tooluniverse-microbiome-research

Microbiome research using MGnify, GTDB, ENA, OLS (ENVO biomes), and EuropePMC. Covers study discovery, taxonomic profiling, host-microbe interaction analysis, and biome-by-condition queries. Use for microbiome study selection, organism-environment associations, and clinical-microbiome literature review. Distinct from analytical workflow (use tooluniverse-metagenomics-analysis for that).

Quality

81%

Does it follow best practices?

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Securityby

Passed

No findings from the security scan

Quality

Content

75%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 highly actionable, well-structured skill body with executable examples and solid methodological guardrails. The main weaknesses are some over-explanation of concepts Claude already knows and the absence of any separate reference files for the large tool table and interpretation guidance.

Suggestions

Trim explanations of well-known concepts (what Shannon/Bray-Curtis/UniFrac are, the definition of dysbiosis) and keep only the non-obvious thresholds and tool-specific guidance.

Consider moving the 18-row Core Tools table and the Interpretation Guidance into a separate REFERENCE.md linked from the body to improve progressive disclosure and reduce inline token weight.

Dimension	Reasoning	Score
Conciseness	Mostly efficient, but the Interpretation Guidance explains concepts Claude already knows (Shannon index, Bray-Curtis/UniFrac, dysbiosis definition) alongside genuinely valuable non-obvious thresholds, and coaching phrases like 'what is the question?' could be trimmed.	3 / 5
Actionability	Quick Start plus five workflows provide fully executable, copy-paste-ready Python with real accessions (MGYS00006860, MGYA00612683) and concrete query formats covering the common cases.	5 / 5
Workflow Clarity	Clear numbered sequences with real checkpoints ('LOOK UP DON'T GUESS', verify pipeline type via MGnify_get_study_detail before proceeding, Synthesis Questions checklist, Evidence Grading); minor gaps as the code workflows lack explicit validate-after-step feedback loops.	4 / 5
Progressive Disclosure	Well-organized sections with easy navigation, but no bundle files exist so everything is inline; the score-5 anchor requires well-signaled one-level-deep references and content appropriately split, which is absent.	4 / 5
	Total	16 / 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 that clearly states capabilities, gives explicit 'Use for' trigger guidance, and disambiguates from a sibling skill. The main gap is trigger-term synonym coverage and slightly category-level rather than granular action verbs.

Suggestions

Add common user synonyms to the trigger clause, e.g. 'metagenome', '16S/amplicon', and 'gut microbiome' so natural phrasings match.

Tighten the 'what' clause toward granular verbs (e.g. 'discover studies, profile taxonomy, query biome-by-condition') to match the score-5 anchor style.

Dimension	Reasoning	Score
Specificity	Names four concrete activities (study discovery, taxonomic profiling, host-microbe interaction analysis, biome-by-condition queries) plus specific tools, but these are activity-category noun phrases rather than the granular verbs of the score-5 anchor.	4 / 5
Completeness	Explicitly answers both 'what' (Covers study discovery, taxonomic profiling...) and 'when' (Use for microbiome study selection...) with concrete trigger phrases.	5 / 5
Trigger Term Quality	Strong natural terms appear (microbiome, taxonomic profiling, host-microbe, biome, clinical-microbiome literature review), but common synonyms users say like metagenome, 16S, amplicon, and gut microbiome are missing.	4 / 5
Distinctiveness Conflict Risk	Provides explicit disambiguation naming the sister skill ('Distinct from analytical workflow (use tooluniverse-metagenomics-analysis for that)'), giving a clear niche with minimal conflict risk.	5 / 5
	Total	18 / 20 Passed

Validation

100%

Warnings & errors only

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-microbiome-research/SKILL.md
Commit: 22661b6

Reviewed: 2 days ago

Table of Contents

Discovery Implementation Validation

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