zaoqu-liu ToolUniverse Router
Route user questions to specialized skills. If no skill matches, use general strategies from references/general-strategies.md.
Routing Workflow
- Extract keywords from user's question
- Scan routing table below for keyword matches
- Take action:
- 1 clear match → invoke that skill NOW using the Skill tool
- Multiple matches → ask user which they prefer (AskUserQuestion)
- No match → use general strategies (load references/general-strategies.md)
- If ambiguous (e.g., "Tell me about aspirin") → ask user to clarify intent
CRITICAL: Actually INVOKE skills — don't describe them or show the routing table to the user.
Language: If the user writes in a non-English language, extract keywords for routing but respond in their language. All tool calls use English terms.
Routing Table
1. Data Retrieval
| Keywords | Action |
|---|---|
| "get", "retrieve", "chemical compound", "PubChem", "ChEMBL", "drug molecule", "SMILES", "InChI" | Skill(skill="tooluniverse-chemical-compound-retrieval") |
| "get", "retrieve", "expression data", "gene expression", "omics dataset", "ArrayExpress", "RNA-seq", "microarray" | Skill(skill="tooluniverse-expression-data-retrieval") |
| "get", "retrieve", "protein structure", "PDB", "AlphaFold", "crystal structure", "3D model" | Skill(skill="tooluniverse-protein-structure-retrieval") |
| "get", "retrieve", "sequence", "DNA sequence", "RNA sequence", "protein sequence", "FASTA" | Skill(skill="tooluniverse-sequence-retrieval") |
2. Research & Profiling
| Keywords | Action |
|---|---|
| "research", "profile", "disease", "syndrome", "disorder", "comprehensive report on [disease]" | Skill(skill="tooluniverse-disease-research") |
| "research", "profile", "drug", "medication", "therapeutic agent", "tell me about [drug]" | Skill(skill="tooluniverse-drug-research") |
| "literature review", "papers about", "publications on", "research articles", "recent studies" | Skill(skill="tooluniverse-literature-deep-research") |
| "research", "profile", "target", "protein target", "gene target", "target validation" | Skill(skill="tooluniverse-target-research") |
3. Clinical Decision Support
| Keywords | Action |
|---|---|
| "drug safety", "adverse events", "side effects", "pharmacovigilance", "pharmacogenomics", "FAERS", "black box warning" | Skill(skill="tooluniverse-pharmacovigilance") |
| "adverse event signal", "safety signal detection", "disproportionality", "PRR", "ROR" | Skill(skill="tooluniverse-adverse-event-detection") |
| "drug safety profile", "drug safety assessment", "comprehensive safety" | Skill(skill="tooluniverse-drug-safety-profiling") |
| "chemical safety", "ADMET", "chemical toxicity", "environmental toxicity", "toxic effects" | Skill(skill="tooluniverse-chemical-safety") |
| "cancer treatment", "precision oncology", "tumor mutation", "targeted therapy", "EGFR", "KRAS", "BRAF" | Skill(skill="tooluniverse-precision-oncology") |
| "cancer driver", "driver gene", "driver mutation", "IntOGen", "cBioPortal" | Skill(skill="tooluniverse-cancer-driver-analysis") |
| "somatic mutation interpretation", "cancer variant", "oncogenic variant", "tumor variant" | Skill(skill="tooluniverse-cancer-variant-interpretation") |
| "immunotherapy response", "checkpoint inhibitor response", "TMB", "MSI", "PD-L1", "ICI response" | Skill(skill="tooluniverse-immunotherapy-response-prediction") |
| "rare disease diagnosis", "differential diagnosis", "phenotype matching", "HPO", "patient with [symptoms]" | Skill(skill="tooluniverse-rare-disease-diagnosis") |
| "variant interpretation", "VUS", "pathogenicity", "clinical significance", "is [variant] pathogenic" | Skill(skill="tooluniverse-variant-interpretation") |
| "clinical guidelines", "practice guidelines", "treatment guidelines", "dosing recommendations", "standard of care" | Skill(skill="tooluniverse-clinical-guidelines") |
| "patient stratification", "precision medicine", "biomarker stratification", "treatment selection" | Skill(skill="tooluniverse-precision-medicine-stratification") |
4. Discovery & Design
| Keywords | Action |
|---|---|
| "find binders", "virtual screening", "hit identification", "compounds for [target]", "IC50", "bioactivity", "binding affinity", "potency", "selectivity", "SAR", "structure-activity", "lead optimization", "hit-to-lead" | Skill(skill="tooluniverse-binder-discovery") |
| "drug repurposing", "new indication", "existing drugs for [disease]", "repurpose [drug]" | Skill(skill="tooluniverse-drug-repurposing") |
| "drug target validation", "target druggability", "validate target", "target assessment" | Skill(skill="tooluniverse-drug-target-validation") |
| "network pharmacology", "polypharmacology", "compound-target network", "multi-target" | Skill(skill="tooluniverse-network-pharmacology") |
| "design protein", "protein binder", "de novo protein", "RFdiffusion", "ProteinMPNN" | Skill(skill="tooluniverse-protein-therapeutic-design") |
| "antibody engineering", "antibody design", "humanization", "affinity maturation" | Skill(skill="tooluniverse-antibody-engineering") |
5. Genomics & Variant Analysis
| Keywords | Action |
|---|---|
| "GWAS study", "genome-wide association", "GWAS catalog", "GWAS for [trait]" | Skill(skill="tooluniverse-gwas-study-explorer") |
| "GWAS trait to gene", "trait-associated genes", "causal genes", "genes for [trait]" | Skill(skill="tooluniverse-gwas-trait-to-gene") |
| "fine-mapping", "credible sets", "causal variants", "statistical refinement" | Skill(skill="tooluniverse-gwas-finemapping") |
| "SNP interpretation", "rsID", "rs[number]", "variant annotation" | Skill(skill="tooluniverse-gwas-snp-interpretation") |
| "polygenic risk", "PRS", "genetic risk", "risk score for [disease]" | Skill(skill="tooluniverse-polygenic-risk-score") |
| "structural variant", "SV", "CNV", "deletion", "duplication", "chromosomal rearrangement" | Skill(skill="tooluniverse-structural-variant-analysis") |
| "VCF", "variant calling", "mutation analysis", "variant annotation pipeline" | Skill(skill="tooluniverse-variant-analysis") |
6. Systems & Network Analysis
| Keywords | Action |
|---|---|
| "protein interactions", "PPI", "interactome", "binding partners", "protein complexes" | Skill(skill="tooluniverse-protein-interactions") |
| "systems biology", "pathway analysis", "network analysis", "gene set enrichment" | Skill(skill="tooluniverse-systems-biology") |
| "metabolomics", "metabolite identification", "metabolic pathway" | Skill(skill="tooluniverse-metabolomics") |
| "epigenomics", "gene regulation", "transcription factor", "TF binding", "enhancers", "chromatin", "ChIP-seq" | Skill(skill="tooluniverse-epigenomics") |
| "gene enrichment", "pathway enrichment", "GO enrichment", "GSEA", "overrepresentation", "gene list analysis" | Skill(skill="tooluniverse-gene-enrichment") |
| "multi-omics", "omics integration", "transcriptomics + proteomics", "integrated analysis" | Skill(skill="tooluniverse-multi-omics-integration") |
| "multi-omic disease", "disease characterization", "genomic + transcriptomic + proteomic" | Skill(skill="tooluniverse-multiomic-disease-characterization") |
7. Screening & Functional Genomics
| Keywords | Action |
|---|---|
| "CRISPR screen", "genetic screen", "screen hits", "essential genes" | Skill(skill="tooluniverse-crispr-screen-analysis") |
| "drug-drug interaction", "DDI", "drug combination", "polypharmacy" | Skill(skill="tooluniverse-drug-drug-interaction") |
| "differential expression", "DESeq2", "RNA-seq analysis", "DE genes", "fold change" | Skill(skill="tooluniverse-rnaseq-deseq2") |
| "proteomics", "mass spectrometry", "protein quantification", "TMT", "iTRAQ", "label-free" | Skill(skill="tooluniverse-proteomics-analysis") |
| "immune repertoire", "TCR", "BCR", "T-cell receptor", "B-cell receptor", "clonotype" | Skill(skill="tooluniverse-immune-repertoire-analysis") |
| "spatial transcriptomics", "Visium", "MERFISH", "seqFISH", "Slide-seq", "spatial gene expression" | Skill(skill="tooluniverse-spatial-transcriptomics") |
| "spatial omics", "spatial proteomics", "spatial multi-omics" | Skill(skill="tooluniverse-spatial-omics-analysis") |
| "microscopy", "image analysis", "cell counting", "colony morphometry", "fluorescence quantification" | Skill(skill="tooluniverse-image-analysis") |
| "phylogenetics", "phylogenetic tree", "sequence alignment", "evolutionary analysis" | Skill(skill="tooluniverse-phylogenetics") |
| "statistical modeling", "regression analysis", "logistic regression", "survival analysis", "Cox" | Skill(skill="tooluniverse-statistical-modeling") |
| "metabolomics analysis", "LC-MS analysis", "metabolite quantification", "metabolic flux" | Skill(skill="tooluniverse-metabolomics-analysis") |
8. Clinical Trials & Study Design
| Keywords | Action |
|---|---|
| "clinical trial design", "trial protocol", "study design", "endpoint selection" | Skill(skill="tooluniverse-clinical-trial-design") |
| "clinical trial matching", "patient-to-trial", "trial eligibility", "find trials for patient" | Skill(skill="tooluniverse-clinical-trial-matching") |
| "GWAS drug discovery", "genetic target validation", "GWAS to drug" | Skill(skill="tooluniverse-gwas-drug-discovery") |
9. Outbreak Response
| Keywords | Action |
|---|---|
| "pathogen", "infectious disease", "outbreak", "emerging infection", "novel virus" | Skill(skill="tooluniverse-infectious-disease") |
10. Infrastructure & Setup
| Keywords | Action |
|---|---|
| "setup", "install", "configure", "API keys", "upgrade", "how to use", "get started", "CLI", "tu command", "MCP vs CLI vs SDK", "what is ToolUniverse", "what can this do", "what databases", "demo", "tutorial", "quickstart", "I'm new" | Skill(skill="setup-tooluniverse") |
| "SDK", "Python SDK", "build AI scientist", "programmatic access", "import tooluniverse", "coding API", "tu build", "typed wrappers" | Skill(skill="tooluniverse-sdk") |
| "install skills", "missing skills", "skill not found", "add skills" | Skill(skill="tooluniverse-install-skills") |
Tie-Breaking Rules
Domain Over Setup: When "how do I", "help me", "explain", or "what is" co-occurs with a domain entity (drug, gene, protein, disease, variant, pathway name), route to the domain skill, NOT setup.
- "how do I find interactions for TP53?" → protein-interactions
- "help me research metformin" → drug-research
- "what is EGFR?" → target-research
- "I'm new, can you research diabetes?" → disease-research
- Only route to setup when NO domain entity present ("how do I use this?")
Specificity Rule: More specific beats general.
- "cancer treatment" → precision-oncology (not disease-research)
Data Type Rule: "get/retrieve/fetch" → retrieval skills.
- "get compound structure" → chemical-compound-retrieval (not drug-research)
Still ambiguous: Ask user with AskUserQuestion.
When to Use General Strategies
Only when no specialized skill matches:
- Meta-questions about ToolUniverse itself (no domain entity)
- Custom workflows combining multiple skills
- User explicitly says "don't use specialized skills"
WARNING: "how do I find interactions for TP53?" is NOT a meta-question — route to protein-interactions.
When using general strategies, load references/general-strategies.md and execute them (run actual queries, don't just describe).
Routing Examples
Clear match: "comprehensive research report on breast cancer" → Skill(skill="tooluniverse-disease-research", args="breast cancer")
Ambiguous: "Tell me about aspirin" → AskUserQuestion: drug profile, safety, chemical data, or repurposing?
No match: "How can I find all tools related to proteomics?" → General strategies: run find_tools queries
Domain + setup keyword: "help me understand BRCA1 variants" → Skill(skill="tooluniverse-variant-interpretation", args="BRCA1")