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winternewt
by winternewt

PRS percentile

percentile
Read-only

Estimate the population percentile (0-100) for a polygenic risk score (PRS) using reference distributions or theoretical approximations.

Instructions

Estimate the population percentile (0-100) for a computed PRS value.

Uses the 3-tier fallback: precomputed reference-panel distributions (best), then a theoretical distribution, then an AUROC approximation. superpopulation is a 1000G code (AFR/AMR/EAS/EUR/SAS).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
prs_scoreYes
pgs_idYes
superpopulationNoEUR
panelNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
pgs_idYesPGS Catalog Score ID.
prs_scoreYesThe PRS value that was scored.
percentileNoEstimated percentile (0-100), or null if unavailable.
methodYes'reference_panel', 'theoretical', 'auroc_approx', or 'unavailable'.
ancestryYes1000G superpopulation used (AFR/AMR/EAS/EUR/SAS).
Behavior4/5

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

Annotations provide readOnlyHint and openWorldHint. The description adds the 3-tier fallback algorithm and superpopulation codes, offering behavioral context beyond annotations. No contradictions.

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 three sentences with no fluff. Purpose is front-loaded, followed by key details on fallback and superpopulation.

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?

Output schema covers return values. Description explains the algorithm and superpopulation, but could clarify the reference distribution source. Still sufficient for understanding.

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

Parameters3/5

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

Schema coverage is 0%, so description compensates partially. It explains superpopulation as a 1000G code with examples (AFR/AMR/EAS/EUR/SAS), but does not detail prs_score or pgs_id. Fallback description adds context for how inputs are used.

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 population percentile (0-100) for a PRS value, with a specific verb and resource. It distinguishes from siblings like absolute_risk or compute_prs.

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

Usage Guidelines3/5

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

The description implies usage for percentile estimation but does not explicitly state when to use vs alternatives or when not to use. No exclusions or context for choosing this over other tools.

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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