187", + "source": "E_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t188", + "source": "Orf3a_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t189", + "source": "Orf9b_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t190", + "source": "Orf6_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t191", + "source": "Orf7a_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t192", + "source": "Orf14_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t193", + "source": "S_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t194", + "source": "Orf7b_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t195", + "source": "M_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t196", + "source": "Orf8_rough_space_endoplasmic_space_reticulum", + "target": "Host_space_translation_space_complex_complex_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t197", + "source": "Orf14_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "Orf14_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t198", + "source": "M_space_ds_space_sgmRNA_rna", + "target": "M_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t199", + "source": "Nsp13", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t200", + "source": "Nsp7", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t201", + "source": "Nsp16", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t202", + "source": "Nsp12", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t203", + "source": "Nsp14", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t204", + "source": "Nsp10", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t205", + "source": "Nsp9", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t206", + "source": "Nsp8", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t207", + "source": "Nsp6_endoplasmic_reticulum", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t208", + "source": "Nsp15", + "target": "Nsp5_epithelial_space_cell", + "sign": true + }, + { + "id": "t209", + "source": "Nsp1", + "target": "pp1a", + "sign": true + }, + { + "id": "t210", + "source": "Nsp2", + "target": "pp1a", + "sign": true + }, + { + "id": "t211", + "source": "pp1a_space_Nsp3-11_endoplasmic_reticulum", + "target": "pp1a", + "sign": true + }, + { + "id": "t212", + "source": "pp1a", + "target": "(+)ss_space_gRNA_rna", + "sign": true + }, + { + "id": "t213", + "source": "pp1ab", + "target": "(+)ss_space_gRNA_rna", + "sign": true + }, + { + "id": "t214", + "source": "(-)ss_space_gRNA_rna_epithelial_space_cell", + "target": "(+)ss_space_gRNA_rna", + "sign": true + }, + { + "id": "t215", + "source": "pp1a", + "target": "Host_space_translation_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t216", + "source": "pp1ab", + "target": "Host_space_translation_space_complex_complex_epithelial_space_cell", + "sign": true + }, + { + "id": "t217", + "source": "Nsp1", + "target": "pp1ab", + "sign": true + }, + { + "id": "t218", + "source": "Nsp2", + "target": "pp1ab", + "sign": true + }, + { + "id": "t219", + "source": "pp1ab_space_Nsp3-16_endoplasmic_reticulum", + "target": "pp1ab", + "sign": true + }, + { + "id": "t220", + "source": "Orf14_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf14_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t221", + "source": "Orf14_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf14_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t222", + "source": "Orf14_space_ds_space_sgmRNA_rna", + "target": "Orf14_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t223", + "source": "E_space_ds_space_sgmRNA_rna", + "target": "E_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t224", + "source": "Orf7b_space_ds_space_sgmRNA_rna", + "target": "Orf7b_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t226", + "source": "Nsp3", + "target": "Nsp3-4_glycosylated", + "sign": true + }, + { + "id": "t227", + "source": "Nsp4_endoplasmic_reticulum", + "target": "Nsp3-4_glycosylated", + "sign": true + }, + { + "id": "t228", + "source": "Nsp3-4_glycosylated", + "target": "Nsp3-4", + "sign": true + }, + { + "id": "t229", + "source": "Nsp7", + "target": "pp1a_space_Nsp6-11", + "sign": true + }, + { + "id": "t230", + "source": "Nsp10", + "target": "pp1a_space_Nsp6-11", + "sign": true + }, + { + "id": "t231", + "source": "Nsp9", + "target": "pp1a_space_Nsp6-11", + "sign": true + }, + { + "id": "t232", + "source": "Nsp8", + "target": "pp1a_space_Nsp6-11", + "sign": true + }, + { + "id": "t233", + "source": "Nsp6_endoplasmic_reticulum", + "target": "pp1a_space_Nsp6-11", + "sign": true + }, + { + "id": "t234", + "source": "Nsp11", + 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"Orf7b_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t258", + "source": "Orf7b_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf7b_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t259", + "source": "N_space_(-)ss_space_sgmRNA_rna", + "target": "N_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t260", + "source": "N_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "N_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t261", + "source": "N_space_ds_space_sgmRNA_rna", + "target": "N_space_space_(-)ss_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t263", + "source": "E_SARS-CoV-2_space_virion", + "target": "E_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "sign": true + }, + { + "id": "t264", + "source": "Nsp3-4", + "target": "pp1a_space_Nsp3-11_endoplasmic_reticulum", + "sign": true + }, + { + "id": "t265", + 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"ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t291", + "source": "S1_endosome", + "target": "ACE2:SPIKE_space_complex_complex_SARS-CoV-2_space_virion", + "sign": true + }, + { + "id": "t292", + "source": "S2_SARS-CoV-2_space_virion", + "target": "CTSB", + "sign": true + }, + { + "id": "t293", + "source": "S1_endosome", + "target": "CTSB", + "sign": true + }, + { + "id": "t294", + "source": "S2_SARS-CoV-2_space_virion", + "target": "CTSL", + "sign": true + }, + { + "id": "t295", + "source": "S1_endosome", + "target": "CTSL", + "sign": true + }, + { + "id": "t296", + "source": "Orf8_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "Orf8_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t297", + "source": "Orf7b_rough_space_endoplasmic_space_reticulum", + "target": "Orf7b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t298", + "source": "Orf7a_space_ds_space_sgmRNA_rna", + "target": "Orf7a_space_(-)ss_space_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t299", + "source": "Orf3a_space_(-)ss_space_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf3a_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t300", + "source": "Orf3a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "target": "Orf3a_space_ds_space_sgmRNA_rna", + "sign": true + }, + { + "id": "t301", + "source": "M_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "target": "M_rough_space_endoplasmic_space_reticulum", + "sign": true + }, + { + "id": "t302", + "source": "M_rough_space_endoplasmic_space_reticulum", + "target": "M_(+)ss_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t303", + "source": "Orf3a_lysosome", + "target": "Orf3a_endoplasmic_space_reticulum-Golgi_space_intermediate_space_compartment", + "sign": true + }, + { + "id": "t304", + "source": "Orf8_rough_space_endoplasmic_space_reticulum", + "target": "Orf8_(+)ss_sgmRNA_rna_epithelial_space_cell", + "sign": true + }, + { + "id": "t305", + "source": "(+)ss_gRNA_rna_epithelial_space_cell", + "target": "(+)ss_gRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t306", + "source": "N_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "N_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t307", + "source": "M_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "M_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t308", + "source": "S_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "S_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t309", + "source": "E_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "E_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t310", + "source": "Orf6__(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf6__(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t311", + "source": "Orf7a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf7a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t312", + "source": "Orf3a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf3a_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t313", + "source": "Orf8_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf8_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t314", + "source": "Orf7a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t315", + "source": "S_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t316", + "source": "Orf6__(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t317", + "source": "E_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t318", + "source": "Orf3a_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t319", + "source": "M_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t320", + "source": "Orf8_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t321", + "source": "N_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t322", + "source": "(+)ss_gRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t323", + "source": "Orf9b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t324", + "source": "Orf14_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t325", + "source": "Orf7b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "DMV_molecular_pore_complex", + "sign": true + }, + { + "id": "t326", + "source": "Orf9b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf9b_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t327", + "source": "Orf14_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf14_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + }, + { + "id": "t328", + "source": "Orf7b_(+)ss_sgmRNA_rna_epithelial_space_cell", + "target": "Orf7b_(+)ss_sgmRNA_rna_double_space_membrane_space_vesicle_space_viral_space_factory", + "sign": true + } + ], + "parameters": [] + }, + "metadata": { + "annotations": { + "license": null, + "authors": [], + "references": [ + "pubmed:34664389" + ], + "time_scale": null, + "time_start": null, + "time_end": null, + "locations": [], + "pathogens": [ + "ncbitaxon:2697049" + ], + "diseases": [ + "doid:0080600" + ], + "hosts": [ + "ncbitaxon:9606" + ], + "model_types": [] + } + } +} \ No newline at end of file