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genbank_genes

Read-only

Map a GenBank/RefSeq nucleotide accession to its NCBI Gene (Entrez) IDs, linking a sequence record to gene-level annotation.

Instructions

Map a GenBank/RefSeq nucleotide accession to its NCBI Gene IDs (elink nuccore→gene).

The returned gene_ids are NCBI Gene (entrezgene) IDs. gene_get takes an HGNC gene symbol, NOT a numeric entrez id, so an id must first be resolved to its symbol — gene_search result rows carry both symbol and entrez_id, so the id→symbol bridge exists via gene_search. Useful bridge from a sequence record to gene-level annotation.

Input Schema

NameRequiredDescriptionDefault
accessionYesGenBank/RefSeq accession, versioned or bare — e.g. NG_017013.2, NC_000023.11

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changedv1.6.0-alpha.10
    • removedInput schema / additionalProperties
      Removed value: -false
  2. Changed2 schema fields changedv1.6.0-alpha.7
    • addedInput schema / properties / accession / minLength
      Added value: +1
    • addedInput schema / properties / accession / pattern
      Added value: +"^[A-Z]{1,6}_?\\d+(?:\\.\\d+)?$"
  3. Addedv0.7.1

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, so the safety and external-network profile is covered. The description still adds substantive value beyond that: it identifies the return values as NCBI entrezgene IDs (not symbols) and warns that they cannot be fed directly into gene_get, which prevents a real downstream misuse. It does not cover failure/empty-result behavior or rate limits, so not a 5.

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 core mapping statement is front-loaded and the crucial caveat (numeric id ≠ symbol) follows immediately. The id→symbol bridge sentence is somewhat repetitive of the preceding sentence and could be tightened, but every element carries useful routing information.

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?

There is no output schema, so the description correctly takes on the job of saying what comes back (a list of entrezgene IDs) and how to use it. What an agent still can't tell is cardinality or the behavior when an accession has no linked gene, which is a modest but real gap for a 1-param lookup.

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?

Only one parameter and schema description coverage is 100%, with the pattern and versioned/bare examples (NG_017013.2, NC_000023.11) already documented in the schema. The description adds no further parameter guidance, so the baseline 3 applies.

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?

Opens with a specific verb+resource+mechanism: 'Map a GenBank/RefSeq nucleotide accession to its NCBI Gene IDs (elink nuccore→gene).' That distinguishes it from genbank_search/genbank_get (which retrieve records) and from gene_get/gene_search (which operate on symbols or gene queries), so an agent can route without opening schemas.

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

Usage Guidelines5/5

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

Explicitly frames the use case as a bridge from a sequence record to gene-level annotation, and names the downstream chain: gene_get takes a symbol not an entrez id, and gene_search rows carry both symbol and entrez_id, so the id→symbol bridge exists via gene_search. This is concrete when-to-use plus named alternatives rather than inference.

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