tooluniverse

name

tooluniverse

description

Router skill for ToolUniverse tasks. First checks if specialized tooluniverse skills (58+ skills covering disease/drug/target research, clinical decision support, genomics, epigenomics, chemical safety, systems biology, and more) can solve the problem, then falls back to general strategies for using 1400+ scientific tools. Covers tool discovery, multi-hop queries, comprehensive research workflows, disambiguation, evidence grading, and report generation. Use when users need to research any scientific topic, find biological data, or explore drug/target/disease relationships.

ToolUniverse Router

Route user questions to specialized skills. If no skill matches, use general strategies from references/general-strategies.md.

Routing Workflow

1. Extract keywords from user's question
2. Scan routing table below for keyword matches
3. 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)
4. 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

1. 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?")

2. Specificity Rule: More specific beats general.

   • "cancer treatment" → precision-oncology (not disease-research)

3. Data Type Rule: "get/retrieve/fetch" → retrieval skills.

   • "get compound structure" → chemical-compound-retrieval (not drug-research)

4. 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")