Spaces:
Running
Running
Example biotech workspace.
Browse files- examples/Bio demo +461 -0
- examples/drug_target_data_sample.csv +6 -0
examples/Bio demo
ADDED
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@@ -0,0 +1,461 @@
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| 1 |
+
{
|
| 2 |
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"env": "LynxKite Graph Analytics",
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| 3 |
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"nodes": [
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| 4 |
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{
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| 5 |
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"id": "Import CSV 1",
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| 6 |
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"type": "basic",
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| 7 |
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"data": {
|
| 8 |
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"title": "Import CSV",
|
| 9 |
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"params": {
|
| 10 |
+
"columns": "<from file>",
|
| 11 |
+
"separator": "<auto>",
|
| 12 |
+
"filename": "examples/drug_target_data_sample.csv"
|
| 13 |
+
},
|
| 14 |
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"display": null,
|
| 15 |
+
"error": null,
|
| 16 |
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"collapsed": null,
|
| 17 |
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| 18 |
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| 19 |
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| 20 |
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| 21 |
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"name": "output",
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| 22 |
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"type": {
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| 23 |
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"type": "None"
|
| 24 |
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}
|
| 25 |
+
}
|
| 26 |
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},
|
| 27 |
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"params": {
|
| 28 |
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"filename": {
|
| 29 |
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"type": {
|
| 30 |
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"type": "<class 'str'>"
|
| 31 |
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},
|
| 32 |
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"default": null,
|
| 33 |
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"name": "filename"
|
| 34 |
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},
|
| 35 |
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"columns": {
|
| 36 |
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"default": "<from file>",
|
| 37 |
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"name": "columns",
|
| 38 |
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"type": {
|
| 39 |
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"type": "<class 'str'>"
|
| 40 |
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}
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| 41 |
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},
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| 42 |
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"separator": {
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| 43 |
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"name": "separator",
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| 44 |
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"default": "<auto>",
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| 45 |
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"type": {
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| 46 |
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"type": "<class 'str'>"
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| 47 |
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}
|
| 48 |
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}
|
| 49 |
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},
|
| 50 |
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"inputs": {},
|
| 51 |
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"type": "basic",
|
| 52 |
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"name": "Import CSV"
|
| 53 |
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},
|
| 54 |
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"__execution_delay": 0.0
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| 55 |
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},
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| 56 |
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"position": {
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| 57 |
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"x": -91.52295913245543,
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| 58 |
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"y": 933.9762681038399
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| 59 |
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},
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| 60 |
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"width": 200.0,
|
| 61 |
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"height": 200.0
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| 62 |
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},
|
| 63 |
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{
|
| 64 |
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"id": "Parse SMILES 1",
|
| 65 |
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"type": "basic",
|
| 66 |
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"data": {
|
| 67 |
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"title": "Parse SMILES",
|
| 68 |
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"params": {
|
| 69 |
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"table": "df",
|
| 70 |
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"save_as": "mols",
|
| 71 |
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"smiles_column": "SMILES"
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| 72 |
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},
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| 73 |
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"display": null,
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| 74 |
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"error": null,
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| 75 |
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"meta": {
|
| 76 |
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"name": "Parse SMILES",
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| 77 |
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"params": {
|
| 78 |
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"table": {
|
| 79 |
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"type": {
|
| 80 |
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"type": "<class 'str'>"
|
| 81 |
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},
|
| 82 |
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"default": "df",
|
| 83 |
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"name": "table"
|
| 84 |
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},
|
| 85 |
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"smiles_column": {
|
| 86 |
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"type": {
|
| 87 |
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"type": "<class 'str'>"
|
| 88 |
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},
|
| 89 |
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"name": "smiles_column",
|
| 90 |
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"default": "SMILES"
|
| 91 |
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},
|
| 92 |
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"save_as": {
|
| 93 |
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"type": {
|
| 94 |
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"type": "<class 'str'>"
|
| 95 |
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},
|
| 96 |
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"name": "save_as",
|
| 97 |
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"default": "mols"
|
| 98 |
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}
|
| 99 |
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},
|
| 100 |
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"inputs": {
|
| 101 |
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"bundle": {
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| 102 |
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"name": "bundle",
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| 103 |
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"type": {
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| 104 |
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"type": "<class 'lynxkite_graph_analytics.lynxkite_ops.Bundle'>"
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| 105 |
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},
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| 106 |
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"position": "left"
|
| 107 |
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}
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| 108 |
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},
|
| 109 |
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"outputs": {
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| 110 |
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"output": {
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| 111 |
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"position": "right",
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| 112 |
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"name": "output",
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| 113 |
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"type": {
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| 114 |
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"type": "None"
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| 115 |
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}
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| 116 |
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}
|
| 117 |
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},
|
| 118 |
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"type": "basic"
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| 119 |
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}
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| 120 |
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},
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| 121 |
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"position": {
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| 122 |
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"x": 381.1847590729871,
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| 123 |
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"y": 945.0
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| 124 |
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},
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| 125 |
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"height": 200.0,
|
| 126 |
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"width": 200.0
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| 127 |
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},
|
| 128 |
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{
|
| 129 |
+
"id": "Graph from molecule similarity 1",
|
| 130 |
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"type": "basic",
|
| 131 |
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"data": {
|
| 132 |
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"title": "Graph from molecule similarity",
|
| 133 |
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"params": {
|
| 134 |
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"table": "df",
|
| 135 |
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"mols_column": "mols",
|
| 136 |
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"average_degree": "3"
|
| 137 |
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},
|
| 138 |
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"display": null,
|
| 139 |
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"error": null,
|
| 140 |
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"collapsed": null,
|
| 141 |
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"meta": {
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| 142 |
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"params": {
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| 143 |
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"mols_column": {
|
| 144 |
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"name": "mols_column",
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| 145 |
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"default": "mols",
|
| 146 |
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"type": {
|
| 147 |
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"type": "<class 'str'>"
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| 148 |
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}
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| 149 |
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},
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| 150 |
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"table": {
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| 151 |
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"type": {
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| 152 |
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"type": "<class 'str'>"
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| 153 |
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},
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| 154 |
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"default": "df",
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| 155 |
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"name": "table"
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| 156 |
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},
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| 157 |
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"average_degree": {
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| 158 |
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"name": "average_degree",
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| 159 |
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"default": 10.0,
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| 160 |
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"type": {
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| 161 |
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"type": "<class 'int'>"
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| 162 |
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}
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| 163 |
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}
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| 164 |
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},
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| 165 |
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"inputs": {
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| 166 |
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"bundle": {
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| 167 |
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"position": "left",
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| 168 |
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"type": {
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| 169 |
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"type": "<class 'lynxkite_graph_analytics.lynxkite_ops.Bundle'>"
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| 170 |
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},
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| 171 |
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"name": "bundle"
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| 172 |
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}
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| 173 |
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},
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| 174 |
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"outputs": {
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| 175 |
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"output": {
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| 176 |
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"type": {
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| 177 |
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"type": "None"
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| 178 |
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},
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| 179 |
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"position": "right",
|
| 180 |
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"name": "output"
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| 181 |
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}
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| 182 |
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},
|
| 183 |
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"name": "Graph from molecule similarity",
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| 184 |
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"type": "basic"
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| 185 |
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},
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| 186 |
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"__execution_delay": 0.0
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| 187 |
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},
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| 188 |
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"position": {
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| 189 |
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"x": 926.4337192214458,
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| 190 |
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"y": 1014.4451876264845
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| 191 |
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},
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| 192 |
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"height": 200.0,
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| 193 |
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"width": 200.0
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| 194 |
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},
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| 195 |
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{
|
| 196 |
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"id": "Visualize graph 1",
|
| 197 |
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"type": "visualization",
|
| 198 |
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"data": {
|
| 199 |
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"title": "Visualize graph",
|
| 200 |
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"params": {
|
| 201 |
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"color_edges_by": "similarity",
|
| 202 |
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"color_nodes_by": "ORGANISM",
|
| 203 |
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"label_by": "DRUG_NAME"
|
| 204 |
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},
|
| 205 |
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"display": {
|
| 206 |
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"animationDuration": 500,
|
| 207 |
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"animationEasingUpdate": "quinticInOut",
|
| 208 |
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"tooltip": {
|
| 209 |
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"show": true
|
| 210 |
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},
|
| 211 |
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"series": [
|
| 212 |
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{
|
| 213 |
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"type": "graph",
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| 214 |
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"lineStyle": {
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| 215 |
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"color": "gray",
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| 216 |
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"curveness": 0.3
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| 217 |
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},
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| 218 |
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"emphasis": {
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| 219 |
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"focus": "adjacency",
|
| 220 |
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|
| 221 |
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"width": 10
|
| 222 |
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}
|
| 223 |
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},
|
| 224 |
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|
| 225 |
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"position": "top",
|
| 226 |
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"formatter": "{b}"
|
| 227 |
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|
| 228 |
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"data": [
|
| 229 |
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{
|
| 230 |
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"id": "0",
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| 231 |
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| 238 |
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"show": true
|
| 239 |
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},
|
| 240 |
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"name": "phencyclidine",
|
| 241 |
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"value": "Torpedo californica"
|
| 242 |
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},
|
| 243 |
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{
|
| 244 |
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"id": "1",
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| 245 |
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| 251 |
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|
| 252 |
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|
| 253 |
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},
|
| 254 |
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"name": "triazolam",
|
| 255 |
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"value": "Homo sapiens"
|
| 256 |
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},
|
| 257 |
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{
|
| 258 |
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"id": "2",
|
| 259 |
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| 265 |
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"label": {
|
| 266 |
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"show": true
|
| 267 |
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},
|
| 268 |
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"name": "gentian violet",
|
| 269 |
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"value": "Homo sapiens"
|
| 270 |
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},
|
| 271 |
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{
|
| 272 |
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"id": "3",
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| 273 |
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| 279 |
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|
| 280 |
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"show": true
|
| 281 |
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},
|
| 282 |
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"name": "ipratropium",
|
| 283 |
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"value": "Homo sapiens"
|
| 284 |
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},
|
| 285 |
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{
|
| 286 |
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"id": "4",
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| 287 |
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| 292 |
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| 293 |
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"label": {
|
| 294 |
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"show": true
|
| 295 |
+
},
|
| 296 |
+
"name": "deoxycholic acid",
|
| 297 |
+
"value": "Homo sapiens"
|
| 298 |
+
}
|
| 299 |
+
],
|
| 300 |
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"links": [
|
| 301 |
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{
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| 302 |
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"source": "3",
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| 303 |
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"value": 0.8813559322033898
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"source": "0",
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},
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{
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"source": "0",
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| 327 |
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"target": "3",
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| 328 |
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"color": "#26818e"
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"value": 0.9047619047619048
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| 332 |
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| 333 |
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{
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| 334 |
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"source": "1",
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| 336 |
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| 337 |
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| 339 |
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"value": 0.9090909090909091
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{
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"source": "1",
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| 344 |
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| 345 |
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"color": "#1ea087"
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| 346 |
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},
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| 347 |
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"value": 0.921875
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| 348 |
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},
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| 349 |
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{
|
| 350 |
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"source": "0",
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| 351 |
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"target": "2",
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| 352 |
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| 353 |
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"color": "#3ebc73"
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| 354 |
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},
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| 355 |
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"value": 0.9375
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| 356 |
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},
|
| 357 |
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{
|
| 358 |
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"source": "1",
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| 359 |
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"target": "4",
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| 360 |
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| 365 |
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{
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| 366 |
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"source": "2",
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| 368 |
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| 385 |
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|
| 387 |
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| 389 |
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| 390 |
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| 391 |
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"position": "left",
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| 392 |
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"type": {
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| 393 |
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"type": "<class 'lynxkite_graph_analytics.lynxkite_ops.Bundle'>"
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| 394 |
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|
| 395 |
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|
| 396 |
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},
|
| 397 |
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"outputs": {},
|
| 398 |
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"type": "visualization",
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| 399 |
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|
| 400 |
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|
| 401 |
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| 409 |
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| 412 |
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|
| 413 |
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|
| 414 |
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| 415 |
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|
| 416 |
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| 417 |
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| 418 |
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| 419 |
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| 420 |
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|
| 421 |
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},
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| 422 |
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"position": {
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|
| 425 |
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},
|
| 426 |
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"name": "Visualize graph"
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| 428 |
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"collapsed": null
|
| 429 |
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},
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| 430 |
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|
| 431 |
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|
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|
| 434 |
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|
| 437 |
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],
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| 438 |
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"edges": [
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| 439 |
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{
|
| 440 |
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"id": "Import CSV 1 Parse SMILES 1",
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| 441 |
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"source": "Import CSV 1",
|
| 442 |
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|
| 443 |
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|
| 446 |
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{
|
| 447 |
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"id": "Parse SMILES 1 Graph from molecule similarity 1",
|
| 448 |
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"source": "Parse SMILES 1",
|
| 449 |
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|
| 450 |
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|
| 452 |
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|
| 453 |
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{
|
| 454 |
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"id": "Graph from molecule similarity 1 Visualize graph 1",
|
| 455 |
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"source": "Graph from molecule similarity 1",
|
| 456 |
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"target": "Visualize graph 1",
|
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|
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}
|
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]
|
| 461 |
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}
|
examples/drug_target_data_sample.csv
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Unnamed: 0,DRUG_NAME,STRUCT_ID,TARGET_NAME,TARGET_CLASS,ACCESSION,GENE,SWISSPROT,ACT_VALUE,ACT_UNIT,ACT_TYPE,ACT_COMMENT,ACT_SOURCE,RELATION,MOA,MOA_SOURCE,ACT_SOURCE_URL,MOA_SOURCE_URL,ACTION_TYPE,TDL,ORGANISM,SMILES,InChI,InChIKey,INN
|
| 2 |
+
9737,phencyclidine,2121,Acetylcholine receptor subunit alpha,Ion channel,P02710,CHRNA1,ACHA_TORCA,6.66,,IC50,Displacement of [3H]PCP from nAChR in Torpedo nobiliana electric organs membranes in presence of 100 uM carbachol by scintillation counting method,CHEMBL,=,,,,,,,Torpedo californica,C1CCN(CC1)C1(CCCCC1)C1=CC=CC=C1,"InChI=1S/C17H25N/c1-4-10-16(11-5-1)17(12-6-2-7-13-17)18-14-8-3-9-15-18/h1,4-5,10-11H,2-3,6-9,12-15H2",JTJMJGYZQZDUJJ-UHFFFAOYSA-N,phencyclidine
|
| 3 |
+
12934,triazolam,2729,GABA A receptor alpha-3/beta-2/gamma-2,Ion channel,P18507|P34903|P47870,GABRG2|GABRA3|GABRB2,GBRG2_HUMAN|GBRA3_HUMAN|GBRB2_HUMAN,8.876,,Ki,,WOMBAT-PK,=,1.0,CHEMBL,,https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL646,POSITIVE ALLOSTERIC MODULATOR,Tclin|Tclin|Tclin|Tclin|Tclin|Tclin|Tclin|Tclin|Tclin,Homo sapiens,CC1=NN=C2CN=C(C3=CC(Cl)=CC=C3N12)C1=C(Cl)C=CC=C1,"InChI=1S/C17H12Cl2N4/c1-10-21-22-16-9-20-17(12-4-2-3-5-14(12)19)13-8-11(18)6-7-15(13)23(10)16/h2-8H,9H2,1H3",JOFWLTCLBGQGBO-UHFFFAOYSA-N,triazolam
|
| 4 |
+
15266,gentian violet,4138,D(2) dopamine receptor,GPCR,P14416,DRD2,DRD2_HUMAN,5.975,,Ki,DRUGMATRIX: Dopamine D2L radioligand binding (ligand: [3H] Spiperone),DRUG MATRIX,=,,,,,,Tclin,Homo sapiens,CN(C)C1=CC=C(C=C1)C(C1=CC=C(C=C1)N(C)C)=C1C=CC(C=C1)=[N+](C)C,"InChI=1S/C25H30N3/c1-26(2)22-13-7-19(8-14-22)25(20-9-15-23(16-10-20)27(3)4)21-11-17-24(18-12-21)28(5)6/h7-18H,1-6H3/q+1",LGLFFNDHMLKUMI-UHFFFAOYSA-N,gentian violet
|
| 5 |
+
6488,ipratropium,1475,Muscarinic acetylcholine receptor M1,GPCR,P11229,CHRM1,ACM1_HUMAN,9.31,,Ki,,WOMBAT-PK,=,,,,,,Tclin,Homo sapiens,CC(C)[N+]1(C)[C@H]2CC[C@@H]1C[C@@H](C2)OC(=O)C(CO)C1=CC=CC=C1,"InChI=1S/C20H30NO3/c1-14(2)21(3)16-9-10-17(21)12-18(11-16)24-20(23)19(13-22)15-7-5-4-6-8-15/h4-8,14,16-19,22H,9-13H2,1-3H3/q+1/t16-,17+,18+,19?,21?",OEXHQOGQTVQTAT-BHIXFJMTSA-N,ipratropium
|
| 6 |
+
17453,deoxycholic acid,4988,G-protein coupled bile acid receptor 1,GPCR,Q8TDU6,GPBAR1,GPBAR_HUMAN,6.2,,EC50,,IUPHAR,=,,,,,AGONIST,Tchem,Homo sapiens,C[C@H](CCC(O)=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C,"InChI=1S/C24H40O4/c1-14(4-9-22(27)28)18-7-8-19-17-6-5-15-12-16(25)10-11-23(15,2)20(17)13-21(26)24(18,19)3/h14-21,25-26H,4-13H2,1-3H3,(H,27,28)/t14-,15-,16-,17+,18-,19+,20+,21+,23+,24-/m1/s1",KXGVEGMKQFWNSR-LLQZFEROSA-N,deoxycholic acid
|