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.

CyIdentifiable.java

Implemented in CyNode, CyEdge, CyNetwork, CyTable, and CyRow.

SUIDFactory.java

Not a Data Model.

CyDisposable.java

Not useful in automation contexts. Applicable to Cytoscape internal implementations.

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 named SUID List_

Though a useful possibility, this is more of a convenience format.

```json
[
  {
    "name": "Network",
    "SUID": 52
  },
  ...
]

CyNetwork as cytoscape.js

See cytoscape.js

CyNetworkFactory.java

Not a Data Model.

CyNetworkManager.java

Not a Data Model.

CyNetworkTableManager.java

Not a Data Model.

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 CyColumns

[
   {
      "name": "name",
      "type": "String",
      "immutable": true,
      "primaryKey": false
   },
   ...
]

As a Single Column

{
  "name": "name",
  "values": [
    "Node 2",
    "Node 1"
  ]
}

CyTableFactory.java

Not a Data Model.

CyTableManager.java

Not a Data Model.

CyTableMetadata.java

Could be useful to identify relationships between tables and networks. Unknown if useful to scripters.

CyTableUtil.java

Not a Data Model.

SavePolicy.java

Applicable to CyNetwork and CyTable. This could be useful to identify tables that won't be saved for automation scripters.

VirtualColumnInfo.java