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cross-disease-shared-biomarker-network-research-planner

Generates complete cross-disease shared-biomarker bioinformatics research designs from a user-provided disease pair and validation direction. Always use this skill whenever a user wants to design, plan, or build a multi-dataset study linking two related diseases through shared DEGs, enrichment, PPI hub genes, public validation, regulatory-network analysis, immune infiltration, drug-gene interaction screening, and optional qRT-PCR or cell-line validation. Covers five study patterns (shared-DEG discovery, hub-gene prioritization, regulatory-network interpretation, immune/drug follow-up, bioinformatics-plus-validation) and always outputs four workload configs (Lite / Standard / Advanced / Publication+) with recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path, and a strictly verified reference literature retrieval layer with real references only.

Quality

87%

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SKILL.md
Quality
Evals
Security

Quality

Content

77%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-structured, highly actionable planning skill with excellent workflow sequencing (mandatory dependency validation with a revise-before-output loop) and clean one-level-deep progressive disclosure across eight real reference files. The main weaknesses are redundancy — roughly half of the 23 Hard Rules restate requirements already specified in the steps and output sections — and a few vague comparative descriptors in the config tables.

Suggestions

Deduplicate the Hard Rules: fold rules that restate Sections D/G/I/J/C.5 requirements (rules 15, 17, 18, 20–23) into a short checklist that references those sections, and merge rules 11–13 into Step 4.5's existing rules.

Replace relative adjectives in the config table ('richer public validation', 'stronger reviewer-facing limitations') with concrete, countable module lists so the Advanced and Publication+ rows are as actionable as the Standard row.

Drop the 'Sample Triggers' section or merge it into the Input Validation examples, since the two lists substantially overlap.

DimensionReasoningScore

Conciseness

The body is dense, directive, and free of explanations of concepts Claude already knows (no 'what is a PPI network' padding), but it is noticeably redundant: the 23 Hard Rules restate mandates already detailed in the execution steps and Sections A–J (rules 11–13 duplicate Step 4.5; 15/17 duplicate Section G; 18 duplicates Step 5; 20–23 duplicate Sections C.5, I, D, and J), and 'Sample Triggers' partially overlaps the Input Validation examples. This fits 'Mostly efficient but... could be tightened' rather than 2, because the repetition is instructional emphasis, not concept explanation or fluff.

3 / 5

Actionability

Concrete, executable guidance throughout: exact input format with four worked examples, a verbatim redirect script, pattern-selection and config tables, explicit dependency formulas ('overlap + hub genes + public validation + immune infiltration'), a verbatim Dataset Disclaimer line, defined output sections A–J, and specific retrieval counts — appropriate for an instruction-only skill. Minor gaps keep it below 5: several config descriptors rely on relative adjectives ('richer public validation', 'stronger reviewer-facing limitations', 'clearer claim-boundary control') rather than concrete module lists, and there is no worked example of a finished plan output.

4 / 5

Workflow Clarity

Seven steps are sequenced in fixed order with an explicit pre-output validation checkpoint: Step 5 ('Dependency Consistency Check (mandatory before output)') with the feedback loop 'If any dependency inconsistency is found, revise the plan before outputting', an input fallback in Step 1 ('infer a reasonable default and state assumptions'), a stop-and-redirect for out-of-scope requests, and a fallback plan requirement in Section J. This matches 'Clear sequence with explicit validation steps; feedback loops for error recovery; checklists for complex processes'.

5 / 5

Progressive Disclosure

SKILL.md functions as a well-organized overview with eight clearly signaled, one-level-deep references ('→ Detailed pattern logic: [references/study-patterns.md]', etc.), all of which exist and contain no nested references. Detailed material (8-field step template, config tables, module and method libraries, citation standards) is appropriately split into the reference files, matching 'Clear overview with well-signaled one-level-deep references; content appropriately split; easy navigation'.

5 / 5

Total

17

/

20

Passed

Description

92%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, highly specific description that explicitly answers both what the skill does and when to use it, with comprehensive deliverable coverage. The only notable gap is that frequently mentioned platform names (GEO, TCGA, HPA) are missing from the trigger vocabulary.

Suggestions

Add the platform names users naturally mention (GEO, TCGA, HPA, GEPIA) to the trigger clause, e.g. 'when a user wants a multi-dataset GEO/TCGA study linking two related diseases'.

Include the natural phrasing 'common differentially expressed genes' alongside 'shared DEGs' to catch users who say 'common DEGs' or 'overlapping DEGs'.

Trim the output enumeration slightly ('figure plan, validation strategy, minimal executable version, publication upgrade path' could compress) so trigger terms carry more of the description's weight.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions and deliverables comprehensively: 'Generates complete cross-disease shared-biomarker bioinformatics research designs', covering 'shared DEGs, enrichment, PPI hub genes, public validation, regulatory-network analysis, immune infiltration, drug-gene interaction screening, and optional qRT-PCR or cell-line validation', plus concrete outputs ('four workload configs (Lite / Standard / Advanced / Publication+)', 'step-by-step workflow, figure plan, validation strategy, minimal executable version, publication upgrade path'). It matches the anchor 'Lists multiple specific concrete actions; comprehensive coverage' rather than 4, since output coverage is exhaustive with no evident gaps.

5 / 5

Completeness

Both questions are explicitly answered: the 'what' is 'Generates complete cross-disease shared-biomarker bioinformatics research designs...' with enumerated outputs, and the 'when' is an explicit trigger clause 'Always use this skill whenever a user wants to design, plan, or build a multi-dataset study linking two related diseases...'. This matches the anchor 'Clearly and explicitly answers both what AND when with concrete trigger phrases'; the 'Use when...' guideline cap at 3 does not apply since the clause is present.

5 / 5

Trigger Term Quality

Good keyword coverage with natural domain terms and verb synonyms: 'design, plan, or build', 'shared biomarker', 'hub genes', 'DEGs', 'immune infiltration', 'qRT-PCR', 'validation direction'. However, the platform names users in this domain naturally say — 'GEO', 'TCGA', 'HPA', 'GEPIA' — appear only in the skill body, not the description, and common phrasings like 'common differentially expressed genes' are absent. Fits 'Good keyword coverage; a few natural terms missing' rather than 5's comprehensive synonym/extension coverage.

4 / 5

Distinctiveness Conflict Risk

The description carves a clear niche — cross-disease (two-disease) shared-biomarker bioinformatics study design — with distinct triggers ('disease pair', 'shared DEGs', 'cross-disease'), which minimally conflicts with adjacent skills (e.g., single-disease planners). Matches 'Clear niche with distinct triggers; minimal conflict risk' rather than 4, since the two-disease scoping language sharply separates it from related skill families.

5 / 5

Total

19

/

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/cross-disease-shared-biomarker-network-research-planner/SKILL.md

Reviewed

Table of Contents

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