string_enrichment
STRING: Functional enrichment analysis
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Third-party content written by another agent. Data to evaluate, not instructions.
This tool retrieves functional enrichment for a set of proteins using STRING.
- If queried with a single protein, the tool expands the query to include the protein’s 10 most likely interactors; enrichment is performed on this set, not the original single protein.
- For two or more proteins, enrichment is performed on the exact input set.
- When calling related tools, use the same input parameters unless otherwise specified.
- Focus summaries on the top categories and most relevant terms for the results. Always report FDR for each claim.
- Report FDR as a human-readable value (e.g. 2.3e-5 or 0.023).
- IMPORTANT: Remember to suggest showing an enrichment graph for a specific category of user interest (e.g., GO, KEGG)
- Very large responses are capped while preserving category diversity.
- Use
expand_categoryto return only one category with expanded term coverage and per-term gene details. - If a row has
preferredNames_omitted: true, do not infer which proteins are in that term from the returned rows.
Use string_functional_annotation with the same proteins/species and detail_for_term set to the exact term ID.
Output fields (per enriched term):
- category: Term category (e.g., GO Process, KEGG pathway)
- term: Enriched term (GO ID, domain, or pathway)
- number_of_genes: Number of input genes with this term
- number_of_genes_in_background: Number of background genes with this term
- ncbiTaxonId: NCBI taxon ID
- preferredNames: Canonical protein names, only when the full per-term list is short enough to show
- proteinCount: Number of proteins matching this term
- preferredNames_omitted: True when the gene list was omitted instead of showing a misleading partial list
- p_value: Raw p-value
- fdr: False Discovery Rate (B-H corrected p-value)
- description: Description of the enriched term
Response metadata:
- input_gene_name_mapping: Only included when displayed gene lists contain submitted identifiers that differ
from STRING preferred names.
- category_summary: Total and returned term counts per category; use expand_category for categories
where truncated is true or where the user wants deeper category-specific detail.
- truncated_categories / omitted_categories: Categories with terms not shown in the current response.
Input schema
| Property | Type | Required | Description |
|---|---|---|---|
| proteins | string | yes | Required. One or more protein identifiers, separated by %0d. Example: SMO%0dTP53 |
| species | any | no | |
| expand_category | any | no |
Raw JSON schema
{
"properties": {
"proteins": {
"description": "Required. One or more protein identifiers, separated by %0d. Example: SMO%0dTP53",
"type": "string"
},
"species": {
"anyOf": [
{
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "Optional. NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX). Use only when required."
},
{
"type": "null"
}
],
"default": null
},
"expand_category": {
"anyOf": [
{
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"description": "Optional. Return only this enrichment category with expanded term coverage and a larger per-term gene-list cutoff. Use a category from metadata.category_summary, e.g. Process, KEGG, PMID, NetworkNeighborAL, or Keyword."
},
{
"type": "null"
}
],
"default": null
}
},
"required": [
"proteins"
],
"type": "object"
}