tooluniverse by mims-harvard/tooluniverse
npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse将用户问题路由至专用技能。若无匹配技能,则使用参考资料/通用策略.md中的通用策略。
关键:实际调用技能——不要向用户描述技能或展示路由表。
语言:如果用户使用非英语语言提问,提取关键词用于路由,但用用户的语言进行回应。所有工具调用均使用英语术语。
| 关键词 | 操作 |
|---|---|
| "get", "retrieve", "chemical compound ", "PubChem", "ChEMBL", "drug molecule", "SMILES", "InChI" |
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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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "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") |
| 关键词 | 操作 |
|---|---|
| "pathogen ", "infectious disease", "outbreak", "emerging infection", "novel virus" | Skill(skill="tooluniverse-infectious-disease") |
| 关键词 | 操作 |
|---|---|
| "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") |
仅在无专用技能匹配时使用:
警告:"how do I find interactions for TP53?" 不是元问题——应路由至 protein-interactions。
使用通用策略时,加载参考资料/通用策略.md并执行它们(运行实际查询,不要仅描述)。
明确匹配:"comprehensive research report on breast cancer" → Skill(skill="tooluniverse-disease-research", args="breast cancer")
意图模糊:"Tell me about aspirin" → AskUserQuestion: 药物概况、安全性、化学数据,还是药物再利用?
无匹配:"How can I find all tools related to proteomics?" → 通用策略:运行 find_tools 查询
领域 + 设置关键词:"help me understand BRCA1 variants" → Skill(skill="tooluniverse-variant-interpretation", args="BRCA1")
每周安装量
175
代码库
GitHub 星标数
1.2K
首次出现
2026年2月4日
安全审计
安装于
codex167
opencode165
gemini-cli162
github-copilot159
amp154
kimi-cli153
Route user questions to specialized skills. If no skill matches, use general strategies from references/general-strategies.md.
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.
| 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") |
| 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") |
| 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") |
| " ", "precision oncology", "tumor mutation", "targeted therapy", "EGFR", "KRAS", "BRAF" |
| 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") |
| " ", "polypharmacology", "compound-target network", "multi-target" |
| 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]" |
| 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" |
| 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" |
| 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") |
| Keywords | Action |
|---|---|
| "pathogen ", "infectious disease", "outbreak", "emerging infection", "novel virus" | Skill(skill="tooluniverse-infectious-disease") |
| 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") |
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.
Specificity Rule : More specific beats general.
Data Type Rule : "get/retrieve/fetch" → retrieval skills.
Still ambiguous : Ask user with AskUserQuestion.
Only when no specialized skill matches:
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).
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")
Weekly Installs
175
Repository
GitHub Stars
1.2K
First Seen
Feb 4, 2026
Security Audits
Gen Agent Trust HubPassSocketPassSnykWarn
Installed on
codex167
opencode165
gemini-cli162
github-copilot159
amp154
kimi-cli153
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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") |
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") |
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") |
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") |
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") |