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 ranked interaction partners for one protein from STRING. STRING’s limit=0 returns the complet…

STRING_get_interaction_partners tool specification

Tool Information:

  • Name: STRING_get_interaction_partners

  • Type: BaseRESTTool

  • Description: Get ranked interaction partners for one protein from STRING. STRING’s limit=0 returns the complete partner list for this endpoint, so ToolUniverse requests all partners then applies exact client-side pagination: start with offset=0 and continue with metadata.next_offset while metadata.has_more is true. metadata.total_results is exact. Returns detailed confidence scores by evidence type.

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) Number of ranked partners in this client-side page (default 10)

  • offset (integer) (optional) Zero-based ranked-partner offset. Continue with metadata.next_offset while metadata.has_more is true.

  • 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 carriage return characters (r).

Parameters:

  • identifiers (string) (required) Protein identifier(s). For multiple proteins, separate with ‘r’ (carriage return character). Examples: ‘TP53’, ‘BRCA1rBRCA2rTP53’, ‘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)