Standard Cytoscape JSON Models - cytoscape/cytoscape-automation GitHub Wiki

This page lists the accepted JSON representations of the Cytoscape Application Data Model. Using these models when Cytoscape objects are returned from automation functions or commands constitutes a best practice. The Cytoscape JSON Utilities Sample contains a reference implementation of how to produce these using utilities within Cytoscape, and should be used wherever possible instead of re-implementing any representation.

CyNode.java

CyNode as SUID List

[
   63,
   ...
]

CyNode as Single Object

{
  "data": {
    "id": 63,
    "SUID": 63,
    "shared name": "Node 1",
    "name": "Node 1",
    "selected": false,
    "int_column": 1
  }
}

CyEdge.java

CyEdges as an SUID List

[
   83,
   ...
]

CyEdge as Single Object

{
  "data": {
    "source": 62,
    "target": 63,
    "SUID": 83,
    "shared name": "Node 2 (interacts with) Node 1",
    "shared interaction": "interacts with",
    "name": "Node 2 (interacts with) Node 1",
    "selected": false,
    "interaction": "interacts with"
  }
}

CyNetwork.java

CyNetworks as an SUID list

[
   52,
   ...
]

CyNetwork as a Single Object

{
    "shared name": "Network",
    "name": "Network",
    "SUID": 52,
    "__Annotations": [
      ""
    ],
    "selected": true
  }

CyNetwork as cytoscape.js

See cytoscape.js

CyTable.java

[
  ...
  {
    "SUID": 54,
    "title": "Network default network",
    "public": true,
    "mutable": "PERMANENTLY_IMMUTABLE",
    "primaryKey": "SUID",
    "rows": [
      {
        "shared name": "Network",
        "name": "Network",
        "SUID": 52,
        "__Annotations": [
          ""
        ],
        "selected": true
      }
    ]
  },
  ...
]

CyRow.java

[
  ...
  {
    "SUID": 63,
    "shared name": "Node 1",
    "name": "Node 1",
    "selected": true,
    "int_column": 1
  },
  ...
]

CyColumn.java

As a List of Column Names

[
  "Column 1",
  "Column 2"
  ...
]

As a Single Column

{
  "name": "int_column",
  "type": "Integer",
  "immutable": false,
  "primaryKey": false,
  "values": [
    1,
    null
  ]
}