This function gets a NetPathMiner default value for a variable.
NPMdefaults(value)The defuult value for the given variable.
NetPathMiner defines the following defaults:
small.comp.ls Dataframe of ubiquitous metabolites. Used by rmSmallCompounds.
bridge Dataframe of attributes supported by Brigde Database. Used by fetchAttribute.
bridge.organisms A list of bridge supported organisms. Used by fetchAttribute.
bridge.web The base URL for Brigde Database webservices. Used by fetchAttribute.
# Get the default list of small compounds (uniquitous metabolites).
NPMdefaults("small.comp.ls")
#> reactome.name name
#> 1 adenosine 5'-monophosphate [extracellular region] AMP
#> 2 ADP [cytosol] ADP
#> 3 ADP [endoplasmic reticulum membrane] ADP
#> 4 ADP [endosome] ADP
#> 5 ADP [extracellular region] ADP
#> 6 ADP [intracellular] ADP
#> 7 ADP [mitochondrial matrix] ADP
#> 8 ADP [nucleoplasm] ADP
#> 9 ADP [plasma membrane] ADP
#> 10 ADP [platelet dense granule lumen] ADP
#> 11 AMP [cytosol] AMP
#> 12 AMP [intracellular] AMP
#> 13 AMP [mitochondrial matrix] AMP
#> 14 AMP [nucleoplasm] AMP
#> 15 AMP [peroxisomal matrix] AMP
#> 16 ATP [cytosol] ATP
#> 17 ATP [endoplasmic reticulum membrane] ATP
#> 18 ATP [endosome] ATP
#> 19 ATP [extracellular region] ATP
#> 20 ATP [intracellular] ATP
#> 21 ATP [mitochondrial matrix] ATP
#> 22 ATP [nucleoplasm] ATP
#> 23 ATP [peroxisomal matrix] ATP
#> 24 ATP [plasma membrane] ATP
#> 25 ATP [platelet dense granule lumen] ATP
#> 26 CO2 [cytosol] CO2
#> 27 CO2 [endoplasmic reticulum lumen] CO2
#> 28 CO2 [intracellular] CO2
#> 29 CO2 [mitochondrial intermembrane space] CO2
#> 30 CO2 [mitochondrial matrix] CO2
#> 31 CO2 [nucleoplasm] CO2
#> 32 CO2 [peroxisomal matrix] CO2
#> 33 CoA-SH [intracellular] CoA
#> 34 CoA-SH [mitochondrial matrix] CoA
#> 35 FAD [cytosol] FAD
#> 36 FAD [endoplasmic reticulum membrane] FAD
#> 37 FAD [intracellular] FAD
#> 38 FAD [mitochondrial inner membrane] FAD
#> 39 FAD [mitochondrial intermembrane space] FAD
#> 40 FAD [mitochondrial matrix] FAD
#> 41 FAD [mitochondrial outer membrane] FAD
#> 42 FAD [peroxisomal matrix] FAD
#> 43 FADH2 [intracellular] FADH2
#> 44 FADH2 [mitochondrial inner membrane] FADH2
#> 45 FADH2 [mitochondrial matrix] FADH2
#> 46 GDP [cytosol] GDP
#> 47 GDP [endoplasmic reticulum lumen] GDP
#> 48 GDP [endosome] GDP
#> 49 GDP [extracellular region] GDP
#> 50 GDP [Golgi lumen] GDP
#> 51 GDP [intracellular] GDP
#> 52 GDP [mitochondrial matrix] GDP
#> 53 GDP [nucleoplasm] GDP
#> 54 GDP [plasma membrane] GDP
#> 55 GDP [platelet dense granule lumen] GDP
#> 56 GTP [cytoplasmic vesicle membrane] GTP
#> 57 GTP [cytosol] GTP
#> 58 GTP [endosome] GTP
#> 59 GTP [ER to Golgi transport vesicle membrane] GTP
#> 60 GTP [extracellular region] GTP
#> 61 GTP [intracellular] GTP
#> 62 GTP [mitochondrial matrix] GTP
#> 63 GTP [nucleoplasm] GTP
#> 64 GTP [plasma membrane] GTP
#> 65 GTP [platelet dense granule lumen] GTP
#> 66 H+ [clathrin sculpted acetylcholine transport vesicle lumen] H+
#> 67 H+ [clathrin sculpted monoamine transport vesicle lumen] H+
#> 68 H+ [cytosol] H+
#> 69 H+ [early endosome lumen] H+
#> 70 H+ [endoplasmic reticulum lumen] H+
#> 71 H+ [endosome lumen] H+
#> 72 H+ [extracellular region] H+
#> 73 H+ [Golgi lumen] H+
#> 74 H+ [intracellular] H+
#> 75 H+ [late endosome lumen] H+
#> 76 H+ [lysosomal lumen] H+
#> 77 H+ [mitochondrial inner membrane] H+
#> 78 H+ [mitochondrial intermembrane space] H+
#> 79 H+ [mitochondrial matrix] H+
#> 80 H+ [nuclear envelope] H+
#> 81 H+ [peroxisomal matrix] H+
#> 82 H+ [phagocytic vesicle lumen] H+
#> 83 H+ [phagolysosome] H+
#> 84 H+ [platelet dense tubular network lumen] H+
#> 85 H+ [synaptic vesicle] H+
#> 86 H2O [cytosol] H2O
#> 87 H2O [endoplasmic reticulum lumen] H2O
#> 88 H2O [extracellular region] H2O
#> 89 H2O [intracellular] H2O
#> 90 H2O [lysosomal lumen] H2O
#> 91 H2O [mitochondrial intermembrane space] H2O
#> 92 H2O [mitochondrial matrix] H2O
#> 93 H2O [nucleoplasm] H2O
#> 94 H2O [peroxisomal matrix] H2O
#> 95 H2O [plasma membrane] H2O
#> 96 H2O [secretory granule] H2O
#> 97 NAD+ [cytosol] NAD+
#> 98 NAD+ [intracellular] NAD+
#> 99 NAD+ [mitochondrial matrix] NAD+
#> 100 NAD+ [peroxisomal matrix] NAD+
#> 101 NADH [cytosol] NADH
#> 102 NADH [intracellular] NADH
#> 103 NADH [mitochondrial matrix] NADH
#> 104 NADH [peroxisomal matrix] NADH
#> 105 NADP+ [cytosol] NADP+
#> 106 NADP+ [endoplasmic reticulum lumen] NADP+
#> 107 NADP+ [extracellular region] NADP+
#> 108 NADP+ [intracellular] NADP+
#> 109 NADP+ [mitochondrial matrix] NADP+
#> 110 NADP+ [nuclear envelope] NADP+
#> 111 NADP+ [peroxisomal matrix] NADP+
#> 112 NADP+ [phagolysosome] NADP+
#> 113 NADPH [cytosol] NADPH
#> 114 NADPH [endoplasmic reticulum lumen] NADPH
#> 115 NADPH [extracellular region] NADPH
#> 116 NADPH [intracellular] NADPH
#> 117 NADPH [mitochondrial matrix] NADPH
#> 118 NADPH [nuclear envelope] NADPH
#> 119 NADPH [peroxisomal matrix] NADPH
#> 120 NADPH [phagolysosome] NADPH
#> 121 Orthophosphate [plasma membrane] Orthophosphate
#> 122 Orthophosphate [platelet dense granule lumen] Orthophosphate
#> 123 Pi [cytosol] Pi
#> 124 Pi [endoplasmic reticulum lumen] Pi
#> 125 Pi [extracellular region] Pi
#> 126 Pi [intracellular] Pi
#> 127 Pi [mitochondrial matrix] Pi
#> 128 Pi [nucleoplasm] Pi
#> 129 UTP [cytosol] UTP
#> 130 UTP [extracellular region] UTP
#> 131 UTP [intracellular] UTP
#> 132 UTP [mitochondrial matrix] UTP
#> 133 UTP [nucleoplasm] UTP
#> 134 O2 O2
#> 135 PPi PPi
#> miriam.kegg.compound miriam.chebi miriam.cas miriam.pubchem.compound
#> 1 C00020 CHEBI:16027 61-19-8 3322
#> 2 C00008 CHEBI:16761 58-64-0 3310
#> 3 C00008 CHEBI:16761 58-64-0 3310
#> 4 C00008 CHEBI:16761 58-64-0 3310
#> 5 C00008 CHEBI:16761 58-64-0 3310
#> 6 C00008 CHEBI:16761 58-64-0 3310
#> 7 C00008 CHEBI:16761 58-64-0 3310
#> 8 C00008 CHEBI:16761 58-64-0 3310
#> 9 C00008 CHEBI:16761 58-64-0 3310
#> 10 C00008 CHEBI:16761 58-64-0 3310
#> 11 C00020 CHEBI:16027 61-19-8 3322
#> 12 C00020 CHEBI:16027 61-19-8 3322
#> 13 C00020 CHEBI:16027 61-19-8 3322
#> 14 C00020 CHEBI:16027 61-19-8 3322
#> 15 C00020 CHEBI:16027 61-19-8 3322
#> 16 C00002 CHEBI:15422 56-65-5 3304
#> 17 C00002 CHEBI:15422 56-65-5 3304
#> 18 C00002 CHEBI:15422 56-65-5 3304
#> 19 C00002 CHEBI:15422 56-65-5 3304
#> 20 C00002 CHEBI:15422 56-65-5 3304
#> 21 C00002 CHEBI:15422 56-65-5 3304
#> 22 C00002 CHEBI:15422 56-65-5 3304
#> 23 C00002 CHEBI:15422 56-65-5 3304
#> 24 C00002 CHEBI:15422 56-65-5 3304
#> 25 C00002 CHEBI:15422 56-65-5 3304
#> 26 C00011 CHEBI:16526 124-38-9 3313
#> 27 C00011 CHEBI:16526 124-38-9 3313
#> 28 C00011 CHEBI:16526 124-38-9 3313
#> 29 C00011 CHEBI:16526 124-38-9 3313
#> 30 C00011 CHEBI:16526 124-38-9 3313
#> 31 C00011 CHEBI:16526 124-38-9 3313
#> 32 C00011 CHEBI:16526 124-38-9 3313
#> 33 C00010 CHEBI:15346 85-61-0 3312
#> 34 C00010 CHEBI:15346 85-61-0 3312
#> 35 C00016 CHEBI:16238 146-14-5 3318
#> 36 C00016 CHEBI:16238 146-14-5 3318
#> 37 C00016 CHEBI:16238 146-14-5 3318
#> 38 C00016 CHEBI:16238 146-14-5 3318
#> 39 C00016 CHEBI:16238 146-14-5 3318
#> 40 C00016 CHEBI:16238 146-14-5 3318
#> 41 C00016 CHEBI:16238 146-14-5 3318
#> 42 C00016 CHEBI:16238 146-14-5 3318
#> 43 C01352 CHEBI:17877 4556
#> 44 C01352 CHEBI:17877 4556
#> 45 C01352 CHEBI:17877 4556
#> 46 C00035 CHEBI:17552 146-91-8 3337
#> 47 C00035 CHEBI:17552 146-91-8 3337
#> 48 C00035 CHEBI:17552 146-91-8 3337
#> 49 C00035 CHEBI:17552 146-91-8 3337
#> 50 C00035 CHEBI:17552 146-91-8 3337
#> 51 C00035 CHEBI:17552 146-91-8 3337
#> 52 C00035 CHEBI:17552 146-91-8 3337
#> 53 C00035 CHEBI:17552 146-91-8 3337
#> 54 C00035 CHEBI:17552 146-91-8 3337
#> 55 C00035 CHEBI:17552 146-91-8 3337
#> 56 C00044 CHEBI:15996 86-01-1 3346
#> 57 C00044 CHEBI:15996 86-01-1 3346
#> 58 C00044 CHEBI:15996 86-01-1 3346
#> 59 C00044 CHEBI:15996 86-01-1 3346
#> 60 C00044 CHEBI:15996 86-01-1 3346
#> 61 C00044 CHEBI:15996 86-01-1 3346
#> 62 C00044 CHEBI:15996 86-01-1 3346
#> 63 C00044 CHEBI:15996 86-01-1 3346
#> 64 C00044 CHEBI:15996 86-01-1 3346
#> 65 C00044 CHEBI:15996 86-01-1 3346
#> 66 C00080 CHEBI:15378 3380
#> 67 C00080 CHEBI:15378 3380
#> 68 C00080 CHEBI:15378 3380
#> 69 C00080 CHEBI:15378 3380
#> 70 C00080 CHEBI:15378 3380
#> 71 C00080 CHEBI:15378 3380
#> 72 C00080 CHEBI:15378 3380
#> 73 C00080 CHEBI:15378 3380
#> 74 C00080 CHEBI:15378 3380
#> 75 C00080 CHEBI:15378 3380
#> 76 C00080 CHEBI:15378 3380
#> 77 C00080 CHEBI:15378 3380
#> 78 C00080 CHEBI:15378 3380
#> 79 C00080 CHEBI:15378 3380
#> 80 C00080 CHEBI:15378 3380
#> 81 C00080 CHEBI:15378 3380
#> 82 C00080 CHEBI:15378 3380
#> 83 C00080 CHEBI:15378 3380
#> 84 C00080 CHEBI:15378 3380
#> 85 C00080 CHEBI:15378 3380
#> 86 C00001 CHEBI:15377 7732-18-5 3303
#> 87 C00001 CHEBI:15377 7732-18-5 3303
#> 88 C00001 CHEBI:15377 7732-18-5 3303
#> 89 C00001 CHEBI:15377 7732-18-5 3303
#> 90 C00001 CHEBI:15377 7732-18-5 3303
#> 91 C00001 CHEBI:15377 7732-18-5 3303
#> 92 C00001 CHEBI:15377 7732-18-5 3303
#> 93 C00001 CHEBI:15377 7732-18-5 3303
#> 94 C00001 CHEBI:15377 7732-18-5 3303
#> 95 C00001 CHEBI:15377 7732-18-5 3303
#> 96 C00001 CHEBI:15377 7732-18-5 3303
#> 97 C00003 CHEBI:15846 53-84-9 3305
#> 98 C00003 CHEBI:15846 53-84-9 3305
#> 99 C00003 CHEBI:15846 53-84-9 3305
#> 100 C00003 CHEBI:15846 53-84-9 3305
#> 101 C00004 CHEBI:16908 58-68-4 3306
#> 102 C00004 CHEBI:16908 58-68-4 3306
#> 103 C00004 CHEBI:16908 58-68-4 3306
#> 104 C00004 CHEBI:16908 58-68-4 3306
#> 105 C00006 CHEBI:18009 53-59-8 3308
#> 106 C00006 CHEBI:18009 53-59-8 3308
#> 107 C00006 CHEBI:18009 53-59-8 3308
#> 108 C00006 CHEBI:18009 53-59-8 3308
#> 109 C00006 CHEBI:18009 53-59-8 3308
#> 110 C00006 CHEBI:18009 53-59-8 3308
#> 111 C00006 CHEBI:18009 53-59-8 3308
#> 112 C00006 CHEBI:18009 53-59-8 3308
#> 113 C00005 CHEBI:16474 2646-71-1 3307
#> 114 C00005 CHEBI:16474 2646-71-1 3307
#> 115 C00005 CHEBI:16474 2646-71-1 3307
#> 116 C00005 CHEBI:16474 2646-71-1 3307
#> 117 C00005 CHEBI:16474 2646-71-1 3307
#> 118 C00005 CHEBI:16474 2646-71-1 3307
#> 119 C00005 CHEBI:16474 2646-71-1 3307
#> 120 C00005 CHEBI:16474 2646-71-1 3307
#> 121 C00009 CHEBI:26078 7664-38-2 3311
#> 122 C00009 CHEBI:18367 7664-38-2 3311
#> 123 C00009 CHEBI:18367 7664-38-2 8144764
#> 124 C00009 CHEBI:18367 7664-38-2 8144764
#> 125 C00009 CHEBI:18367 7664-38-2 8144764
#> 126 C00009 CHEBI:18367 7664-38-2 8144764
#> 127 C00009 CHEBI:18367 7664-38-2 8144764
#> 128 C00009 CHEBI:18367 7664-38-2 8144764
#> 129 C00075 CHEBI:15713 63-39-8 3375
#> 130 C00075 CHEBI:15713 63-39-8 3375
#> 131 C00075 CHEBI:15713 63-39-8 3375
#> 132 C00075 CHEBI:15713 63-39-8 3375
#> 133 C00075 CHEBI:15713 63-39-8 3375
#> 134 C00007 CHEBI:15379 7782-44-7 977
#> 135 C00013 CHEBI:29888 2466-09-3 1023