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Absolute risk

absolute_risk
Read-onlyIdempotent

Estimate absolute disease risk from a polygenic risk score z-score by combining it with population prevalence and effect-size data.

Instructions

Estimate absolute disease risk from a PRS z-score and population prevalence.

Joins the score's trait to prevalence + effect-size data. z_score is the PRS in standard deviations from the population mean. Raises if the required prevalence / effect-size data is unavailable for this score.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
sexNo
pgs_idYes
z_scoreYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
methodYesEstimation method: 'or_per_sd' or 'auc_bivariate'
caveatsNoWarnings about estimation quality (e.g. 'cohort prevalence used, not population')
confidenceYesData quality confidence: 'high', 'moderate', or 'low'
risk_ratioYesRisk ratio vs population average (e.g. 1.64x)
absolute_riskYesEstimated absolute risk (e.g. 0.18 = 18% lifetime risk)
prevalence_typeYesType of prevalence: 'lifetime', 'point', or 'cohort'
prevalence_sourceYesWhere the prevalence data came from
effect_size_citationNoPaper citation for the OR/AUROC used (e.g. 'Smith et al. 2023, JAMA (PMID: 12345678)')
population_prevalenceYesPopulation baseline prevalence (e.g. 0.11 = 11%)
Behavior4/5

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

Beyond annotations (readOnlyHint, idempotentHint, etc.), the description discloses that the tool raises an error if prevalence/effect-size data is missing. This adds meaningful behavioral context without contradicting the annotations.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is remarkably concise with three front-loaded sentences. Key information (purpose, join behavior, parameter meaning, error condition) is included without redundancy or extraneous detail.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

The tool has an output schema, so return values are covered. The description explains the main functionality, parameter z_score, and the error case. It could clarify that prevalence and effect-size data come from internal sources, but it's mostly complete for a 3-parameter tool.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 0%, so the description must explain all parameters. Only z_score is explicitly described (as PRS in standard deviations). pgs_id is implied but not detailed, and sex is not mentioned at all. This is insufficient compensation for the lack of schema descriptions.

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

Purpose5/5

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

The description clearly states the tool estimates absolute disease risk from a PRS z-score and population prevalence, with a specific verb 'estimate' and resource 'absolute disease risk'. It adds context about joining data and error conditions, making the purpose precise and unambiguous.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implicitly guides usage by specifying requirements (z-score and available prevalence data) and the error case when data is unavailable. While no sibling tools exist to compare against, this provides clear context for when the tool is applicable.

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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