ToolUniverse — 1000+ Scientific Tools

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

Drug Safety

Disease-Target

Literature

ADMET Prediction

Molecular Docking

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