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Annotations

annotations
Read-onlyIdempotent

Sequence-level annotations (e.g. MUTAGEN, LOW_CONFIDENCE_REGIONS).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
typeNoAnnotation type filter (optional).
qualifierYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
annotationsNoList of sequence annotations
uniprotAccessionNoUniProt accession code

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

C2.9/5.0
Behavior3/5

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

The annotations already declare the tool as read-only, open-world, idempotent, and non-destructive. The description adds context about the nature of the data (sequence-level annotations) but does not disclose any additional behavioral traits, such as potential filters or default behavior, so it stays at a baseline level.

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?

The description is extremely brief and contains no wasted words. However, it is a sentence fragment rather than a complete sentence, which slightly reduces its structural quality, but still earns high marks for conciseness.

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?

For a simple 2-parameter tool with an output schema, the description is adequate but has clear gaps: it lacks an explicit purpose verb and usage guidance. The examples partially compensate, but the tool would benefit from stating that it retrieves annotations for a given qualifier.

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 schema covers 50% of parameters (type has a description, qualifier does not). The description adds meaning by giving examples of annotation types (MUTAGEN, LOW_CONFIDENCE_REGIONS) and the examples show qualifier usage with a UniProt-like ID, but it does not explicitly explain the role of the qualifier parameter.

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

Purpose3/5

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

The description identifies the resource as 'sequence-level annotations' with examples, but lacks an explicit verb like 'get' or 'list'. The name 'annotations' implies retrieval, and the examples make it clearer, but the purpose is not as directly stated as it could be.

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?

The description offers no guidance on when to use this tool or how it compares to alternatives. The examples imply usage with a qualifier, but there is no explicit context about when to choose this over sibling tools like 'uniprot' or 'entity_profile'.

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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