Inputs

The tools can handle inputs in both CX and CX2 format. Please refer to respective documentations for the details how to create CX and CX2 files, or use ndex2-client python package.

• HIERARCHY directory

  A RO-Crate generated by cellmaps_generate_hierarchy or directory with similar structure, containing all necessary files:

  • hierarchy.cx or hierarchy.cx2

    Network hierarchy in CX or CX2 (HCX) format.

    [
      {
        "CXVersion": "1.0",
        "hasFragments": false
      },
      {
        "metaData": [
          {
            "elementCount": 1,
            "name": "attributeDeclarations"
          },
          {
            "elementCount": 1,
            "name": "networkAttributes"
          },
          {
            "elementCount": 3,
            "name": "nodes"
          },
          {
            "elementCount": 2,
            "name": "edges"
          }
        ]
      },
      {
        "attributeDeclarations": [removed for readability of the example]
      },
      {
        "networkAttributes": [
          {
            "name": "Sample Network",
            "description": "This is a sample network for demonstration."
            "ndexSchema": "hierarchy_v0.1",
            "HCX::modelFileCount": 2,
            "HCX::interactionNetworkName": "hierarchy_parent.cx2"
          }
        ]
      },
      {
        "nodes": [
          {
            "id": 0,
            "v": {
              "name": "Node1",
              "represents": "Data1"
              "HCX::isRoot": true,
              "HCX::members": [
                0,
                1,
                2]
            }
          },
          {
            "id": 1,
            "v": {
              "name": "Node2",
              "represents": "Data2"
              "HCX::isRoot": false,
              "HCX::members": [
                1]
            }
          },
          {
            "id": 2,
            "v": {
              "name": "Node3",
              "represents": "Data3"
              "HCX::isRoot": true,
              "HCX::members": [
                2]
            }
          }
        ]
      },
      {
        "edges": [
          {
            "id": 0,
            "s": 0,
            "t": 1
          },
          {
            "id": 1,
            "s": 0,
            "t": 2
          }
        ]
      },
      {
        "status": [
          {
            "error": "",
            "success": true
          }
        ]
      }
    ]
    

    • hierarchy_parent.cx2:

      The parent or primary network used as a reference for generating the hierarchy in CX or CX2 format.

    [
        {
            "CXVersion": "2.0",
            "hasFragments": false
        },
        {
            "metaData": [
                {"elementCount": 1, "name": "attributeDeclarations"},
                {"elementCount": 1, "name": "networkAttributes"},
                {"elementCount": 3, "name": "nodes"},
                {"elementCount": 2, "name": "edges"}
            ]
        },
        {
            "attributeDeclarations": [
                {
                    "networkAttributes": {"name": {"d": "string"}, "description": {"d": "string"}},
                    "nodes": {"name": {"a": "n", "d": "string"}, "represents": {"a": "r", "d": "string"}},
                    "edges": {"interaction": {"a": "i", "d": "string"}, "Weight": {"d": "double"}}
                }
            ]
        },
        {
            "networkAttributes": [
                {"name": "Example PPI Network", "description": "Simplified Protein-Protein Interaction network example"}
            ]
        },
        {
            "nodes": [
                {"id": 0, "v": {"n": "ProteinA", "r": "ProteinA"}},
                {"id": 1, "v": {"n": "ProteinB", "r": "ProteinB"}},
                {"id": 2, "v": {"n": "ProteinC", "r": "ProteinC"}}
            ]
        },
        {
            "edges": [
                {"id": 0, "s": 0, "t": 1, "v": {"Weight": 0.5, "i": "interacts-with"}},
                {"id": 1, "s": 0, "t": 2, "v": {"Weight": 0.6, "i": "interacts-with"}},
            ]
        }
    ]
    

  • ro-crate-metadata.json:

    Metadata in RO-Crate_ format, a community effort to establish a lightweight approach to packaging research data with their metadata.

    It contains general information about the data i.a. ID, Type, Name, Description, contextual definitions, Software detail, as well as datasets details of each individual part of the data.

    For example, the metadata for the content of hierarchy.cx provides unique id, context, type, url, name, keywords, etc. The url can be used to view the hierarchy in Cytoscape_ Web.