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tooluniverse-gene-regulatory-networks

Gene regulatory network analysis — TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence (knockout/overexpression). Use for 'which TF regulates gene X', 'which genes does TF Y target', regulatory pathway reconstruction. Distinguishes direct (binding) vs indirect (co-expression) regulatory evidence.

Quality

85%

Does it follow best practices?

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SecuritybySnyk

Low

Low-risk findings worth noting

SKILL.md
Quality
Evals
Security

Quality

Content

63%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, largely concrete skill body: sequenced phases, five question-to-tool-chain patterns, and copy-paste tool payloads with explicit evidence grading. Its weaknesses are a monolithic layout with no reference files, some redundant or Claude-known explanatory content, and one internal contradiction (Common Mistake #1 vs Phase 1's jaspar_get_matrix) plus a missing executable Python pattern.

Suggestions

Move the per-tool API reference (parameter tables, return shapes, and library lists) into a references/ file (e.g., references/tool_reference.md) and keep SKILL.md as a workflow overview with one-line pointers, shrinking the always-loaded body.

Delete the 'Common histone marks and their meaning' table and the duplicate Enrichr-direction guidance (it already appears as Common Mistakes #4) — Claude knows histone mark biology and the duplication wastes tokens.

Fix the internal contradiction: Common Mistake #1 says to use 'jaspar_search_matrices' NOT 'jaspar_get_matrix', yet Phase 1 documents jaspar_get_matrix as a valid tool for detailed motif info; also add one concrete example of the Python analysis pattern the 'COMPUTE, DON'T DESCRIBE' section mandates.

DimensionReasoningScore

Conciseness

The tool parameter/return documentation is non-obvious, skill-specific knowledge that earns its tokens, but the 'Common histone marks and their meaning' table is textbook biology Claude already knows, and the Enrichr-direction guidance is stated twice (Phase 2 'IMPORTANT' and Common Mistakes #4). This fits 'mostly efficient but includes some unnecessary explanation or could be tightened'; it is not 4 because the duplication and biology primer exceed 'minor instances'.

3 / 5

Actionability

Every tool has concrete parameter tables and copy-paste-ready JSON payloads (e.g., '{"search": "TP53", "limit": 5}') with documented return shapes — mostly executable guidance with minor gaps. It is not 5 because 'COMPUTE, DON'T DESCRIBE' mandates Python analysis yet no executable Python invocation pattern is shown, and Common Mistake #1 ('NOT jaspar_get_matrix') directly contradicts Phase 1, which documents jaspar_get_matrix as a valid tool; it is not 3 because the contradiction is localized and the rest is fully concrete.

4 / 5

Workflow Clarity

Phases 0–7 are explicitly sequenced and the five 'Common Use Patterns' map real question shapes to ordered tool chains, with 'LOOK UP DON'T GUESS... verify library names before calling enrichr' and the T1–T4 evidence grading acting as checkpoints. It is not 5 because there are no explicit verify→fix→retry feedback loops; it is not 3 because checkpoints are explicit rather than implicit and the destructive/batch cap does not apply to read-only data retrieval.

4 / 5

Progressive Disclosure

No bundle files exist, so the full API reference for ~15 tools (~200 lines of parameters and return shapes) is inlined in a 290-line SKILL.md. Section headers are well organized, but the per-tool reference is exactly the 'content that should be separate is inline' of anchor 3. It is not 4 because moving tool API details to a references/ file would materially shrink the always-loaded body; it is not 2 because the structure is good and nothing is buried.

3 / 5

Total

14

/

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: concrete capability list, explicit third-person voice, natural quoted trigger queries covering both directions of the TF–target relationship, and a distinctive niche. It matches the strongest reference examples in structure and quality.

DimensionReasoningScore

Specificity

The description enumerates multiple concrete capabilities — 'TF-target inference (JASPAR motifs, ChIP-seq), motif scanning, eQTL integration, perturbation evidence (knockout/overexpression)' — with comprehensive, non-generic coverage, matching the top anchor. It is not 4 because the gaps are trivial, not 'minor gaps in coverage'.

5 / 5

Completeness

It explicitly answers both 'what' (the first sentence lists the capabilities) and 'when' ('Use for “which TF regulates gene X”, “which genes does TF Y target”, regulatory pathway reconstruction'), mirroring the score-5 exemplar structure. It is not 4 because the 'when' clause is explicit with concrete trigger phrases rather than merely present.

5 / 5

Trigger Term Quality

Quoted natural user phrasings ('which TF regulates gene X', 'which genes does TF Y target', 'regulatory pathway reconstruction') plus domain keywords (eQTL, ChIP-seq, knockout/overexpression) give comprehensive natural-term coverage. It is not 4 because the interrogative triggers capture the natural ways users ask this question, and no file extensions apply in this domain.

5 / 5

Distinctiveness Conflict Risk

'Gene regulatory network analysis', 'TF-target inference', and the quoted TF/gene-centric triggers carve a clear niche with minimal overlap risk against unrelated skills. It is not 4 because the trigger phrasings would not plausibly fire a different skill.

5 / 5

Total

20

/

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

mims-harvard/ToolUniverse

Path

plugin/skills/tooluniverse-gene-regulatory-networks/SKILL.md

Reviewed

Table of Contents

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