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STRING Database MCP Server

STRING: Resolves protein identifiers to metadata

string_resolve_proteins

Maps one or more protein identifiers to their corresponding STRING metadata, including: gene symbol, description, sequence, domains, species, and internal STRING ID.

This method is useful for translating raw identifiers into readable, annotated protein entries.

Example input: "TP53%0dSMO"

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
speciesNo
proteinsYesRequired. One or more input protein identifiers (gene symbols, UniProt IDs, etc.), separated by carriage return (%0d). Example: TP53%0dSMO
show_sequenceNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

TDQS

A4/5.0
Behavior3/5

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

With no annotations provided, the description carries the full burden. It accurately implies a read-only mapping operation and lists what data to expect, but it does not disclose error handling, edge cases (e.g., invalid identifiers), or any operational constraints. The output schema helps, but the description could be more explicit about behavior such as separator handling or the effect of the show_sequence flag.

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

Conciseness5/5

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

The description is compact and front-loaded: it states the core function in the first sentence, adds a brief use-case statement, and gives a concrete example. No redundant or vague wording is present.

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 purpose, a typical scenario, and an example input. Since an output schema exists, return values are already structured. However, it omits mention of the optional species and show_sequence parameters and does not discuss potential limitations, so it is not fully complete for a tool with three parameters.

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

Parameters3/5

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

Schema description coverage is low (33% per context), and while the description adds value via the input example ('TP53%0dSMO') and the concept of multiple identifiers, it does not explain the 'species' or 'show_sequence' parameters. The schema itself provides some description for these, but the description does not compensate fully for the low coverage.

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 uses a specific verb ('Maps') and clearly identifies the resource (protein identifiers) and the target (STRING metadata). It enumerates the metadata fields (gene symbol, description, sequence, domains, species, internal STRING ID), which distinguishes it from sibling tools like string_sequence_search or string_functional_annotation.

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 a clear use case ('useful for translating raw identifiers into readable, annotated protein entries'), which gives context on when to apply the tool. However, it does not explicitly mention alternatives or when not to use it, 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.