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biobankjapan-phewas-skill

Fetch compact BioBank Japan PheWAS summaries for single variants by accepting rsID, GRCh38, or GRCh37 input and resolving to the required GRCh37 query. Use when a user wants concise BBJ association results for one variant

68

Quality

83%

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

88%Weight 40%Scale 1-5

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

A tight, highly actionable body with executable examples, complete input/output contracts, and clear behavior rules for a simple single-purpose lookup skill. The main weaknesses are slight duplication of max_results/input guidance and an inaccurate claim that no other runtime files are needed despite the imported variant_resolution module.

Suggestions

Fix the References section to acknowledge `scripts/variant_resolution.py` (imported by the main script) instead of claiming the import package is limited to SKILL.md and `biobankjapan_phewas.py`.

Consolidate the duplicated `max_results` guidance (Operating rules vs Execution behavior) into a single place to remove redundancy.

State the accepted input keys once — either in the Input section with a pointer from Operating rules, or vice versa — to trim the repeated GRCh37/GRCh38/rsID/variant enumeration.

DimensionReasoningScore

Conciseness

The body is lean and assumes Claude's competence — no concept over-explanation, no padding — but `max_results` guidance is duplicated ('start with `max_results=10` and only increase it...' in Operating rules vs 'Increase `max_results` gradually...' in Execution behavior) and the accepted input keys are stated in both Operating rules and Input. Minor trimmable redundancy fits anchor 4 rather than 5.

4 / 5

Actionability

Fully executable guidance: a copy-paste-ready bash invocation ('echo ... | python scripts/biobankjapan_phewas.py'), four concrete JSON input patterns covering every accepted key, exact output field names, and an explicit error contract ('Failure returns `ok=false` with `error.code` and `error.message`'). Matches anchor 5.

5 / 5

Workflow Clarity

A simple, single-purpose skill (~41 lines, read-only lookup) where the single action — pipe exactly one variant JSON object to the script — is unambiguous, with a built-in retry/feedback loop (surface `truncated`, increase `max_results` only when the first slice is insufficient) and a failure contract. Per the simple-skill scoring note, this matches anchor 5; no destructive/batch validation cap applies.

5 / 5

Progressive Disclosure

Sections are well organized for a sub-50-line skill and the referenced path `scripts/biobankjapan_phewas.py` exists. However the bundle also contains `scripts/variant_resolution.py`, which the main script imports (`from variant_resolution import ...`), yet the body states 'keep the import package limited to this file and `scripts/biobankjapan_phewas.py`' — an unacknowledged runtime dependency. Minor organization gap fits anchor 4 rather than 5.

4 / 5

Total

18

/

20

Passed

Description

78%Weight 40%Scale 1-5

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

A strong, third-person description with concrete capabilities, an explicit 'Use when...' clause, and a highly distinctive niche. It could be slightly more comprehensive in enumerating summary contents and broaden its trigger phrases beyond the single BBJ-focused 'when' clause.

Suggestions

Broaden the 'when' trigger with more concrete phrasing a user would naturally say, e.g. 'Use when the user asks for BioBank Japan or BBJ PheWAS results, variant-phenotype associations, or BBJ lookups for an rsID or genomic coordinate.'

Enumerate one or two concrete summary contents (e.g. phenotype association statistics, odds ratios) so the 'what' is comprehensive rather than just naming the fetch/resolution mechanics.

Spell out or add common synonyms such as 'phenotype-wide association study' alongside 'PheWAS' to improve trigger term coverage.

DimensionReasoningScore

Specificity

Names the domain ('BioBank Japan PheWAS') and several concrete actions ('Fetch compact... summaries', 'accepting rsID, GRCh38, or GRCh37 input', 'resolving to the required GRCh37 query'), but does not enumerate what the summaries contain, leaving minor gaps in coverage. Fits anchor 4 rather than 5 because the action list is not fully comprehensive, and above anchor 3 because more than 1-2 specific actions are stated.

4 / 5

Completeness

Explicitly answers both 'what' (fetch compact BBJ PheWAS summaries by resolving rsID/GRCh38/GRCh37 input to the GRCh37 query) and 'when' ('Use when a user wants concise BBJ association results for one variant'). The single 'when' clause is explicit but somewhat narrow and uses the 'BBJ' abbreviation rather than multiple concrete trigger phrases, so it fits anchor 4 rather than 5.

4 / 5

Trigger Term Quality

Includes natural domain terms users would say — 'BioBank Japan', 'PheWAS', 'variant', 'rsID', 'BBJ', 'association results' — but misses common synonyms and variations such as 'phenotype-wide association' or 'phenotype association'. Good coverage with a few natural terms missing, matching anchor 4, not 5.

4 / 5

Distinctiveness Conflict Risk

Occupies a clear niche (BioBank Japan PheWAS lookups for single variants) with distinct triggers ('rsID', 'GRCh37/GRCh38', 'PheWAS'); virtually no overlap risk with other skills. Matches anchor 5.

5 / 5

Total

17

/

20

Passed

Validation

100%

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
openai/plugins
Reviewed

Table of Contents

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