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genbank_genes

Read-only

Map a GenBank/RefSeq nucleotide accession to NCBI Gene IDs, linking sequence records to gene-level annotations for downstream gene lookups.

Instructions

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

The returned gene_ids are entrezgene IDs usable directly with MyGene-backed gene tools (gene_get, gene_search). Useful bridge from a sequence record to gene-level annotation.

Input Schema

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

TDQS

A4.2/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and openWorldHint=true, covering safety. The description adds valuable behavioral detail: it uses the elink nuccore→gene mechanism and returns entrezgene IDs that are directly compatible with MyGene-backed tools. This goes beyond just saying 'maps an accession.'

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?

Two sentences, with the core mapping stated first and supporting detail (returned ID type, downstream compatibility) second. No wasted words or redundant restatement of the tool name.

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?

For a single-parameter read-only lookup with no output schema, the description covers the essential points: what input is expected, how the mapping happens, what the output is (gene IDs), and how those IDs can be used. Minor gaps like zero/multiple hit behavior and exact response shape are not disclosed, but the description is complete enough for correct invocation.

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 coverage is 100% and the parameter description already includes examples ('NG_017013.2, NC_000023.11') and versioning detail. The description repeats the GenBank/RefSeq context but doesn't add meaning beyond the schema. Baseline 3 is appropriate.

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 and resource: 'Map a GenBank/RefSeq nucleotide accession to its NCBI Gene IDs.' This clearly distinguishes it from sibling tools like genbank_search/genbank_get (which retrieve sequence records) and gene_search (which searches for genes by other criteria).

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 phrase 'Useful bridge from a sequence record to gene-level annotation' gives clear context for when to use this tool. It does not explicitly state alternatives or when not to use it, but the mapping purpose is distinctive enough that an agent can infer the appropriate scenario.

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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