ebi-pdbe-update_workspace

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

The annotations declare readOnlyHint=true, but the description explicitly states the tool supports 'adding/removing scenes and structures, component or annotation layers, and changing layer visibility,' which are mutating operations. This is a direct contradiction. Additionally, destructiveHint=false conflicts with removing scenes/structures.

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 front-loaded with the core purpose and then provides operational details in a logical order. It is somewhat long but each sentence adds relevant context about host routing, ID matching, and validation.

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 (huge schema, no output schema, mutation behavior), the description covers many important operational traits: no global server state, host routing to existing Apps, validation when no operations are provided, and that the App does not calculate scientific measurements. It still omits the compact_response behavior.

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?

The description explains expected_revision as concurrency control and calls operations 'atomic,' and it notes the workspace should be the latest complete version. However, it does not mention the compact_response parameter at all, and with only 25% schema description coverage, the description does not fully compensate for the gap.

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 states a specific verb and resource: 'Compose or restore a molecular workspace in the shared viewer.' It is clear what the tool does, though it does not explicitly differentiate itself from the many sibling PDB data tools.

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?

It gives clear context for when to use it: 'Supply the latest complete workspace from tool results or App context, expected_revision, and atomic operations' and 'No operations validates and restores a saved workspace.' It also explains host routing behavior. However, it lacks an explicit when-not-to-use statement or named alternative.

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