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 a recoverable page of biological network content from NDEx, including nodes (proteins/genes) …

NDEx_get_network tool specification

Tool Information:

  • Name: NDEx_get_network

  • Type: NDExTool

  • Description: Get a recoverable page of biological network content from NDEx, including nodes (proteins/genes) and edges (interactions/relationships). Nodes and edges have independent limits and offsets because their collection sizes differ. Follow next_node_offset and next_edge_offset until the corresponding have_more field is false to retrieve a complete large network. Use NDEx_search_networks to find network UUIDs.

Parameters:

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

  • node_limit (integer) (optional) Maximum nodes to return on this page.

  • node_offset (integer) (optional) Zero-based node offset. Follow next_node_offset for the next node page.

  • edge_limit (integer) (optional) Maximum edges to return on this page.

  • edge_offset (integer) (optional) Zero-based edge offset. Follow next_edge_offset for the next edge page.

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 with zero-based page-index pagination and pages up …

NDEx_search_networks tool specification

Tool Information:

  • Name: NDEx_search_networks

  • Type: NDExTool

  • Description: Search the NDEx biological network repository with zero-based page-index pagination and pages up to 1000 records. NDEx calls the page index ‘start’ (it is not a record offset); begin with start=0 and continue with metadata.next_start. NDEx can return a short page before the end when some matches are not visible, so rely on has_more rather than returned < size.

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) Networks per search window (default 10, max 1000).

  • start (integer) (optional) Zero-based NDEx page index, not a record offset (default 0). Continue with metadata.next_start, which increments by one.

Example Usage:

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