compare_genomes

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

No annotations are provided, so the description carries the full behavioral burden. It discloses the output contents (lineage, LCA, differing ranks, metrics), which is genuinely useful, but says nothing about permissions, error cases (e.g., mismatched or missing genomes), or result size/limits. The operation is obviously a non-mutating read, so the safety gap is minor, but the completeness gap is real.

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?

Two tight sentences with zero filler. The purpose is front-loaded and the return summary follows immediately, each sentence earning its place.

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?

With no output schema, the description usefully enumerates the return fields, and a two-parameter read tool needs little else. It stops short of covering failure modes or edge cases (missing/invalid genome IDs, cross-domain comparison behavior), which keeps it from a 5.

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?

Schema coverage is 100%: both gid1 and gid2 are documented with example accession formats directly in the schema. The description adds only that the arguments are genomes being compared; it contributes no format, ordering, or constraint detail beyond the schema, so the baseline 3 applies.

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?

States a specific verb and resource ('Compare two genomes taxonomically') and enumerates exactly what is computed (shared lineage, LCA, differing ranks, metric diffs). This cleanly distinguishes it from single-genome siblings like get_genome, get_taxonomy, and get_tree_path.

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?

Usage is strongly implied by the comparative framing — an agent can infer this is the tool for pairwise genome comparison versus the single-entity siblings — but there is no explicit when-to-use, when-not, or named alternative. Adequate but with a clear gap.

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