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ncbi_efetch

Fetch full biological records and sequences from NCBI databases using efetch. Supports multiple output formats like XML, FASTA, and GenBank.

Instructions

Fetch full records using efetch. Returns actual data (sequences, records, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
dbNoAlias for `database`.
idsNoIDs to fetch. Accepts either a list of strings (e.g., ["123", "456"]) or a comma-separated string ("123,456").
retmodeNoReturn mode (text, xml, json where applicable)text
rettypeNoReturn type (xml, fasta, gb, etc.)xml
databaseNoNCBI database name (alias: `db`)
Behavior2/5

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

With no annotations, the description must disclose all behavioral traits. It only states that it returns actual data but fails to mention that it is a read-only operation, any authentication requirements, rate limits, or that it requires prior IDs from a search. The description is insufficient for safe invocation.

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 extremely concise with two short sentences. It front-loads the core purpose and adds a brief note about output. Every word earns its place with no redundancy.

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

Completeness2/5

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

Given the lack of output schema and the presence of 5 parameters, the description is too minimal. It does not explain what 'full records' means in different database contexts, how to interpret the return format, or how this tool fits into a workflow with ncbi_esearch and ncbi_esummary. The description leaves significant gaps for an agent to understand fully.

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?

The input schema covers all 5 parameters with descriptions, achieving 100% schema coverage. The tool description adds no additional meaning beyond the schema, so the baseline score of 3 is appropriate. The description does not explain how parameters like 'retmode' and 'rettype' interact with different databases.

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?

The description clearly identifies the action ('fetch'), the resource ('full records'), and the method ('efetch'). It states that it returns actual data, which distinguishes it from search tools that only return IDs. However, it does not explicitly differentiate from sibling tools like ncbi_esummary, which returns summaries rather than full records.

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

Usage Guidelines2/5

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

No guidance is provided on when to use this tool versus alternatives. There is no mention of prerequisites, database selection, or whether it complements earlier search steps. The description is too generic to help an agent decide when to invoke this tool.

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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