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RNAcentral MCP Server

RNAcentral MCP Server

Official
by RNAcentral

map_rna_id

Converts RNAcentral URS IDs to external database identifiers and back, optionally filtered by taxon, to support cross-database RNA sequence lookup.

Instructions

Bidirectional ID mapping for RNA sequences. Maps between RNAcentral URS IDs and external database identifiers.

Args: identifier: RNAcentral URS ID (e.g., "URS0000759B6D") or External ID (e.g., "MIMAT0000062") taxon: Optional taxon name or NCBI Taxonomy ID. Prefer scientific names (e.g. "Homo sapiens", "Mus musculus") if available.

Input Schema

NameRequiredDescriptionDefault
taxonNo
identifierYes

Output Schema

NameRequiredDescriptionDefault
resultYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv0.2.1

TDQS

A3.5/5.0
Behavior3/5

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

No annotations are provided, so the description carries the full behavioral burden. It discloses the bidirectional mapping behavior, but says nothing about what happens with ambiguous identifiers (one ID mapping to many external IDs), unmatched IDs, or result cardinality — an output schema exists but the description does not frame the semantics of multiple matches.

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?

Two short front-loaded sentences establish purpose, followed by a compact Args block. The second sentence slightly restates the first but earns its place by naming the specific identifier namespaces.

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

Completeness3/5

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

With only two parameters, an output schema, and no annotations, the core is covered, but an agent still cannot predict behavior for ambiguous or unknown IDs and how the taxon narrows results. The gap is moderate rather than severe.

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?

Schema description coverage is 0%, so the description must compensate, and it does: it states that identifier accepts either a URS ID (with example "URS0000759B6D") or an external ID ("MIMAT0000062"), and that taxon accepts a name or NCBI Taxonomy ID with a preference for scientific names. Only the taxon's effect on filtering results is left unstated.

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

Purpose4/5

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

States a specific verb and resource: bidirectional mapping between RNAcentral URS IDs and external database identifiers. This is clearly distinct from siblings like search_sequence or query_rnacentral, though it never names those alternatives.

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

Usage Guidelines3/5

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

"Bidirectional" implies the tool is used whenever an ID must be converted in either direction, but there is no explicit when-to-use versus when-not-to-use guidance and no mention of an alternative tool for resolution or lookup. Usage is only inferable.

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