onekgpd

Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.

Quality

92%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

85%

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is highly actionable with executable commands, clear sequenced workflows, and clean one-level-deep references to verified bundle files. The main weakness is redundancy between Quick Start and the Typical Workflows section plus repeated coordinate-provenance emphasis.

Suggestions

Collapse the 'Quick Start' and 'Which individuals, then which variants they carry' workflow into a single worked example to remove the near-duplicate command block.

Consolidate the coordinate-provenance warning so it is stated once in its dedicated section and merely cross-referenced elsewhere, rather than re-explained in Scope, the CAUTION block, and Common Mistakes.

Dimension	Reasoning	Score
Conciseness	Mostly efficient and free of basic-concept padding, but the 'Quick Start' and 'Which individuals, then which variants they carry' workflow are near-duplicates, and the coordinate-provenance warning is repeated across Scope, the Coordinate Provenance section, a CAUTION block, and Common Mistakes.	2 / 3
Actionability	Provides fully executable `uv run scripts/onekgpd_api.py ...` invocations with concrete flags and a real example coordinate (BRCA1 chr17:43044292-43170245), copy-paste ready and complete.	3 / 3
Workflow Clarity	Sequences multi-step queries explicitly (Quick Start steps 1-4, Typical Workflows) with a count-before-select checkpoint, a truncated→raise-limit/page-size feedback loop, and a Common Mistakes checklist with fixes.	3 / 3
Progressive Disclosure	SKILL.md is a well-organized overview that signals one-level-deep references to real bundle files (references/onekgpd_commands.md for full argument tables/schemas, references/annotation_vocabularies.md for controlled vocabularies), with detailed material appropriately split out.	3 / 3
	Total	11 / 12 Passed

Description

100%

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is specific, well-triggered, and complete, naming concrete individual-level query actions and an explicit 'Use when' clause tied to the 1000 Genomes Project. It is clearly niche-scoped and unlikely to fire for the wrong skill.

Dimension	Reasoning	Score
Specificity	Lists multiple concrete actions ('which individuals carry variants matching specific criteria in a gene or region', 'which individuals are homozygous-reference at a position', 'relatedness between two specified individuals'), matching the level-3 anchor.	3 / 3
Completeness	Explicitly states both what it does ('Query the 1000 Genomes Project dataset... at the level of individual participants') and when to use it via an explicit 'Use when a question is about individuals or variants in the 1000 Genomes Project cohort' clause.	3 / 3
Trigger Term Quality	Covers natural terms a genomics user would say — '1000 Genomes Project', 'individuals', 'variants', 'homozygous-reference', 'relatedness', 'allele frequencies', 'gnomAD', 'AlphaMissense' — with good variation rather than jargon.	3 / 3
Distinctiveness Conflict Risk	Scoped to a single named dataset and individual-level queries with distinct triggers ('1000 Genomes Project cohort', 'homozygous-reference', 'relatedness'), making conflict with other skills unlikely.	3 / 3
	Total	12 / 12 Passed

Validation

100%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository: K-Dense-AI/scientific-agent-skills
Path: skills/onekgpd/SKILL.md
Commit: 757b63b

Reviewed: about 12 hours ago

Table of Contents

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