STRING through GeneFoundry

Explore STRING protein association networks and their supporting evidence channels.

Research area
Genes & proteins
Namespace
stringdb
Listed tools
10
Upstream source
STRING

Research tasks

  • Resolve protein identifiers with organism context
  • Inspect interaction partners and network evidence

Start with tool discovery

The catalog lists stringdb_get_interaction_partners as a representative tool. After connecting your client, inspect the tools and input requirements returned by the service before submitting a query.

Identifiers to prepare

  • STRING protein identifier
  • Gene symbol or synonym
  • UniProt accession with organism context

Source version not supplied by this website catalog.

All available tools (10)

The router surfaces these tools namespaced under stringdb_*:

resolve_protein_identifiersMaps common protein names, gene symbols, UniProt IDs, and other identifiers

Router invocation: stringdb_resolve_protein_identifiers()

Maps common protein names, gene symbols, UniProt IDs, and other identifiers to STRING database identifiers. The STRING database uses an intelligent mapping system to find the best matching identifier for each input. **Supported identifier types:** - Gene symbols (e.g., p53, BRCA1, CDK2) - UniProt IDs (e.g., P04637, P38398) - Ensembl IDs (e.g., ENSP00000269305) - RefSeq IDs (e.g., NP_000537) - Common protein names **Species support:** - Humans (9606), Mouse (10090), E. coli (511145), and 2000+ other species - If no species is specified, STRING attempts cross-species mapping

Input parameters

  • echo_query(boolean) — Include input identifiers in the output
  • identifiers(array) [required] — List of protein identifiers to resolve
  • species(any) — NCBI taxon identifier (e.g., 9606 for human)
search_protein_interactionsGet protein-protein interaction network.

Router invocation: stringdb_search_protein_interactions()

Get protein-protein interaction network. Retrieves the protein-protein interaction network for the given proteins. If only one protein is provided and add_nodes is 0, additional nodes will be automatically added to show the interaction neighborhood. Args: request: Network interaction request service: StringDB service instance logger: Logger instance Returns: List of protein-protein interactions Raises: HTTPException: If the request fails

Input parameters

  • add_nodes(integer) — Number of additional nodes to add to the network
  • identifiers(array) [required] — List of protein identifiers
  • network_type(string) — Network type: functional or physical
  • required_score(number) — Minimum confidence score (0.0-1.0)
  • show_query_node_labels(boolean) — Use submitted names as node labels
  • species(any) — NCBI taxon identifier
get_interaction_partnersGet interaction partners for proteins.

Router invocation: stringdb_get_interaction_partners()

Get interaction partners for proteins. Retrieves all interaction partners for the given proteins, not just interactions between the input proteins. Useful for finding all proteins that interact with your proteins of interest. Args: request: Interaction partners request client: StringDB HTTP client logger: Logger instance Returns: List of interaction partners Raises: HTTPException: If the request fails

Input parameters

  • identifiers(array) [required] — List of protein identifiers
  • limit(integer) — Maximum number of interaction partners per protein
  • network_type(string) — Network type: functional or physical
  • required_score(number) — Minimum confidence score (0.0-1.0)
  • species(any) — NCBI taxon identifier
get_network_linkGet shareable link to STRING webpage for the network.

Router invocation: stringdb_get_network_link()

Get shareable link to STRING webpage for the network. This endpoint generates a shareable URL that leads to the STRING database website showing the protein interaction network for the specified proteins. The link includes all visualization parameters and can be shared with others. The generated link allows users to: - View the network interactively on the STRING website - Access additional features like network customization - Share the exact network view with collaborators

Input parameters

  • identifiers(array) [required] — List of protein identifiers
  • network_flavor(string) — Network visualization style
  • network_type(string) — Network type: functional or physical
  • output_format(string) — STRING serialization of the shareable link. All four formats convey the same URL: 'json' returns it structured in 'url'; 'tsv', 'tsv-no-header' and 'xml' return STRING's text in 'formatted' with the URL also extracted into 'url'. (STRING's psi-mi/image/svg link formats are not offered — they carry no link payload.)
  • required_score(number) — Minimum confidence score (0.0-1.0)
  • species(any) — NCBI taxon identifier
compute_functional_enrichmentPerform functional enrichment analysis.

Router invocation: stringdb_compute_functional_enrichment()

Perform functional enrichment analysis.

Input parameters

  • background_string_identifiers(any) — Optional custom background proteome, given as STRING identifiers (e.g. '9606.ENSP00000269305'). MUST be a superset of the query identifiers; STRING rejects a background that omits any query protein.
  • category(any) — Optional term-category filter. When set, only enrichment terms in this STRING category are returned (e.g. 'KEGG' for pathways, 'Process' for GO biological process, 'DISEASES' for disease associations). Omit to return terms across all categories.
  • identifiers(array) [required] — List of protein identifiers
  • limit(integer) — Maximum number of enrichment terms to return, taken as the most significant (lowest FDR) first. 'total_count' still reports the full number of matching terms, so a smaller limit never hides how many exist.
  • species(any) — NCBI taxon identifier
compute_ppi_enrichmentPerform protein-protein interaction enrichment analysis.

Router invocation: stringdb_compute_ppi_enrichment()

Perform protein-protein interaction enrichment analysis.

Input parameters

  • background_string_identifiers(any) — Optional custom background proteome, given as STRING identifiers (e.g. '9606.ENSP00000269305'). MUST be a superset of the query identifiers; STRING rejects a background that omits any query protein.
  • identifiers(array) [required] — List of protein identifiers
  • required_score(number) — Minimum confidence score (0.0-1.0)
  • species(any) — NCBI taxon identifier
get_functional_annotationsGet functional annotations for proteins.

Router invocation: stringdb_get_functional_annotations()

Get functional annotations for proteins.

Input parameters

  • allow_pubmed(boolean) — Include PubMed annotations
  • identifiers(array) [required] — List of protein identifiers
  • only_pubmed(boolean) — Return only PubMed annotations
  • species(any) — NCBI taxon identifier
get_protein_homology_scoresRetrieve homology scores for proteins showing sequence similarity to proteins from other species. This endpoint helps identify evolutionarily related proteins across different organisms. Returns structured JSON data.

Router invocation: stringdb_get_protein_homology_scores()

Retrieve homology scores for proteins showing sequence similarity to proteins from other species. This endpoint helps identify evolutionarily related proteins across different organisms. Returns structured JSON data.

Input parameters

  • identifiers(array) [required] — List of protein identifiers
  • species(any) — NCBI taxon identifier
get_protein_homology_best_hitsGet the best homology hits between proteins from different species. This endpoint is useful for finding the closest evolutionary relatives of proteins across species boundaries. Returns structured JSON data.

Router invocation: stringdb_get_protein_homology_best_hits()

Get the best homology hits between proteins from different species. This endpoint is useful for finding the closest evolutionary relatives of proteins across species boundaries. Returns structured JSON data.

Input parameters

  • identifiers(array) [required] — List of protein identifiers
  • species(any) — Source species NCBI taxon identifier
  • species_b(any) — Target species NCBI taxon identifiers
get_network_imageGenerate a protein network visualization image as base64 (MCP surface).

Router invocation: stringdb_get_network_image()

Generate a protein network visualization image as base64 (MCP surface).

Input parameters

  • add_color_nodes(integer) — Number of colored nodes to add
  • add_white_nodes(integer) — Number of white nodes to add
  • hide_disconnected_nodes(boolean) — Hide proteins not connected to any other protein
  • hide_node_labels(boolean) — Hide protein names from the image
  • identifiers(array) [required] — List of protein identifiers
  • image_format(string) — Image format: PNG, high-res PNG, or SVG
  • network_flavor(string) — Network visualization style
  • network_type(string) — Network type: functional or physical
  • required_score(number) — Minimum confidence score (0.0-1.0)
  • show_query_node_labels(boolean) — Use submitted names as protein labels
  • species(any) — NCBI taxon identifier

Database & release provenance

Data mode
none
Attestation
unhosted
Release version
v4.1.6
Container image:ghcr.io/berntpopp/stringdb-link@sha256:86cff15b3c3e3364f1920a1fa9ce7e7c91d934072135cc03cddf6b860ec2d67d

Inspect canonical provenance artifact: genefoundry.org/provenance (JSON)

Review the response

Keep the source record link and submitted identifiers with your notes. Record the dataset version and retrieval date when available. This page does not contain a captured STRING response.

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