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tooluniverse-gene-disease-association

Gene-disease association analysis across DisGeNET, OpenTargets, Monarch, OMIM, GenCC, Orphanet, Gene2Phenotype (G2P). Cross-references multiple sources for evidence-graded association reports with concordance scoring (5/5 sources agree → strong, 1/5 → weak). Use for 'which diseases is gene X associated with' or 'which genes cause disease Y' queries with quantitative confidence, including clinical-panel-based curation (developmental disorders, cancer, cardiac, skeletal, eye, skin panels).

Quality

86%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tooluniverse-gene-disease-association in mims-harvard/ToolUniverse

SKILL.md
Quality
Evals
Security

Quality

Content

78%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-sequenced multi-database workflow with executable code, prerequisite/fallback handling, and strong error-recovery guidance. The main structural weakness is that everything lives in one long SKILL.md with no bundle files — the per-database tool reference and troubleshooting content would benefit from being split into one-level-deep reference files.

Suggestions

Split the per-database tool-call catalog (Phases 2–6) into a references/ file (e.g., references/tool-catalog.md), keeping SKILL.md to the workflow overview, core principles, and synthesis guidance.

Move the detailed Troubleshooting entries into a references/troubleshooting.md or trim to the most common failure modes, keeping only API-key setup and ID-resolution pitfalls inline.

Add explicit inline validation checkpoints to the phase workflow (e.g., 'confirm Ensembl/HGNC IDs resolved before Phase 3/4 calls; if empty, re-run MyGene_query_genes') instead of relying on the Troubleshooting section alone.

DimensionReasoningScore

Conciseness

The body is dense and tool-specific with almost no filler — API-key requirements, fallbacks, exact parameter values, and known upstream failures (the EnsemblPheno HTTP 500 note) all earn their tokens. A few sections could be trimmed, e.g., the multi-sentence G2P/GenCC concordance commentary and parts of the evidence-hierarchy paragraph restate domain knowledge Claude already has, so it sits at 'efficient; minor instances of over-explanation' rather than the lean score-5 anchor.

4 / 5

Actionability

Fully executable, copy-paste-ready guidance: complete initialization (`from tooluniverse import ToolUniverse; tu.load_tools()`), exact tool names with real parameters (`DisGeNET_get_gda(gene=..., source="CURATED", min_score=0.3, limit=25)`), concrete output consumption (`g2p_hits["data"]["results"][0]["stable_id"]`), an example synthesis table, and specific troubleshooting fixes. This matches the score-5 anchor of copy-paste-ready code covering the common cases.

5 / 5

Workflow Clarity

The 7-phase workflow is clearly sequenced with an ASCII overview, entry-point alternatives (gene vs disease query), input dependencies noted ('Both require pre-resolved Ensembl/EFO IDs'), and a thorough Troubleshooting section giving error→fix feedback loops for each tool. It falls short of the score-5 anchor because validation checkpoints (verify IDs resolved, confirm non-empty results before synthesis) live in Troubleshooting rather than as explicit inline checkpoints in the phase sequence.

4 / 5

Progressive Disclosure

No references/, scripts/, or assets/ directories exist, and the single ~250-line SKILL.md inlines roughly 150 lines of per-tool API reference (all seven phases' call signatures, G2P/GenCC/Orphanet details, troubleshooting entries) that clearly belongs in separate reference files — mirroring the score-3 anchor of well-structured content with inline material that should be split out. Section organization itself is good, which keeps it above score 2.

3 / 5

Total

16

/

20

Passed

Description

88%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: concrete, third-person, and comprehensive about both capabilities and trigger conditions, with quoted user phrasings and a distinctive concordance-scoring hook. The only gaps are a few natural synonym phrasings and minor trigger overlap with closely related sibling skills.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions — 'association analysis across' seven named databases, 'cross-references multiple sources for evidence-graded association reports', 'concordance scoring (5/5 sources agree → strong, 1/5 → weak)', and 'clinical-panel-based curation' with named panels — covering the domain comprehensively. It is not merely the score-4 anchor because the coverage of actions (query, cross-reference, score, curate by panel) is complete rather than having minor gaps.

5 / 5

Completeness

Explicitly answers 'what' ('gene-disease association analysis across [databases]... evidence-graded association reports with concordance scoring') and 'when' with a concrete 'Use for...' clause quoting two literal trigger phrases. This matches the score-5 anchor: both what and when are clearly and explicitly stated with concrete trigger phrases.

5 / 5

Trigger Term Quality

Includes natural query phrasings users would actually say ('which diseases is gene X associated with', 'which genes cause disease Y') plus the seven database names and panel terms — good keyword coverage. It falls short of the score-5 anchor because common synonyms like 'linked to', 'risk gene', or 'disease-causing gene' are absent.

4 / 5

Distinctiveness Conflict Risk

The niche is well-defined (multi-database gene-disease association scoring) with distinctive terms (concordance scoring, clinical panels, named databases), giving minimal generic conflict risk. However, sibling skills exist (e.g., tooluniverse-rare-disease-diagnosis, tooluniverse-disease-research referenced in the body), and the 'which genes cause disease Y' trigger overlaps with them — mostly distinct with minor overlap risk, matching the score-4 anchor.

4 / 5

Total

18

/

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

relative_links

Relative link issues: 4 suspicious

Warning

Total

15

/

16

Passed

Repository

mims-harvard/ToolUniverse

Path

plugins/tooluniverse/skills/tooluniverse-gene-disease-association/SKILL.md

Reviewed

Table of Contents

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