tooluniverse-precision-oncology
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options for specific mutations (EGFR, KRAS, BRAF, etc.), therapy resistance, or clinical trial eligibility.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-precision-oncology --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
What it does
Provides actionable treatment recommendations for cancer patients based on molecular profile, using multiple knowledge bases (CIViC, ClinVar, OpenTargets, ClinicalTrials.gov) and structure-based analysis. It prioritizes output as a report that is created first and updated progressively, ensuring each recommendation includes evidence, and focuses on clinical actions rather than data dumps.
How it works
- Phase 1: Profile Validation: verifies variant nomenclature and resolves gene identifiers, then confirms cancer type.
- Phase 2: Variant Interpretation: retrieves CIViC evidence for variants and gathers COSMIC, GDC/TCGA, DepMap, OncoKB, cBioPortal, Human Protein Atlas, and OpenTargets data to build a variant significance table with target validation and expression.
- Phase 2.5: Tumor Expression Context (NEW): analyzes tumor-specific expression context using CELLxGENE, ChIPAtlas, and cancer-specific expression patterns, producing expression validation output.
- Phase 3: Treatment Options: aggregates FDA-approved therapies, NCCN-recommended options, and off-label options with supporting evidence to produce a prioritized treatment list.
- Phase 3.5: Pathway & Network Analysis (NEW): uses KEGG/Reactome and protein interaction data to provide context for potential drug combinations.
- Phase 4: Resistance Analysis (if prior therapy): identifies known resistance mechanisms and uses structure-based and network analyses to explain resistance and propose strategies.
- Phase 5: Clinical Trial Matching: filters active trials by indication and biomarker and outputs matched trials.
- Phase 5.5: Literature Evidence (NEW): gathers PubMed, BioRxiv/MedRxiv, and OpenAlex to support literature.
- Phase 6: Report Synthesis: compiles executive summary, prioritized treatments, and next steps.
When to use it
Apply when oncology questions involve: treatment options for a mutation (e.g., EGFR, KRAS, BRAF), therapy resistance, or clinical trial eligibility.
What it can touch
Uses tools such as CIViC, ClinVar, OpenTargets, ClinicalTrials.gov, and structure-based analysis as described in the workflow to gather evidence and context.
Caveats
The skill lists tools and data sources, and emphasizes evidence-graded outputs and clinical focus. It does not claim outcomes not stated, and it requires proper tool access as specified in the workflow. License status is NOASSERTION per the provided metadata.
# Precision Oncology Treatment Advisor Provide actionable treatment recommendations for cancer patients based on their molecular profile using CIViC, ClinVar, OpenTargets, ClinicalTrials.gov, and structure-based analysis. **KEY PRINCIPLES**: 1. **Report-first** - Create report file FIRST, update progressively 2. **Evidence-graded** - Every recommendation has evidence level 3. **Actionable output** - Prioritized treatment options, not data dumps 4. **Clinical focus** - Answer "what should we do?" not "what exists?" 5. **English-first queries** - Always use English terms in tool calls (mutations, drug names, cancer types), even if the user writes in another language. Only try original-language terms as a fallback. Respond in the user's language --- ## When to Use Apply when user asks: - "Patient has [cancer] with [mutation] - what treatments?" - "What are options for EGFR-mutant lung cancer?" - "Patient failed [drug], what's next?" - "Clinical trials for KRAS G12C?" - "Why isn't [drug] working anymore?" --- ## Phase 0: Tool Verification **CRITICAL**: Verify tool parameters before first use. | Tool | WRONG | CORRECT | |------|-------|---------| | `civic_get_variant` | `variant_name` |
- When to Use
- Phase 0: Tool Verification
- Workflow Overview
- Phase 1: Profile Validation
- 1.1 Resolve Gene Identifiers
- 1.2 Validate Variant Nomenclature
- Phase 2: Variant Interpretation
- 2.1 CIViC Evidence Query
- 2.2 COSMIC Somatic Mutation Analysis (NEW)
- 2.3 GDC/TCGA Pan-Cancer Analysis (NEW)
- 2.4 DepMap Target Validation (NEW)
- 2.5 OncoKB Actionability Assessment (NEW)
- 2.6 cBioPortal Cross-Study Analysis (NEW)
- 2.7 Human Protein Atlas Expression (NEW)
What does the tooluniverse-precision-oncology skill do?
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options for specific mutations (EGFR, KRAS, BRAF, etc.), therapy resistance, or clinical trial eligibility.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tooluniverse-precision-oncology --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.