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STRING Database MCP Server

STRING: Get interactive network link (web UI)

string_network_link

Retrieves a stable URL to an interactive STRING network for one or more proteins.

  • For a single protein: includes the protein and its top 10 most likely interactors.

  • For multiple proteins: includes all known interactions within the query set.

  • If the user asks for "physical interactions", "complexes", or "binding", set network_type to "physical".

The input may include one numeric value per protein, such as fold change, effect size, or score. These values are visualized as colored halos around the nodes, allowing overlay of protein-level measurements on the network.

Example: PTEN 2.1 SMO -1.3

If numeric values are provided:

  • positive values are shown in blue

  • negative values are shown in red

  • larger absolute values produce stronger halo intensity

If the user provides numeric values together with the proteins, preserve them in the query.

If few or no interactions are shown, consider lowering required_score.

For large queries (>100 proteins):

  • use network_flavor="confidence"

  • increase required_score (e.g. 700)

Always display the link as a markdown hyperlink (hide the raw URL).

Input parameters should match those used in related STRING tools unless otherwise specified.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
speciesNo
proteinsYesRequired. One or more protein IDs, optionally followed by one numeric value per protein. Example: PTEN 0.234 SMO -3.445 Use newline (%0d) between entries. Tabs and spaces are accepted as separators.
network_typeNo
extend_networkNo
network_flavorNo
required_scoreNo
hide_disconnected_nodesNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

TDQS

A4.5/5.0
Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description fully discloses key behaviors: the network content for single vs multiple proteins, how numeric values are visualized as halos with color coding, the markdown link instruction, and the suggestion to lower required_score when few interactions appear. This provides a clear behavioral model for the agent.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with bullet points and an example, making it easy to parse. It is longer than strictly necessary but every section serves a purpose: usage scenarios, numeric value semantics, and best practices. The only minor redundancy is repeating the numeric value color logic in two places.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The description covers the main usage contexts, edge cases (large queries, few interactions), and output presentation (markdown hyperlink). With an output schema present, return values are already specified. The only missing piece is explicit handling of invalid protein IDs or error cases, but these are likely covered by the output schema or standard error handling.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The description adds meaningful context beyond the schema, especially for the proteins parameter with a concrete example and separator notes, and for network_type with the 'physical interactions' trigger. However, species, extend_network, and hide_disconnected_nodes are only covered by the schema's own descriptions, which are already self-explanatory. The description's note on matching parameters to related STRING tools is a useful cross-tool convention.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool 'Retrieves a stable URL to an interactive STRING network for one or more proteins.' The verb 'retrieves' and the specific resource 'interactive STRING network URL' make the purpose explicit. It also distinguishes from siblings like string_visual_network by specifying 'web UI' link generation.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides detailed when-to-use guidance for different query types (single protein vs multiple proteins), when to set network_type, required_score adjustments, and large query handling. However, it does not explicitly name alternative sibling tools or state when not to use this tool, so it falls short of a 5.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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TDQS

A3.6/5.0
Disambiguation2/5

Several tool pairs have overlapping purposes: string_network_link and string_visual_network both return network URLs with nearly identical behavior, and string_all_interaction_partners vs string_interactions_query_set both query interactions, differing subtly in scope. The enrichment/annotation tools also share boundaries, making it difficult for agents to disambiguate without reading detailed descriptions.

Naming Consistency3/5

All tools share the 'string_' prefix, but the pattern is inconsistent: some are verb-first (create_file, resolve_proteins), some are noun-first (interactions_query_set, network_link), and some are bare nouns (enrichment, homology). This mixed convention reduces predictability.

Tool Count4/5

At 17 tools, the server is slightly above the ideal range, but it covers a broad domain: interactions, networks, enrichment, annotation, homology, species resolution, and sequence search. The count is justified by the complexity of the STRING database.

Completeness4/5

The tool set covers core STRING workflows: querying interactions, constructing networks, computing enrichment, retrieving annotations, identifying homologs, mapping IDs, and exporting data. Minor gaps exist (e.g., direct edge-list tables and intricate interaction score details), but the overall surface is robust.