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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

87%

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SecuritybySnyk

Low

Low-risk findings worth noting

The canonical home for this skill is tooluniverse-cancer-classification in mims-harvard/ToolUniverse

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 excels at actionability and workflow design — concrete tool calls, a validated-codes table, explicit validation steps, and fallback chains make it easy to execute correctly. Its weaknesses are token efficiency and structure: a long inline domain primer explains oncology concepts Claude already knows and would be better split into a reference file.

Suggestions

Move the 'Tumor Classification Reasoning (CRITICAL)' domain background (staging vs grading, histological vs molecular axes, biomarker interpretation, actionability levels) into a references/ file such as references/tumor-classification.md, keeping in SKILL.md only the tool-relevant guidance (e.g., 'pass the validated OncoTree code to OncoKB') plus a one-line pointer — this fixes both conciseness and progressive disclosure.

Delete or compress the passages that restate textbook knowledge, e.g. the TNM definition ('T=tumor size, N=lymph nodes, M=metastasis') and the Grade 1-3 explanation, down to a single line each since they drive no tool calls.

Document the actual response envelope (e.g., whether results come back as `results["data"]` and whether `OncoTree_get_type` returns a `status` field) in the Phase 1/2 field lists so the Python patterns are copy-paste consistent with the documented schema.

DimensionReasoningScore

Conciseness

The tool sections are lean (param tables, verified codes, fallback chains), but the "Tumor Classification Reasoning (CRITICAL)" section spends roughly 70 lines on textbook oncology Claude already knows — "Stage (TNM): How far has it spread? T=tumor size, N=lymph nodes, M=metastasis", "Grade: How abnormal do the cells look?", and the histological-vs-molecular primer — which goes beyond the 'minor trims' of the anchor above.

3 / 5

Actionability

Concrete executable calls with parameters appear throughout — `OncoTree_search(query="breast cancer")`, `OncoKB_annotate_variant(gene="EGFR", variant="L858R", tumor_type="LUAD")`, a verified-codes table, and fallback chains — covering the common cases. The minor gap is that the Python patterns rely on a response shape (`results["data"][0]["code"]`, `detail["status"] == "success"`) that is not documented in the Phase 1/2 response-field descriptions.

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"), an evidence-grading table, and explicit error-recovery feedback loops (404 on an alias falls back to `OncoTree_search`; no results falls back to tissue-level search), matching the top anchor. No destructive or batch operations, so no cap applies.

5 / 5

Progressive Disclosure

No bundle files exist (no references/, scripts/, or assets/), and everything — including the separable oncology domain primer (staging vs grading, biomarker interpretation, actionability levels) — is inlined in a single ~190-line SKILL.md. Internal section headers are well organized, but content that clearly belongs in a reference file is inline with no references to signal, matching the 'some structure' anchor rather than the 'most content appropriately placed' anchor.

3 / 5

Total

15

/

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.

A strong description: dense with concrete capabilities, explicit third-person what-statements, and a four-scenario 'Use for' trigger clause using natural domain vocabulary. It would both trigger correctly for the intended tasks and stay out of the way of unrelated skills.

DimensionReasoningScore

Specificity

The description lists multiple specific 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 no coverage gaps, matching the comprehensive anchor.

5 / 5

Completeness

It explicitly answers both what (translate/resolve/cross-reference, sentence 1) and when ("Use for standardizing cancer-type nomenclature... building cohorts... mapping tumor-board notes... ensuring consistent terminology"), with four concrete trigger scenarios, matching the top anchor.

5 / 5

Trigger Term Quality

It covers the natural phrases this domain's users would actually say — "OncoTree codes", "tumor descriptions", "cancer subtypes", "tissue hierarchy", "EHR free-text", "OncoKB", "GDC", "tumor-board notes", "cancer-genomics pipelines" — comprehensively including synonyms; no meaningful natural term is missing.

5 / 5

Distinctiveness Conflict Risk

The niche — OncoTree cancer-type coding with OncoKB/GDC integration — has distinct triggers and minimal conflict risk; the named vocabularies and tools make accidental triggering of a generic terminology or document skill very unlikely.

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

plugins/tooluniverse/skills/tooluniverse-cancer-classification/SKILL.md

Reviewed

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