tooluniverse-sdk

Agent Building

Build AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` function API, direct class instantiation), tool loading, batch execution, MCP server integration, and embedding-based tool search. Use for SDK programming, custom tool composition, benchmarking pipelines, and integrating ToolUniverse into research workflows.

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ToolUniverse Python SDK

3 calling patterns -- start with pattern 1:

tu.run({"name": ..., "arguments": ...}) -- single tool call, dict API (most portable)
tu.tools.ToolName(param=value) -- function API (recommended for interactive use)
Direct class instantiation -- advanced, bypasses caching/hooks

Installation

pip install tooluniverse              # Standard
pip install tooluniverse[embedding]   # Embedding search (GPU)
pip install tooluniverse[all]         # All features

export OPENAI_API_KEY="sk-..."  # Required for LLM tool search
export NCBI_API_KEY="..."       # Optional

Quick Start

from tooluniverse import ToolUniverse

tu = ToolUniverse()
tu.load_tools()  # REQUIRED before any tool call

# Find tools
tools = tu.run({"name": "Tool_Finder_Keyword", "arguments": {"description": "protein structure", "limit": 10}})

# Execute (dict API)
result = tu.run({"name": "UniProt_get_entry_by_accession", "arguments": {"accession": "P05067"}})

# Execute (function API)
result = tu.tools.UniProt_get_entry_by_accession(accession="P05067")

Core Patterns

Batch Execution

calls = [
    {"name": "UniProt_get_entry_by_accession", "arguments": {"accession": "P05067"}},
    {"name": "UniProt_get_entry_by_accession", "arguments": {"accession": "P12345"}},
]
results = tu.run_batch(calls)

Scientific Workflow

def drug_discovery_pipeline(disease_id):
    tu = ToolUniverse(use_cache=True)
    tu.load_tools()
    try:
        targets = tu.tools.OpenTargets_get_associated_targets_by_disease_efoId(efoId=disease_id)
        compound_calls = [
            {"name": "ChEMBL_search_molecule_by_target",
             "arguments": {"target_id": t['id'], "limit": 10}}
            for t in targets['data'][:5]
        ]
        compounds = tu.run_batch(compound_calls)
        return {"targets": targets, "compounds": compounds}
    finally:
        tu.close()

Configuration

# Caching
tu = ToolUniverse(use_cache=True)
stats = tu.get_cache_stats()
tu.clear_cache()

# Hooks (auto-summarization of large outputs)
tu = ToolUniverse(hooks_enabled=True)

# Load specific categories
tu.load_tools(categories=["proteins", "drugs"])

Critical Notes

Always call load_tools() before using any tools
Tool Finder returns nested structure: access via tools['tools'] after isinstance(tools, dict) check
Tool names are case-sensitive: UniProt_get_entry_by_accession not uniprot_get_...
Check required params: tu.all_tool_dict["ToolName"]['parameter'].get('required', [])
Cache deterministic calls (ML predictions, DB queries); don't cache real-time data

Error Handling

from tooluniverse.exceptions import ToolError, ToolUnavailableError, ToolValidationError

try:
    result = tu.tools.some_tool(param="value")
except ToolUnavailableError:
    ...  # Tool service down
except ToolValidationError as e:
    tool_info = tu.all_tool_dict["some_tool"]
    print(f"Required: {tool_info['parameter'].get('required', [])}")

Tool Categories

Category	Tools	Use Cases
Proteins	UniProt, RCSB PDB, AlphaFold	Protein analysis, structure
Drugs	DrugBank, ChEMBL, PubChem	Drug discovery, compounds
Genomics	Ensembl, NCBI Gene, gnomAD	Gene analysis, variants
Diseases	OpenTargets, ClinVar	Disease-target associations
Literature	PubMed, Europe PMC	Literature search
ML Models	ADMET-AI, AlphaFold	Predictions, modeling
Pathways	KEGG, Reactome	Pathway analysis

Resources

Docs: https://zitniklab.hms.harvard.edu/ToolUniverse/
GitHub: https://github.com/mims-harvard/ToolUniverse
See REFERENCE.md for detailed guides.