compare_alleles

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

With no annotations, the description carries the full burden and does well: it discloses that inference is live (and that results carry `source: live`), that outputs are model predictions for research prioritization, and that no pathogenic/benign call is made. It stops short of stating latency, cost, or whether repeated calls are deterministic, which would be valuable for a live-inference tool.

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?

Front-loads the core action in the first sentence, then separates mechanics from the clinical-use caveat. Every sentence carries information; the only minor cost is the parenthetical about score_variant, which reads more like implementation detail than agent-facing guidance.

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 and no annotations, the description covers the essentials an agent needs: what is ranked, that inference is live, the supported variant classes, and the interpretation limits. Missing only operational details (runtime, determinism, error behavior) that would complete the picture for a live-inference call.

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 description coverage is 100%, so chromosome, position, ref, and alts are already documented, including patterns and the 1-20 alt limit. The description adds only implicit semantics (that indels/MNVs are expressed through ref/alts), so the baseline of 3 is appropriate.

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 ('Rank the alternate alleles of one position by predicted effect'), which makes the operation clear. It does not explicitly differentiate itself from close siblings like compare_variants or compare_variants_same_gene, so an agent must infer the boundary from the names alone.

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?

Gives useful scope guidance by naming the variant classes it handles ('single-nucleotide variants, indels and multi-nucleotide variants') and clarifies that inference is live. However, it never says when to prefer this tool over predict_variant_effect, compare_variants, or batch_score_variants, which is the main routing question for an agent.

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