String Ext Tools

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

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

Available Tools

STRING_get_enrichment (Type: STRINGExtTool)

Perform functional enrichment analysis on a set of proteins using the STRING database. Tests whet…

STRING_get_enrichment tool specification

Tool Information:

  • Name: STRING_get_enrichment

  • Type: STRINGExtTool

  • Description: Perform functional enrichment analysis on a set of proteins using the STRING database. Tests whether the input protein list is statistically enriched for Gene Ontology terms, KEGG pathways, Reactome pathways, WikiPathways, InterPro domains, TISSUES, DISEASES, COMPARTMENTS, and other functional categories. Returns enriched terms with p-values, FDR-corrected q-values, and the matching proteins. Useful for interpreting gene lists from RNA-seq, GWAS, proteomics experiments.

Parameters:

  • identifiers (string) (required) Newline-separated list of protein identifiers (gene names or STRING IDs). Example: ‘BRCA1nBRCA2nTP53nATM’. Minimum 2 proteins, recommended 5-100 for meaningful enrichment.

  • species (integer) (optional) NCBI taxonomy ID (default 9606 for human). Examples: 9606 (human), 10090 (mouse), 7227 (fly), 6239 (worm).

  • background_string_identifiers ([‘string’, ‘null’]) (optional) Optional newline-separated background gene set. If not provided, the entire genome proteome is used as background.

Example Usage:

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

STRING_get_functional_annotations (Type: STRINGExtTool)

Get comprehensive functional annotations for a protein from STRING database. Returns per-protein …

STRING_get_functional_annotations tool specification

Tool Information:

  • Name: STRING_get_functional_annotations

  • Type: STRINGExtTool

  • Description: Get comprehensive functional annotations for a protein from STRING database. Returns per-protein annotations from Gene Ontology (Process, Function, Component), KEGG pathways, Reactome, WikiPathways, InterPro domains, Pfam, HPO phenotypes, DISEASES, TISSUES expression, and COMPARTMENTS subcellular localization. Different from STRING_functional_enrichment which tests for statistical enrichment of a protein SET - this tool returns all known annotations for individual proteins. Example: ‘TP53’ returns 1,877 annotations across 13 categories including 655 biological processes, 462 HPO phenotypes, 212 disease associations.

Parameters:

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

  • species (integer) (optional) NCBI taxonomy ID (default 9606 for human). Examples: 9606 (human), 10090 (mouse), 7227 (fly), 6239 (worm).

  • category (string) (optional) Filter by annotation category. Options: ‘Process’ (GO BP), ‘Function’ (GO MF), ‘Component’ (GO CC), ‘KEGG’, ‘RCTM’ (Reactome), ‘WikiPathways’, ‘InterPro’, ‘Pfam’, ‘HPO’, ‘DISEASES’, ‘TISSUES’, ‘COMPARTMENTS’, ‘Keyword’. Leave null for all categories.

Example Usage:

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