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tooluniverse-data-integration-analysis

Integrate computed statistical results (DEGs, GWAS hits, associations) with biological context from ToolUniverse databases (UniProt, GO, Reactome, ClinVar, OpenTargets). Use for adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findings, and going beyond p-values to mechanism.

58

Quality

67%

Does it follow best practices?

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SecuritybySnyk

Passed

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tessl review fix ./plugins/tooluniverse/skills/tooluniverse-data-integration-analysis/SKILL.md

The canonical home for this skill is tooluniverse-data-integration-analysis in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

56%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.

The content is well-structured as a clear five-step workflow but leans instructional rather than executable, and embeds concept explanations and reference tables that add tokens. With no bundle files, progressive disclosure is limited to section organization.

Suggestions

Replace conceptual explanations of DAGs, Mendelian randomization, and confounders/mediators/colliders with concise reminders or move them to a reference file, since Claude already knows these frameworks.

Add concrete, runnable Python examples for the analysis steps (e.g., enrichment via ToolUniverse + scipy/statsmodels) instead of only descriptive guidance and find_tools() query strings.

Move the evidence-grading table and finding-type mapping table into a separate reference file referenced from the body to reduce token load and improve progressive disclosure.

DimensionReasoningScore

Conciseness

The body is mostly efficient but spends tokens explaining causal reasoning concepts Claude already knows (DAGs, confounders/mediators/colliders, Mendelian randomization) and reproduces large reference tables that could be trimmed.

3 / 5

Actionability

Guidance is framed as conceptual steps and discovery queries ('find_tools(...)') rather than concrete executable code; tool-discovery calls are actionable but most analysis guidance is descriptive and lacks runnable examples.

3 / 5

Workflow Clarity

A clear five-step sequence with explicit ordering and per-step structure is present, including falsification/cross-validation steps, though validation checkpoints are conceptual rather than concrete verification commands.

4 / 5

Progressive Disclosure

The skill is a single self-contained file with well-organized sections but no bundle files and no external references; large reference tables and evidence-grading detail are inlined rather than split into separate files.

3 / 5

Total

13

/

20

Passed

Description

78%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.

The description is specific, well-differentiated, and covers both what and when with a clear 'Use for' clause. It is slightly above the midpoint on specificity and trigger coverage due to high-level action phrasing rather than fully concrete operations.

DimensionReasoningScore

Specificity

Description names the domain and multiple concrete actions ('adding gene function/pathway/disease annotations to a result list, building biological narrative around statistical findings, and going beyond p-values to mechanism') but the actions are somewhat high-level rather than enumerating specific concrete operations.

4 / 5

Completeness

Clearly states what it does (integrate computed statistical results with biological context) and provides a 'Use for' when-clause, but the when guidance lists use cases rather than a single explicit natural trigger phrase.

4 / 5

Trigger Term Quality

Includes natural domain terms users would say (DEGs, GWAS hits, associations, gene function, pathways, p-values, mechanism) with good coverage, though a few common synonyms and explicit file/extension-like triggers are missing.

4 / 5

Distinctiveness Conflict Risk

Has a clear niche (post-analysis biological interpretation via ToolUniverse databases) and explicitly distinguishes itself from adjacent skills, with minimal overlap risk.

5 / 5

Total

17

/

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.

Validation16 / 16 Passed

Validation for skill structure

No warnings or errors.

Repository
mims-harvard/ToolUniverse
Reviewed

Table of Contents

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