skills.rest
mims-harvard
mims-harvardOFFICIAL
Explore all skills by this author →
Website𝕏@marinkazitnikGitHub

tooluniverse-cancer-classification

Translate free-text tumor descriptions into validated OncoTree codes with UMLS and NCI cross-references.

1.7k|254|Updated Mar 3, 2025
Search Tags:#oncology#variant annotation#umls#oncotree#onkokb#cancer classification#tumor nomenclature
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-cancer-classification
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-cancer-classification
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-cancer-classification
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-cancer-classification

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Cancer type names appear as inconsistent free text across EHR notes, tumor-board reports, and research pipelines, making cohort building and variant annotation unreliable. This Skill standardizes tumor nomenclature by resolving free-text descriptions to validated OncoTree ontology codes with UMLS and NCI cross-references.

Core Features & Use Cases

  • Free-Text Cancer Search: Query OncoTree with tumor names or acronyms to retrieve codes, hierarchy levels, tissue of origin, and external vocabulary references.
  • Code Validation and Hierarchy Navigation: Confirm candidate codes, list all 32 tissue categories, and explore subtypes before downstream use.
  • Downstream Variant Annotation: Pass validated OncoTree codes to OncoKB for tumor-type-specific therapeutic levels and to GDC for TCGA mutation frequencies.
  • Use Case: A researcher annotating an EGFR L858R variant resolves "lung adenocarcinoma" to the validated code LUAD, then calls OncoKB with that tumor type to obtain the Level 1 FDA-approved therapy indication instead of a less specific pan-cancer level.

Quick Start

Ask the agent to find the OncoTree code for a tumor description such as "pancreatic ductal adenocarcinoma" and validate it before using it in an OncoKB variant annotation.

Frequently Asked Questions about tooluniverse-cancer-classification

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I find the OncoTree code for a cancer type?▼

Use OncoTree_search with a free-text query such as a tumor name or acronym to get matching codes with tissue, hierarchy level, and parent information. Then validate the candidate code with OncoTree_get_type before using it downstream.

How do I annotate a variant for a specific tumor type in OncoKB?▼

Pass a validated OncoTree code as the tumor_type parameter to OncoKB_annotate_variant along with gene and variant. Providing the tumor type returns tumor-specific therapeutic levels instead of less specific pan-cancer levels.

Why does OncoTree_get_type return 404 for GBM?▼

GBM is not a valid OncoTree code; the correct code for Glioblastoma, IDH-Wildtype is GB. Common acronyms often differ from official codes, so always validate with OncoTree_get_type or fall back to OncoTree_search.

Can I list all cancer subtypes within a tissue category?▼

Yes. Call OncoTree_list_tissues to get the 32 tissue categories, then run OncoTree_search with the tissue name to retrieve all cancer types in that tissue. Filter results by main_type or level for finer subtype groupings.

What are the limitations of OncoTree-based cancer classification?▼

Very rare or novel tumor subtypes may not exist in the OncoTree ontology and return no search matches. Codes are also case-sensitive and evolve across versions, so deprecated names require checking the history field of OncoTree_get_type.

Related Skills

Explore More Education & Research Skills→
nahisahonahisaho
3

scientific-precision-oncology

Annotate cancer variants across CIViC, OncoKB, cBioPortal, COSMIC, and GDC/TCGA.

Community
Advanced
maziyarpanahimaziyarpanahi
5.0k

linking-umls-concepts

Map OpenMed clinical entities to UMLS Concept Unique Identifiers via the UTS API.

Community
Advanced
Hung-3008Hung-3008
1

monarch-database

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations.

Community
Advanced
brazil-benchbrazil-bench
11

pdd

Transform rough ideas into design and implementation plans with structured prompts.

Official
Basic