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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.

Input 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

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

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds useful context that entries carry license and coverage caveats and browser reachability, but says nothing about ordering, pagination, or how the catalog is scoped.

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?

A single front-loaded sentence with no filler, and the most decision-relevant attribute (what each database covers) appears early. It is a verbless fragment, which slightly weakens immediate actionability.

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?

An output schema exists, so return-value detail is not required, and the description sensibly summarises what the output contains. However, for a tool whose schema carries nested _subject/_files record parameters that seem unrelated to listing databases, the description does nothing to resolve that ambiguity, leaving a real gap.

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% and each of the three parameters (domain enum, _files, _subject) is documented in the schema. The description adds no filtering or parameter-level meaning beyond that, so the baseline of 3 applies — notably it does not explain what the _subject/_files record parameters mean for a catalog-listing call.

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 identifies the resource (the catalog of authoritative databases) and enumerates the attributes surfaced per entry — coverage, browser reachability, license/caveat — so an agent can tell this is a catalog-listing tool. It never states an explicit verb ('list') and does not contrast itself with lookup_*/query_database/find_accessions siblings, which keeps it short of a 5.

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?

There is no when-to-use or when-not-to-use guidance, no mention of prerequisites, and no named alternative. The only implied usage is 'inspect what is available', which an agent must infer from the noun phrase alone.

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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