String Network Tools

Configuration File: string_network_tools.json Tool Type: Local Tools Count: 2

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

Available Tools

STRING_get_interaction_partners (Type: BaseRESTTool)

Get interaction partners for a single protein from STRING database. Returns a ranked list of prot…

STRING_get_interaction_partners tool specification

Tool Information:

  • Name: STRING_get_interaction_partners

  • Type: BaseRESTTool

  • Description: Get interaction partners for a single protein from STRING database. Returns a ranked list of proteins that interact with the query protein, along with detailed confidence scores by evidence type (experimental, database, text-mining, etc.). Different from STRING_get_network which returns all edges in a network - this returns a simple partner list focused on one protein. Useful for finding what proteins a given protein interacts with.

Parameters:

  • identifiers (string) (required) Protein identifier (gene name or STRING ID). Examples: ‘TP53’, ‘BRCA1’, ‘EGFR’, ‘9606.ENSP00000269305’

  • species (integer) (optional) NCBI taxonomy ID (9606=human, 10090=mouse, 7227=fly, 6239=worm)

  • limit (integer) (optional) Maximum number of interaction partners to return

  • required_score ([‘integer’, ‘null’]) (optional) Minimum combined STRING score (0-1000). 400=medium, 700=high, 900=highest confidence.

Example Usage:

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

STRING_get_network (Type: BaseRESTTool)

Get the protein-protein interaction network for one or more proteins from STRING database. Return…

STRING_get_network tool specification

Tool Information:

  • Name: STRING_get_network

  • Type: BaseRESTTool

  • Description: Get the protein-protein interaction network for one or more proteins from STRING database. Returns all interactions (edges) between the query proteins and their neighbors, including confidence scores broken down by evidence type (experiments, co-expression, databases, text-mining, etc.). Different from STRING_get_functional_annotations (which returns GO/pathway annotations) and STRING_get_enrichment (which tests enrichment of a set). Use this to build or visualize PPI networks. Multiple proteins can be separated by newlines (%0d).

Parameters:

  • identifiers (string) (required) Protein identifier(s). For multiple proteins, separate with ‘%0d’ (URL-encoded newline). Examples: ‘TP53’, ‘BRCA1%0dBRCA2%0dTP53’, ‘9606.ENSP00000269305’

  • species (integer) (optional) NCBI taxonomy ID. Examples: 9606 (human), 10090 (mouse), 7227 (Drosophila), 6239 (C. elegans)

  • limit (integer) (optional) Maximum number of interaction partners to include (per protein). 0 = only interactions among input proteins.

  • required_score ([‘integer’, ‘null’]) (optional) Minimum combined STRING score (0-1000). 400=medium, 700=high, 900=highest confidence. Default: 400.

Example Usage:

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