compare_protective_risk

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 it runs live inference via score_variant with the SDK's recommended scorers, that the result carries `source: live`, that it accepts SNVs, indels and MNVs, and that outputs are AlphaGenome model predictions with no pathogenic/benign call. It does not cover cost, latency, or rate limits of live inference.

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?

Three short paragraphs, front-loaded with what the tool does and its key caveat, with no filler. The live-inference note and the research-use disclaimer each occupy one tight sentence.

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?

For a two-nested-parameter tool with no annotations and no output schema, the description covers behaviour (live inference, source marker), accepted variant types, and the interpretive limits of the output. An agent has enough to call it correctly, though a hint about which sibling to prefer would close the remaining gap.

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 visible schema documents each nested field (chromosome, position, ref, alt, variant_id), and the description adds semantics the schema cannot: the protective_variant/risk_variant labels are supplied by the caller and are not validated or judged by the tool. That meaningfully guides how the two required objects should be assigned.

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: it compares two caller-labelled variants and reports predicted effect sizes per modality, and explicitly clarifies it does not assign protective/risk direction. This is clear, though it never names or contrasts with close siblings such as compare_variants, compare_alleles, or compare_variants_same_gene.

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 gives one implicit when-not: it does not judge which allele is protective or a risk, which tells the agent not to use it for classification. However, with 20+ siblings including several near-identical comparison tools, no alternative is named and no condition for selecting this over them is given.

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