tooluniverse

name	tooluniverse
description	Access 1000+ scientific tools through ToolUniverse for drug discovery, protein analysis, genomics, literature search, clinical data, ADMET prediction, molecular docking, and more. Use when the user needs biomedical or scientific research capabilities.

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

1. tooluniverse_search("drug adverse events") → find FAERS tools
2. tooluniverse_run("FAERS_count_reactions_by_drug_event", ...) → get adverse events
3. tooluniverse_run("FAERS_get_drug_label_info", ...) → get drug label

Disease Target Discovery

1. tooluniverse_run("OpenTargets_get_associated_targets_by_disease_efoId", ...) → targets
2. tooluniverse_run("UniProt_get_entry_by_accession", ...) → protein details
3. tooluniverse_run("PubTator_search_publications", ...) → supporting literature

Compound Property Analysis

1. tooluniverse_search("ADMET prediction") → find prediction tools
2. Run multiple ADMET predictions (BBB, toxicity, bioavailability, solubility)
3. 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_search with 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