Ppi Tools

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

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

Available Tools

BioGRID_get_interactions (Type: BioGRIDRESTTool)

Query protein and genetic interactions from the BioGRID database. BioGRID is a comprehensive data…

BioGRID_get_interactions tool specification

Tool Information:

  • Name: BioGRID_get_interactions

  • Type: BioGRIDRESTTool

  • Description: Query protein and genetic interactions from the BioGRID database. BioGRID is a comprehensive database of physical and genetic interactions with detailed experimental evidence.

Parameters:

  • gene_names (array) (required) List of gene names or protein identifiers

  • organism (string) (optional) Organism name (e.g., ‘Homo sapiens’, ‘Mus musculus’)

  • interaction_type (string) (optional) Type of interaction (‘physical’, ‘genetic’, ‘both’)

  • evidence_types (array) (optional) List of evidence types to include

  • limit (integer) (optional) Maximum number of interactions to return (default: 100)

  • format (string) (optional) Output format (‘json’ or ‘tab’, default: ‘json’)

Example Usage:

query = {
    "name": "BioGRID_get_interactions",
    "arguments": {
        "gene_names": ["item1", "item2"]
    }
}
result = tu.run(query)

STRING_get_protein_interactions (Type: STRINGRESTTool)

Query protein-protein interactions from the STRING database. STRING is a comprehensive database o…

STRING_get_protein_interactions tool specification

Tool Information:

  • Name: STRING_get_protein_interactions

  • Type: STRINGRESTTool

  • Description: Query protein-protein interactions from the STRING database. STRING is a comprehensive database of known and predicted protein-protein interactions with confidence scores and functional annotations.

Parameters:

  • protein_ids (array) (required) List of protein identifiers (UniProt IDs, gene names, etc.)

  • species (integer) (optional) NCBI taxonomy ID (default: 9606 for human)

  • confidence_score (number) (optional) Minimum confidence score (0-1, default: 0.4)

  • limit (integer) (optional) Maximum number of interactions to return (default: 50)

  • network_type (string) (optional) Type of network (‘full’, ‘physical’, ‘functional’)

Example Usage:

query = {
    "name": "STRING_get_protein_interactions",
    "arguments": {
        "protein_ids": ["item1", "item2"]
    }
}
result = tu.run(query)