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jean — Molecular Biology & Genomics

list_databases

Read-only

The authoritative databases available, with what each one covers, whether it is reachable from the browser, and any license or coverage caveat. Call this before searching if unsure which source answers a question.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
_filesNoThe project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
domainNorestrict to one subject area (all areas when unset).
_subjectNoThe record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYeshow many authorities the filter left
sourcesYesevery authority in the requested domain: its id, what it covers, its measured browser transport verdict, and any license or coverage caveat

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior3/5

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

Annotations already declare this is a read-only, non-destructive, closed-world operation, so the safety profile is covered. The description adds useful content context—authoritative sources, browser reachability, license caveats—but does not disclose operational traits like pagination, auth requirements, or rate limits.

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, both earning their place. The first front-loads what the tool returns, and the second front-loads the usage condition, with no redundant restatement of the tool name or annotations.

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?

An output schema exists, so return values do not need explanation here. The description covers purpose and usage well for a catalog-style tool, though it omits any mention of the domain filter, leaving that entirely to the schema.

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 100%, so the schema itself fully documents the parameters, including the domain enum and the nested _subject object. The description adds no additional parameter meaning, which yields the baseline score of 3.

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 states a specific resource—authoritative databases—and enumerates exactly what it returns for each: coverage, browser reachability, and license/coverage caveats. The second sentence explicitly distinguishes it from search/query siblings by positioning it as the pre-search source-selection step.

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?

It gives clear context: 'Call this before searching if unsure which source answers a question.' That names the trigger condition well, but it does not explicitly name alternative tools or state when not to call it, which keeps it just 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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