Ppi Tools#

Configuration File: ppi_tools.json Tool Type: Local Tools Count: 4

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

Available Tools#

STRING_functional_enrichment (Type: STRINGRESTTool)#

Identify enriched biological functions, pathways, and processes for a protein set using STRING (S…

STRING_functional_enrichment tool specification

Tool Information:

  • Name: STRING_functional_enrichment

  • Type: STRINGRESTTool

  • Description: Identify enriched biological functions, pathways, and processes for a protein set using STRING (Search Tool for Retrieval of Interacting Genes/Proteins) database. Performs statistical enrichment analysis against GO (Gene Ontology) terms, KEGG pathways, Reactome pathways, and other annotation databases. Returns significantly enriched terms with FDR-corrected p-values. Minimum 3-4 proteins required for meaningful statistical analysis. No API key required. Use for: discovering pathways enriched in protein network, identifying biological processes, finding shared functions among proteins, interpreting omics data (proteomics, interactomics), hypothesis generation.

Parameters:

  • protein_ids (array) (required) List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins recommended for meaningful enrichment.

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

  • category (string) (optional) Enrichment category: ‘Process’ (GO Biological Process), ‘Component’ (GO Cellular Component), ‘Function’ (GO Molecular Function), ‘KEGG’, ‘Reactome’, ‘WikiPathways’, ‘COMPARTMENTS’, ‘TISSUES’, ‘DISEASES’

Example Usage:

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

STRING_get_protein_interactions (Type: STRINGRESTTool)#

Alternative method to retrieve protein interactions from STRING (Search Tool for Retrieval of Int…

STRING_get_protein_interactions tool specification

Tool Information:

  • Name: STRING_get_protein_interactions

  • Type: STRINGRESTTool

  • Description: Alternative method to retrieve protein interactions from STRING (Search Tool for Retrieval of Interacting Genes/Proteins). STRING uses limit to expand network nodes and can return more pairwise edges than that value; this wrapper sorts all returned edges by confidence and exposes a recoverable local page. Start with interaction_offset=0 and continue with next_interaction_offset while has_more is true. Recommend using STRING_get_network for most analyses. No API key required.

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 interactions in this returned page. STRING also uses this value for upstream network expansion, so total_interactions can exceed limit; use interaction_offset to retrieve the remaining edges from the same expanded network.

  • interaction_offset (integer) (optional) Zero-based number of score-sorted interaction edges to skip. Start at 0 and continue with metadata.next_interaction_offset.

  • 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)

STRING_map_identifiers (Type: STRINGRESTTool)#

Map protein identifiers to STRING (Search Tool for Retrieval of Interacting Genes/Proteins) datab…

STRING_map_identifiers tool specification

Tool Information:

  • Name: STRING_map_identifiers

  • Type: STRINGRESTTool

  • Description: Map protein identifiers to STRING (Search Tool for Retrieval of Interacting Genes/Proteins) database IDs. Essential first step before using other STRING tools - converts your protein names (gene symbols, UniProt IDs, Ensembl IDs) to STRING’s internal identifiers. STRING database contains 14M+ proteins from 5,000+ organisms with functional association networks. No API key required (public API with rate limits). Use for: preparing protein lists for network analysis, converting between identifier types, validating protein names exist in STRING, batch identifier conversion.

Parameters:

  • protein_ids (array) (required) List of protein identifiers to map (UniProt IDs, gene names, Ensembl IDs, RefSeq IDs)

  • species (integer) (optional) NCBI taxonomy ID (default: 9606 for human, 10090 for mouse)

  • limit (integer) (optional) Maximum number of matches per identifier (default: 1)

  • echo_query (integer) (optional) Include query identifier in response (1=yes, 0=no, default: 1)

Example Usage:

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

STRING_ppi_enrichment (Type: STRINGRESTTool)#

Test if your protein set has more interactions than expected by chance (PPI = Protein-Protein Int…

STRING_ppi_enrichment tool specification

Tool Information:

  • Name: STRING_ppi_enrichment

  • Type: STRINGRESTTool

  • Description: Test if your protein set has more interactions than expected by chance (PPI = Protein-Protein Interaction enrichment). Compares observed interactions in your network to random expectation - significant enrichment suggests proteins work together functionally. Returns enrichment p-value and expected vs observed interaction counts. Useful for validating that your protein list forms a real functional module rather than random proteins. No API key required. Use for: validating protein complex predictions, testing if proteins form functional module, quality control for network analysis, distinguishing real complexes from random protein lists, assessing functional coherence.

Parameters:

  • protein_ids (array) (required) List of protein identifiers (UniProt IDs, gene names, Ensembl IDs). Minimum 3 proteins required.

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

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

Example Usage:

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