A unified Python library for biological concept lookup across 29+ biomedical knowledge sources including BioPortal, OLS, UMLS, ChEMBL, DisGeNET, and more. Built for bioinformatics researchers, knowledge graph developers, and biomedical data scientists.

• 🔍 29+ Knowledge Sources: Comprehensive coverage of biomedical ontologies and databases
• ⚡ Unified API: Single interface for all sources with consistent results
• 🔄 Multi-source Annotation: Cross-reference concepts across multiple databases
• 📊 RDF Export: Convert results to RDF format for knowledge graphs
• 💾 Intelligent Caching: Built-in caching system for performance optimization
• 🔄 Async Support: Asynchronous operations for scalable applications
• 🧪 Comprehensive Testing: Full test suite with unit and integration tests
• 📚 Rich Documentation: Extensive examples and API documentation

pip install biomedical-knowledge-lookup
# or
poetry add biomedical-knowledge-lookup
# or from source
git clone https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup.git
cd biomedical-knowledge-lookup
poetry install

from knowledge_lookup import CentralKnowledgeLookup, KnowledgeSource

# Initialize the lookup system
lookup = CentralKnowledgeLookup()

# Search for concepts across multiple sources
results = await lookup.search_concepts(
    "diabetes mellitus",
    sources=[KnowledgeSource.BIOPORTAL, KnowledgeSource.OLS, KnowledgeSource.UMLS]
)

# Get detailed information about a specific concept
concept_details = await lookup.get_concept_details("DOID:9351")

# Export results to RDF
rdf_graph = lookup.export_to_rdf(results)

from knowledge_lookup import MultiSourceAnnotator

# Annotate text with concepts from multiple sources
annotator = MultiSourceAnnotator()
annotations = await annotator.annotate_text(
    "Type 2 diabetes is associated with insulin resistance",
    confidence_threshold=0.7
)

# Get consensus annotations across sources
consensus = annotator.get_consensus_annotations(annotations)

knowledge_lookup/
├── adapters/           # Individual source adapters
├── models.py          # Data models and enums
├── central_lookup.py  # Main lookup coordinator
├── multi_source_annotator.py  # Cross-source annotation
├── rdf_converter.py   # RDF export utilities
├── cache.py          # Caching system
└── base.py           # Abstract base classes

• Getting Started Guide
• API Reference
• Adapter Documentation
• Examples
• Contributing Guide

• Documentation Improvement Summary
• Project Overview

Explore interactive examples in the examples/ directory:

• Basic concept lookup
• Multi-source annotation
• RDF export and knowledge graph construction
• Performance benchmarking

Some sources require API keys. Set them as environment variables:

export BIOPORTAL_API_KEY="your_key_here"
export UMLS_API_KEY="your_key_here"
# ... etc

Or create a .env file:

BIOPORTAL_API_KEY=your_key_here
UMLS_API_KEY=your_key_here

from knowledge_lookup import LookupConfig

config = LookupConfig(
    rate_limits={
        KnowledgeSource.BIOPORTAL: 10,  # requests per second
        KnowledgeSource.OLS: 20,
    },
    cache_enabled=True,
    cache_dir="./cache"
)

lookup = CentralKnowledgeLookup(config)

# Run all tests
poetry run pytest

# Run specific test categories
poetry run pytest -m "unit"        # Unit tests only
poetry run pytest -m "integration" # Integration tests
poetry run pytest -m "not slow"    # Skip slow tests

# Run with coverage
poetry run pytest --cov=knowledge_lookup

We welcome contributions! Please see our Contributing Guide for details.

1. Extend KnowledgeSourceAdapter in base.py
2. Implement required methods: search_concepts(), get_concept_details()
3. Add to adapters/__init__.py
4. Add tests in tests/unit/test_adapters/
5. Update documentation

git clone https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup.git
cd biomedical-knowledge-lookup
poetry install
poetry run pre-commit install

This project is licensed under the MIT License - see the LICENSE file for details.

• Built upon the AID-PAIS Knowledge Graph project
• Thanks to all contributors and the biomedical research community
• Special thanks to the maintainers of the various knowledge sources

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Email: jonas.heinicke@helmholtz-hzi.de

If you use this library in your research, please cite:

@software{heinicke_biomedical_knowledge_lookup_2025,
  author = {Heinicke, Jonas},
  title = {Biomedical Knowledge Lookup: Unified biological concept lookup across 29+ biomedical knowledge sources},
  url = {https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup},
  version = {1.0.0},
  year = {2025}
}

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