string-database

STRING Database

Use the STRING MCP tools as the source of truth for protein interaction, network, enrichment, annotation, evidence, species, and homolog questions.

Grounding Rules

• Use STRING tool output for factual claims about interactions, functions, pathways, enrichment, annotations, homologs, and species availability.
• If no species is provided, use human, NCBI taxon ID 9606.
• Do not guess, assemble, or derive STRING links or image URLs. Only show exact links and image URLs returned by tools.
• If a requested claim is not supported by the current tool output in context, retrieve the relevant STRING data with parameters specific to the new claim.
• If identifiers are ambiguous, resolve them with string_resolve_proteins before analysis.
• If the input is an amino acid sequence rather than an identifier, use string_sequence_search.
• If a species name or taxon is uncertain, use string_query_species.
• If a requested STRING capability is unavailable through the tools, use string_help when a matching help topic exists.
• Avoid repeating the same tool call with identical inputs unless the user asks to retry.

Tool Selection

Use string_resolve_proteins to map gene symbols, UniProt IDs, or other protein identifiers to STRING metadata.

Use string_interactions_query_set to retrieve interactions among the submitted proteins. Functional queries use the integrated typed network flavor by default, which can include physical and directed regulatory attributes when STRING reports them. Verify a physical relationship from a positive physical.association_confidence and a directed regulatory relationship from a nonempty regulatory.directions list; do not infer either from a typed network image alone. For binding, complex, co-complex, or physical-interaction questions, set network_type to physical. For directed regulatory relationships, regulators, targets, or signaling direction, set network_type to regulatory.

Use string_all_interaction_partners when the user asks what a protein interacts with, or asks for partners beyond the submitted set. For regulatory partners, network_type=regulatory returns both incoming and outgoing directed relationships.