Standard Cytoscape JSON Models

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
  ]
}