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tpmi-phewas-skill

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

72

Quality

90%

Does it follow best practices?

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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 skill body: exact I/O contracts, concrete input patterns, and a runnable example with clear error and truncation handling appropriate to a simple read-only lookup. Its one real defect is that the References section misdescribes the bundle by omitting the variant_resolution.py dependency, plus slight rule duplication across sections.

Suggestions

Update the References section to acknowledge scripts/variant_resolution.py as part of the bundle (tpmi_phewas.py imports resolve_query_variant from it), so the stated file inventory matches reality.

Merge the duplicated max_results and save_raw guidance from 'Operating rules' and 'Execution behavior' into a single location to remove redundancy and tighten token usage.

DimensionReasoningScore

Conciseness

The body is lean and assumes competence — no concept explanations, just rules, I/O contracts, and one example. Minor trimming is possible: max_results and save_raw guidance each appear redundantly across "Operating rules" and "Execution behavior" (e.g., "start with max_results=10 and only increase it" vs "Increase max_results gradually"), keeping it just below the level 5 'every token earns its place' anchor.

4 / 5

Actionability

Fully executable guidance: exact script path, stdin JSON contract, four concrete input patterns with real values ("{\"grch38\":\"6:160540105-T-C\",\"max_results\":10}"), enumerated output field names, failure shape (ok=false with error.code/message), and a copy-paste bash example covering the common case. Matches the level 5 anchor.

5 / 5

Workflow Clarity

This is a simple single-task skill (~40 lines) whose single action is unambiguous: resolve the one accepted input to a canonical GRCh38 query, run scripts/tpmi_phewas.py, report the canonical variant, count, and truncation status. Error recovery and truncation feedback paths (ok=false/error, truncated -> raise max_results; save_raw for full payloads) are explicit, and the operation is read-only so the destructive/batch validation cap does not apply. Fits the simple-skill level 5 exception.

5 / 5

Progressive Disclosure

The body is under 50 lines, well sectioned, and correctly references scripts/tpmi_phewas.py which exists in the bundle. However, the References section's claim to "keep the import package limited to this file and scripts/tpmi_phewas.py" is inaccurate against the actual bundle: scripts/variant_resolution.py is present and is imported by tpmi_phewas.py yet is never mentioned, a minor navigation/organization gap that keeps it below level 5.

4 / 5

Total

18

/

20

Passed

Description

87%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 description: it states concrete capabilities (three accepted input formats, GRCh38 resolution) in third person and includes an explicit, specific 'Use when' clause. Trigger coverage is good and the niche is highly distinct, with only minor room to broaden natural-language synonyms.

DimensionReasoningScore

Specificity

Phrases like "accepting rsID, GRCh37, or GRCh38 input" and "resolving to the required GRCh38 query" name several concrete actions (fetch summaries, accept three input formats, resolve coordinates), with only minor gaps such as not mentioning the association output content. It is above level 3 (which expects only 1-2 concrete actions) but below level 5's comprehensive multi-action coverage.

4 / 5

Completeness

Explicitly answers what ("Fetch compact TPMI PheWAS summaries for single variants by accepting rsID, GRCh37, or GRCh38 input and resolving to the required GRCh38 query") and when ("Use when a user wants concise TPMI association results for one variant") with a concrete trigger phrase. This matches the level 5 anchor directly; level 4 would require a weaker or less explicit 'when' clause.

5 / 5

Trigger Term Quality

Includes natural domain terms users would say: "TPMI", "PheWAS", "rsID", "GRCh37", "GRCh38", "variant", "association results". A few natural variations are missing (e.g., "phenome-wide association", "SNP", "look up a variant"), so it falls just short of level 5's comprehensive synonym coverage but is clearly above level 3.

4 / 5

Distinctiveness Conflict Risk

TPMI PheWAS is a clear niche with distinct trigger terms (TPMI, PheWAS, rsID/GRCh38 variant lookup); there is minimal risk of this description firing for an unrelated skill. Matches the level 5 anchor for a clear niche with distinct triggers.

5 / 5

Total

18

/

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

Path

plugins/life-science-research/skills/tpmi-phewas-skill/SKILL.md

Reviewed

Table of Contents

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