tooluniverse-precision-oncology

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 : Report-first - Create report file FIRST, update progressively Evidence-graded - Every recommendation has evidence level Actionable output - Prioritized treatment options, not data dumps Clinical focus - Answer "what should we do?" not "what exists?" 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 "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 Tool WRONG CORRECT civic_get_variant variant_name id (numeric) civic_get_evidence_item variant_id id OpenTargets_* ensemblID ensemblId (camelCase) search_clinical_trials disease condition Workflow Overview Input: Cancer type + Molecular profile (mutations, fusions, amplifications) Phase 1: Profile Validation -> Resolve gene IDs (Ensembl, UniProt, ChEMBL) Phase 2: Variant Interpretation -> CIViC, ClinVar, COSMIC, GDC/TCGA, DepMap, OncoKB, cBioPortal, HPA Phase 2.5: Tumor Expression -> CELLxGENE cell-type expression, ChIPAtlas regulatory context Phase 3: Treatment Options -> OpenTargets + DailyMed (approved), ChEMBL (off-label) Phase 3.5: Pathway & Network -> KEGG/Reactome pathways, IntAct interactions Phase 4: Resistance Analysis -> CIViC + PubMed + NvidiaNIM structure analysis Phase 5: Clinical Trials -> ClinicalTrials.gov search + eligibility Phase 5.5: Literature -> PubMed, BioRxiv/MedRxiv preprints, OpenAlex citations Phase 6: Report Synthesis -> Executive summary + prioritized recommendations Key Tools by Phase Phase 1: Profile Validation MyGene_query_genes - Resolve gene to Ensembl ID UniProt_search - Get UniProt accession ChEMBL_search_targets - Get ChEMBL target ID Phase 2: Variant Interpretation civic_search_variants / civic_get_variant - CIViC evidence COSMIC_get_mutations_by_gene / COSMIC_search_mutations - Somatic mutations GDC_get_mutation_frequency / GDC_get_ssm_by_gene - TCGA patient data GDC_get_gene_expression / GDC_get_cnv_data - Expression and CNV DepMap_get_gene_dependencies / DepMap_get_drug_response - Target essentiality OncoKB_annotate_variant / OncoKB_get_gene_info - Actionability cBioPortal_get_mutations / cBioPortal_get_cancer_studies - Cross-study data HPA_search_genes_by_query / HPA_get_comparative_expression_by_gene_and_cellline - Expression Phase 2.5: Tumor Expression CELLxGENE_get_expression_data / CELLxGENE_get_cell_metadata - Cell-type expression Phase 3: Treatment Options OpenTargets_get_associated_drugs_by_target_ensemblId - Approved drugs DailyMed_search_spls - FDA label details ChEMBL_get_drug_mechanisms_of_action_by_chemblId - Drug mechanism Phase 3.5: Pathway & Network kegg_find_genes / kegg_get_gene_info - KEGG pathways reactome_disease_target_score - Reactome disease relevance intact_get_interaction_network - Protein interactions Phase 4: Resistance Analysis civic_search_evidence_items - Resistance evidence (clinical_significance="Resistance") PubMed_search_articles - Resistance literature NvidiaNIM_alphafold2 / NvidiaNIM_diffdock - Structure-based analysis Phase 5: Clinical Trials search_clinical_trials - Find trials (param: condition , NOT disease ) get_clinical_trial_eligibility_criteria - Eligibility details Phase 5.5: Literature PubMed_search_articles - Published evidence BioRxiv_search_preprints / MedRxiv_search_preprints - Preprints (flag as NOT peer-reviewed) openalex_search_works - Citation analysis References TOOLS_REFERENCE.md - Complete tool documentation with parameters and examples API_USAGE_PATTERNS.md - Detailed code examples for each phase TREATMENT_ALGORITHMS.md - Evidence grading, treatment prioritization, cancer type mappings, DepMap interpretation REPORT_TEMPLATE.md - Report template with output tables EXAMPLES.md - Worked examples (EGFR NSCLC, T790M resistance, KRAS G12C, no actionable mutations) CHECKLIST.md - Quality and completeness checklist