drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/string.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
STRING REST API		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/string.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

STRING REST API

Base URL

https://string-db.org/api

URL Pattern

/api/{output_format}/{method}

• output_format: json, tsv, tsv-no-header, image, svg (not all formats for all endpoints)
• method: endpoint name (see below)

Authentication

No API key required. All endpoints are public.

Key Endpoints

1. Resolve protein identifiers

Map protein names/identifiers to STRING internal IDs. Always do this first to get canonical STRING IDs.

GET /api/json/resolve?identifier={query}&species={taxid}

Parameter	Type	Description
identifier	string	Required. Protein name, gene symbol, or external ID.
species	int	NCBI taxonomy ID (9606 = human, 10090 = mouse). Recommended to avoid ambiguity.

Example:

https://string-db.org/api/json/resolve?identifier=TP53&species=9606

Response:

[
  {
    "stringId": "9606.ENSP00000269305",
    "preferredName": "TP53",
    "ncbiTaxonId": 9606,
    "taxonName": "Homo sapiens",
    "annotation": "Cellular tumor antigen p53; ..."
  }
]

---

2. Get interaction partners (network)

GET /api/json/interaction_partners?identifiers={proteins}&species={taxid}

Parameter	Type	Description
identifiers	string	Required. Protein name(s). Use %0d (newline) to separate multiple.
species	int	NCBI taxonomy ID.
limit	int	Max number of interaction partners to return (per input protein).
required_score	int	Minimum combined score (0-1000). Default: 400. Common thresholds: 400 (medium), 700 (high), 900 (highest).
network_type	string	functional (default, all associations) or physical (physical binding only).

Example:

https://string-db.org/api/json/interaction_partners?identifiers=TP53&species=9606&limit=10&required_score=900

Response:

[
  {
    "stringId_A": "9606.ENSP00000269305",
    "stringId_B": "9606.ENSP00000261842",
    "preferredName_A": "TP53",
    "preferredName_B": "MDM2",
    "ncbiTaxonId": 9606,
    "score": 0.999,
    "nscore": 0,
    "fscore": 0,
    "pscore": 0,
    "ascore": 0.93,
    "escore": 0.994,
    "dscore": 0.9,
    "tscore": 0.981
  }
]

Score channels: nscore (neighborhood), fscore (fusion), pscore (phylogenetic co-occurrence), ascore (co-expression), escore (experimental), dscore (database/curated), tscore (text mining).

---

3. Get network interactions between a set of proteins

GET /api/json/network?identifiers={proteins}&species={taxid}

Parameter	Type	Description
identifiers	string	Required. Protein names separated by %0d (newline-encoded).
species	int	NCBI taxonomy ID.
required_score	int	Minimum combined score (0-1000).
network_type	string	functional or physical.
add_nodes	int	Number of additional interactors to add (expands the network).

Example — network among a set of proteins:

https://string-db.org/api/json/network?identifiers=TP53%0dBRCA1%0dATM%0dCHEK2%0dMDM2&species=9606&required_score=700

Returns all pairwise interactions among the input set.

---

4. Network image

GET /api/image/network?identifiers={proteins}&species={taxid}
GET /api/svg/network?identifiers={proteins}&species={taxid}

Returns a PNG image or SVG of the interaction network.

Example:

https://string-db.org/api/image/network?identifiers=TP53%0dBRCA1%0dMDM2&species=9606

---

5. Functional enrichment analysis

Perform Gene Ontology, KEGG pathway, and other enrichment analysis on a set of proteins.

GET /api/json/enrichment?identifiers={proteins}&species={taxid}

Parameter	Type	Description
identifiers	string	Required. Newline-separated (%0d) protein names.
species	int	NCBI taxonomy ID.

Example:

https://string-db.org/api/json/enrichment?identifiers=TP53%0dBRCA1%0dATM%0dCHEK2%0dCDK2%0dCDKN1A&species=9606

Response:

[
  {
    "category": "Process",
    "term": "GO:0006974",
    "description": "cellular response to DNA damage stimulus",
    "number_of_genes": 6,
    "number_of_genes_in_background": 781,
    "ncbiTaxonId": 9606,
    "inputGenes": "TP53,BRCA1,ATM,CHEK2,CDK2,CDKN1A",
    "preferredNames": "TP53,BRCA1,ATM,CHEK2,CDK2,CDKN1A",
    "p_value": 1.2e-12,
    "fdr": 5.6e-10
  }
]

Categories include: Process (GO Biological Process), Function (GO Molecular Function), Component (GO Cellular Component), KEGG, Pfam, InterPro, SMART, Keyword (UniProt), Reactome, WikiPathways, HPO (Human Phenotype Ontology).

---

6. Get protein annotations/info

GET /api/json/get_string_ids?identifiers={proteins}&species={taxid}

Maps arbitrary names to STRING IDs with annotation text.

Example:

https://string-db.org/api/json/get_string_ids?identifiers=CDK2%0dp53&species=9606

Response:

[
  {
    "queryIndex": 0,
    "queryItem": "CDK2",
    "stringId": "9606.ENSP00000266970",
    "ncbiTaxonId": 9606,
    "taxonName": "Homo sapiens",
    "preferredName": "CDK2",
    "annotation": "Cyclin-dependent kinase 2; ..."
  }
]

---

7. Get homology / best-hit in another species

GET /api/json/homology?identifiers={proteins}&species={taxid}&species_b={taxid_b}

Parameter	Type	Description
identifiers	string	Source protein(s).
species	int	Source species.
species_b	int	Target species for homolog lookup.

Example:

https://string-db.org/api/json/homology?identifiers=TP53&species=9606&species_b=10090

---

8. PPI enrichment (is my set more connected than expected?)

GET /api/json/ppi_enrichment?identifiers={proteins}&species={taxid}

Example:

https://string-db.org/api/json/ppi_enrichment?identifiers=TP53%0dBRCA1%0dATM%0dCHEK2&species=9606

Response:

[
  {
    "number_of_nodes": 4,
    "number_of_edges": 6,
    "average_node_degree": 3.0,
    "local_clustering_coefficient": 1.0,
    "expected_number_of_edges": 1,
    "p_value": 0.000123
  }
]

---

Common Species Taxonomy IDs

Species	Taxon ID
Homo sapiens (human)	9606
Mus musculus (mouse)	10090
Rattus norvegicus (rat)	10116
Drosophila melanogaster (fruit fly)	7227
Saccharomyces cerevisiae (yeast)	4932
Caenorhabditis elegans (worm)	6239
Danio rerio (zebrafish)	7955
Escherichia coli K12	511145
Arabidopsis thaliana	3702

Rate Limits

• No published hard rate limit, but the API is intended for programmatic access at moderate rates.
• Recommended: max 1 request per second.
• For large-scale data downloads, use the flat-file downloads on the STRING website instead.
• If you send too many requests, you may receive HTTP 429 or temporary blocking.
• Multiple identifiers per request is strongly preferred over multiple single-identifier requests.

Error Handling

• Returns HTTP 400 for malformed requests.
• Returns HTTP 404 if no matching protein is found.
• Empty JSON array [] if the query is valid but returns no results (e.g., no interactions above the threshold).
• Include species parameter whenever possible to avoid ambiguous identifier resolution.