encode-toolkit

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

Annotations already provide readOnlyHint=true, destructiveHint=false, openWorldHint=false, and idempotentHint=true, covering safety and idempotency. The description adds valuable context by specifying the types of identifiers returned (PMIDs, DOIs, etc.) and how they can be used with other MCP tools, enhancing behavioral understanding beyond the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with clear sections (purpose, usage, parameters, returns), front-loaded key information, and no wasted sentences. Each part earns its place by adding value, such as listing identifier types and related tools.

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

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

Given the tool's complexity (read-only, idempotent, with optional filtering), the description is complete: it explains purpose, usage, parameters, and return format. With annotations covering safety and an output schema present (implied by 'Returns: JSON'), no additional details are needed for effective use.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description compensates by explaining both parameters: 'experiment_accession' filters by specific experiment, and 'reference_type' filters by type with enumerated values listed. This adds significant meaning beyond the bare schema, though it doesn't detail optionality or defaults.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose with specific verbs ('Get external references') and resources ('linked to tracked experiments'), distinguishing it from siblings like encode_get_citations (which likely retrieves citations rather than external references) and encode_link_reference (which links rather than gets references).

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

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

The description includes an explicit 'WHEN TO USE' section stating to use it for retrieving external references linked to experiments, and it names specific related tools (encode_link_reference, encode_get_citations) for context, providing clear guidance on when to use this tool versus alternatives.

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