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mendelian-randomization-protocol-designer

Generates complete Mendelian randomization study designs from a user-provided exposure and outcome direction. Always use this skill whenever a user wants to design, plan, or build a Mendelian randomization study — even if phrased as "help me write a paper on X", "design an MR study for Y", or "I want to test whether A causally affects B using GWAS". Covers core two-sample MR design, optional bidirectional follow-up, optional multivariable MR, IV selection logic, ancestry alignment, harmonization, IVW as the default primary estimator, weighted median / MR-Egger / MR-PRESSO / leave-one-out sensitivity analyses, Steiger directionality, heterogeneity / pleiotropy checks, and explicit claim-boundary control. Always outputs four workload configs (Lite / Standard / Advanced / Publication+) with a recommended primary plan, stepwise workflow, method rationale, validation ladder, figure plan, minimal executable version, and strictly verified literature guidance with no fabricated references.

Quality

87%

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SKILL.md
Quality
Evals
Security

Quality

Content

71%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 well-engineered instruction-only skill: a hard scope gate, an ordered 8-step process, a fully specified A–L deliverable structure, and exemplary one-level-deep reference delegation with per-section mapping. Its main weakness is token redundancy — the process/deliverable split plus three partially duplicated sections (Sample Triggers, What This Skill Should Not Do, repeated reference mappings) could be consolidated.

Suggestions

Consolidate the 8-step Execution section with the A–L Mandatory Output Structure (e.g., annotate each output section with the step that produces it) — Steps 4–8 currently restate the content of Sections E–L almost point for point.

Delete the Sample Triggers section (it repeats the Input Validation examples verbatim in intent) and fold the non-duplicated lines of 'What This Skill Should Not Do' into the existing Hard Rules, which already cover most of them.

State each reference-module mapping exactly once — in the per-section lines of the Mandatory Output Structure — and drop the duplicated mapping list in Reference Module Integration.

DimensionReasoningScore

Conciseness

The writing itself is disciplined (terse bullets, no explanation of concepts Claude already knows), but the ~300-line body carries real structural redundancy: the 8 Execution Steps restate the A–L Mandatory Output Structure (Step 4 ≈ Section E, Step 5 ≈ Section F, Step 7 ≈ Sections G/H/I, Step 8 ≈ Sections B/L), the Reference Module Integration map is repeated per-section in the output structure, "Sample Triggers" duplicates the Input Validation examples, and "What This Skill Should Not Do" largely restates Hard Rules. Not 4: the duplication goes beyond minor trimmable instances; not 2: there is no padded prose or unnecessary concept explanation.

3 / 5

Actionability

Concrete, executable guidance throughout: exact out-of-scope redirect text to quote, named estimators with a default ("Default primary estimator: IVW"), specific decision rules ("If instrument count is sparse, explicitly downgrade claim strength", "label it as a candidate source type", Dataset Disclaimer placement), a fully specified A–L output structure, and 8 reference files supplying field-level templates (8-field step template, exact disclaimer text, estimator/parameter tables). Not 5: the body directs Claude to "specify" items like "SNP selection threshold logic" without inline values (delegated to references), and there is no worked example of a completed output section; not 3: the guidance is concrete and near-fully executable, not pseudocode-level.

4 / 5

Workflow Clarity

"Execution — 8 Steps (always run in order)" gives a clear sequence, with a hard input-validation gate ("respond with the redirect below and stop"), validation/claim-tier definition in Step 7, and explicit verification checkpoints in Hard Rules ("If references cannot be directly verified, output no formal citation for that slot"; incomplete output if a reference module is skipped). Not 5: the process (Steps 1–8) and the deliverable (Sections A–L) form two parallel structures the reader must reconcile on their own — the interleaving is never spelled out, a minor clarity gap. Not 3: checkpoints are explicit, not merely implied.

4 / 5

Progressive Disclosure

Model progressive disclosure: the body is a process/output overview, and each of the 8 reference files is mapped to the exact output section it serves ("references/workload-configurations.md → use when generating Section B"); all 8 referenced files exist and contain substantive material, and inspection of the bundle shows references are one level deep with no nested references. Not 4: navigation signals, file placement, and split of overview vs. detail leave no organization gaps.

5 / 5

Total

16

/

20

Passed

Description

100%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.

An exemplary description: third-person, information-dense, with an explicit always-use trigger clause that quotes the natural phrasings users would actually produce. It fully answers both what the skill does and when to use it, and its MR-specific framing keeps conflict risk minimal.

DimensionReasoningScore

Specificity

"Generates complete Mendelian randomization study designs", "Covers core two-sample MR design, optional bidirectional follow-up, optional multivariable MR, IV selection logic, ancestry alignment, harmonization, IVW as the default primary estimator, weighted median / MR-Egger / MR-PRESSO / leave-one-out sensitivity analyses, Steiger directionality", and "Always outputs four workload configs (Lite / Standard / Advanced / Publication+)" list multiple specific concrete actions with comprehensive coverage, all in third person. Not 4: coverage of capabilities is comprehensive rather than having minor gaps.

5 / 5

Completeness

Explicitly answers both questions: what ("Generates complete Mendelian randomization study designs... Always outputs four workload configs... with a recommended primary plan, stepwise workflow, method rationale, validation ladder, figure plan") and when ("Always use this skill whenever a user wants to design, plan, or build a Mendelian randomization study — even if phrased as...") with concrete trigger phrases. Not 4: the when-clause is maximally explicit, including edge-case rephrasings, rather than merely present.

5 / 5

Trigger Term Quality

Includes the natural phrases users would actually say, quoted verbatim: "help me write a paper on X", "design an MR study for Y", "I want to test whether A causally affects B using GWAS", plus "design, plan, or build a Mendelian randomization study", "MR", "GWAS", "exposure", "outcome". Not 4: synonym coverage (full term, MR abbreviation, GWAS) plus paraphrased user phrasings is comprehensive rather than missing a few natural terms.

5 / 5

Distinctiveness Conflict Risk

"Mendelian randomization study designs from a user-provided exposure and outcome direction" using "GWAS summary statistics" defines a clear niche with distinct triggers; the trigger requires MR study-design intent, so overlap with generic epidemiology, PRS, or paper-writing skills is minimal. Not 4: the "help me write a paper on X" broadening is explicitly conditioned on MR study design, leaving only minimal conflict risk.

5 / 5

Total

20

/

20

Passed

Validation

93%

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

Validation — 15 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

15

/

16

Passed

Repository

aipoch/medical-research-skills

Path

awesome-med-research-skills/Protocol Design/mendelian-randomization-protocol-designer/SKILL.md

Reviewed

Table of Contents

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