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tooluniverse-cancer-classification

Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies. Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines.

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

70%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 body is a well-sequenced, highly actionable workflow guide with explicit validation steps and fallback chains for the tool domain. Its weaknesses are token efficiency — general oncology education and repeated caveats pad the file — and progressive disclosure, since all reference-grade material is inlined with no bundle files or external references.

Suggestions

Trim or move the general oncology education (staging vs. grading, histological vs. molecular axes, biomarker thresholds like HER2 IHC 3+ / Ki67 >20%) into a references/ file, keeping only the tool-specific interpretation guidance (e.g., 'pass MSI-H to OncoKB as gene="Other Biomarkers"') inline.

Deduplicate: state the GBM→GB alias caveat once (Phase 2 or the codes table) and merge the 'Key Tools' table with the 'Tool Parameter Reference' table into a single table.

Create a references/ directory (e.g., oncotree-codes.md for the code table, biomarker-interpretation.md) and link to it from the body so the SKILL.md reads as a lean overview with well-signaled one-level-deep references.

DimensionReasoningScore

Conciseness

The tool-specific content is dense and useful, but the "Tumor Classification Reasoning" and "Biomarker Interpretation Strategy" sections re-teach general oncology Claude already knows (e.g., "Stage (TNM): How far has it spread? T=tumor size, N=lymph nodes, M=metastasis", "Ki67: Proliferation index... High (>20%) suggests aggressive biology", "HER2: Positive = IHC 3+ or FISH-amplified"). There is also duplication: the GBM→"GB" caveat appears three times (Phase 2, the Common Codes table, and Interpretation Guidance), and tool parameters are tabulated twice (Key Tools and Tool Parameter Reference). This fits the level-3 anchor ("mostly efficient but includes some unnecessary explanation or could be tightened") better than level 4, since multiple sections, not minor instances, could be trimmed.

3 / 5

Actionability

Concrete, specific guidance throughout: exact tool signatures with parameters (e.g., `OncoKB_annotate_variant(gene="EGFR", variant="L858R", tumor_type="LUAD")`), response-field documentation, verified code mappings, and case-sensitivity/404 gotchas. It falls short of the level-5 anchor ("copy-paste ready code") because the "Common Patterns" blocks are illustrative patterns over MCP tool results (e.g., `results["data"][0]["code"]`) rather than fully executable code, and no end-to-end runnable example is given — but it clearly exceeds level 3's pseudocode/incomplete level.

4 / 5

Workflow Clarity

The four-phase workflow is clearly sequenced with an explicit validation checkpoint ("Always validate via `OncoTree_get_type` before using in downstream tools") and error-recovery feedback loops (the Fallback Chains table for 404s and empty searches, plus the Python pattern `if detail["status"] == "success": OncoKB_annotate_variant(...)`). This matches the level-5 anchor (explicit validation steps, feedback loops for error recovery); the domain is read-only lookup/annotation so the destructive/batch validation cap does not apply, and it is clearly above level 4's "minor validation gaps".

5 / 5

Progressive Disclosure

There are no bundle files (references/, scripts/, assets/ are absent) and no pointers to external material — everything, including ~60 lines of general tumor-classification reasoning, biomarker interpretation, staging-vs-grading education, and code lookup tables, is inlined in a single ~190-line SKILL.md. Section headers are clear, but reference-style content that would naturally live in a separate file is inline, matching the level-3 anchor ("some structure but... content that should be separate is inline") rather than level 4's "most content appropriately placed" with clearly signaled references.

3 / 5

Total

15

/

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 description: concrete third-person capability statements, an explicit "Use for..." clause with multiple concrete trigger contexts, and domain-specific terms that clearly distinguish it from other skills. The only weakness is slightly incomplete synonym coverage of natural user phrasings.

DimensionReasoningScore

Specificity

The description lists multiple concrete actions — "Translate free-text tumor descriptions to OncoTree codes", "resolve cancer subtypes/tissue hierarchy", "Cross-references UMLS/NCI vocabularies", "building cohorts in OncoKB or GDC", "mapping tumor-board notes to ontology codes" — with comprehensive coverage of the skill's scope. It clearly exceeds the level-4 anchor ("several specific actions; minor gaps") and matches the level-5 anchor; it is not vague or generic like levels 1-2, and no capability gap is apparent. Third-person voice is used throughout ("Translate", "Cross-references"), per the guidelines.

5 / 5

Completeness

It explicitly answers both questions: what ("Translate free-text tumor descriptions to OncoTree codes and resolve cancer subtypes/tissue hierarchy. Cross-references UMLS/NCI vocabularies") and when ("Use for standardizing cancer-type nomenclature in EHR free-text, building cohorts in OncoKB or GDC, mapping tumor-board notes to ontology codes, and ensuring consistent terminology across cancer-genomics pipelines"). This matches the level-5 anchor exactly — a clear 'what' plus an explicit 'Use for...' clause with concrete trigger contexts — and is well above level 4, where the 'when' is only loosely specified.

5 / 5

Trigger Term Quality

Good natural-term coverage: users would say "OncoTree code", "cancer subtypes", "standardizing cancer-type nomenclature", "cohorts in OncoKB or GDC", "tumor-board notes", "cancer-genomics pipelines". It falls just short of the level-5 anchor ("comprehensive coverage including synonyms and file extensions") because common user phrasings like "tumor type code", "ICD-O", or "WHO classification" are absent — noticeably above the midpoint (level 3's "missing common variations or synonyms") but not full synonym coverage.

4 / 5

Distinctiveness Conflict Risk

The description carves out a clear niche (OncoTree/UMLS/NCI cancer-type coding) with distinct triggers (OncoKB, GDC, tumor-board notes, EHR free-text) that few other skills would claim, matching the level-5 anchor ("clear niche with distinct triggers; minimal conflict risk"). It is not generic or broadly overlapping as in levels 1-3; the vocabulary is specific to cancer ontology standardization.

5 / 5

Total

19

/

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-cancer-classification/SKILL.md

Reviewed

Table of Contents

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