ToolUniverse — 1000+ Scientific Tools
You have access to ToolUniverse, a unified ecosystem of 1000+ scientific tools that covers the full spectrum of biomedical research. These tools are pre-integrated in the sandbox and ready to use through three dedicated tools.
When to Use
Use ToolUniverse tools when the user needs:
- Drug Discovery: target identification, compound screening, ADMET prediction, drug safety, drug-drug interactions, drug repurposing
- Protein Analysis: structure retrieval (PDB/AlphaFold), function lookup (UniProt), interaction networks (STRING/BioGRID), therapeutic design
- Genomics: gene expression, GWAS analysis, variant interpretation (ACMG), enrichment analysis, single-cell RNA-seq
- Literature Search: multi-source paper search (PubMed/PubTator/EuropePMC/Semantic Scholar/OpenAlex), systematic reviews
- Clinical: trial matching, guidelines, pharmacovigilance, precision oncology, rare disease diagnosis
- Molecular: docking (Boltz2), SMILES-based property prediction, compound similarity, molecular visualization
- Omics: transcriptomics, proteomics, metabolomics, multi-omics integration, spatial transcriptomics
Three-Step Workflow
Always follow this sequence: Search → Info → Run
Step 1: Search for tools
tooluniverse_search(query="protein structure prediction", limit=5)
This returns a list of matching tools with names and descriptions. Use natural language to describe what you need.
Step 2: Check tool specification
tooluniverse_info(tool_name="UniProt_get_function_by_accession")
This returns the full parameter schema (required/optional args, types, descriptions). Always check this before running a tool to ensure you provide correct arguments.
Step 3: Execute the tool
tooluniverse_run( tool_name="UniProt_get_function_by_accession", arguments='{"accession": "P05067"}' )
The arguments parameter is a JSON string containing the tool's parameters.
Common Tool Examples
Protein & Gene
| Tool | Arguments Example |
|---|---|
UniProt_get_function_by_accession | {"accession": "P05067"} |
UniProt_get_entry_by_accession | {"accession": "P05067"} |
Drug Safety
| Tool | Arguments Example |
|---|---|
FAERS_count_reactions_by_drug_event | {"medicinalproduct": "aspirin"} |
Disease-Target
| Tool | Arguments Example |
|---|---|
OpenTargets_get_associated_targets_by_disease_efoId | {"efoId": "EFO_0000685"} |
Literature
| Tool | Arguments Example |
|---|---|
PubTator_search_publications | {"query": "CRISPR cancer therapy", "limit": 10} |
ADMET Prediction
| Tool | Arguments Example |
|---|---|
ADMETAI_predict_BBB_penetrance | {"smiles": ["CCO"]} |
ADMETAI_predict_toxicity | {"smiles": ["CCO"]} |
Molecular Docking
| Tool | Arguments Example |
|---|---|
boltz2_docking | {"protein_id": "1ABC", "ligand_smiles": "CCO"} |
Multi-Step Research Patterns
Drug Safety Profile
tooluniverse_search("drug adverse events")→ find FAERS toolstooluniverse_run("FAERS_count_reactions_by_drug_event", ...)→ get adverse eventstooluniverse_run("FAERS_get_drug_label_info", ...)→ get drug label
Disease Target Discovery
tooluniverse_run("OpenTargets_get_associated_targets_by_disease_efoId", ...)→ targetstooluniverse_run("UniProt_get_entry_by_accession", ...)→ protein detailstooluniverse_run("PubTator_search_publications", ...)→ supporting literature
Compound Property Analysis
tooluniverse_search("ADMET prediction")→ find prediction tools- Run multiple ADMET predictions (BBB, toxicity, bioavailability, solubility)
- Synthesize results into a compound profile
Tips
- Tool names follow a pattern:
Database_action_description(e.g.,UniProt_get_entry_by_accession) - First call may be slow (~30s) as ToolUniverse initializes; subsequent calls are fast
- Results can be large: focus on the most relevant fields for the user's question
- When unsure about tool name: use
tooluniverse_searchwith a broad query first - Chain multiple tools for comprehensive analysis — combine data from different sources
- API keys are optional: most tools work without keys, but some (NVIDIA, HuggingFace) may need them for specific functionality
