Ndex Tools

Configuration File: ndex_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ndex_tools.json configuration file.

Available Tools

NDEx_get_network (Type: NDExTool)

Get the full content of a biological network from NDEx including all nodes (proteins/genes) and e…

NDEx_get_network tool specification

Tool Information:

  • Name: NDEx_get_network

  • Type: NDExTool

  • Description: Get the full content of a biological network from NDEx including all nodes (proteins/genes) and edges (interactions/relationships). Returns the network in a structured format with node names, edge source-target pairs, and interaction types. Large networks are truncated (max 200 nodes, 500 edges). Use NDEx_search_networks to find network UUIDs. Example: retrieves the BRCA1 interactome showing all protein interaction partners.

Parameters:

  • uuid (string) (required) NDEx network UUID. Example: ‘34eec19d-ab5a-11ea-aaef-0ac135e8bacf’ (BRCA1 interactome).

Example Usage:

query = {
    "name": "NDEx_get_network",
    "arguments": {
        "uuid": "example_value"
    }
}
result = tu.run(query)

NDEx_get_network_summary (Type: NDExTool)

Get detailed summary information for a specific biological network in NDEx by its UUID. Returns t…

NDEx_get_network_summary tool specification

Tool Information:

  • Name: NDEx_get_network_summary

  • Type: NDExTool

  • Description: Get detailed summary information for a specific biological network in NDEx by its UUID. Returns the network name, description, node and edge counts, owner, DOI, version, creation/modification dates, and custom properties. Use NDEx_search_networks to find network UUIDs first. Example: UUID ‘34eec19d-ab5a-11ea-aaef-0ac135e8bacf’ returns the BRCA1 interactome network with 82 nodes and 118 edges.

Parameters:

  • uuid (string) (required) NDEx network UUID. Get UUIDs from NDEx_search_networks results. Example: ‘34eec19d-ab5a-11ea-aaef-0ac135e8bacf’ (BRCA1 interactome), ‘35e031eb-45d1-11ed-b7d0-0ac135e8bacf’ (p53 pathway).

Example Usage:

query = {
    "name": "NDEx_get_network_summary",
    "arguments": {
        "uuid": "example_value"
    }
}
result = tu.run(query)

NDEx_search_networks (Type: NDExTool)

Search the NDEx biological network repository for published networks by keyword. NDEx hosts thous…

NDEx_search_networks tool specification

Tool Information:

  • Name: NDEx_search_networks

  • Type: NDExTool

  • Description: Search the NDEx biological network repository for published networks by keyword. NDEx hosts thousands of curated protein-protein interaction (PPI) networks, signaling pathways, gene regulatory networks, and metabolic networks from research publications and databases like NCI-PID and SIGNOR. Returns network names, node/edge counts, DOIs, and UUIDs. Example: search ‘BRCA1’ finds interaction networks involving BRCA1; search ‘p53 signaling’ finds p53 pathway networks.

Parameters:

  • query (string) (required) Search query for finding biological networks. Can include gene names, pathway names, diseases, or biological processes. Examples: ‘BRCA1’, ‘p53 signaling’, ‘apoptosis’, ‘insulin pathway’, ‘MAPK cascade’.

  • size (integer) (optional) Maximum number of results to return (default: 10, max: 100).

  • start (integer) (optional) Offset for pagination (default: 0).

Example Usage:

query = {
    "name": "NDEx_search_networks",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)