biomedical-knowledge-lookup 1.0.0__py3-none-any.whl

biomedical_knowledge_lookup-1.0.0.dist-info/METADATA

@@ -0,0 +1,289 @@
+Metadata-Version: 2.4
+Name: biomedical-knowledge-lookup
+Version: 1.0.0
+Summary: Unified biological concept lookup across 29+ biomedical knowledge sources including BioPortal, OLS, UMLS, ChEMBL, DisGeNET, and more
+License: MIT
+License-File: LICENSE
+Keywords: biomedical,ontology,knowledge-graph,bioinformatics,semantic-web,rdf,bioportal,ols,umls
+Author: Jonas Heinicke
+Author-email: jonas.heinicke@helmholtz-hzi.de
+Requires-Python: >=3.10,<4.0
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Dist: aiohttp (>=3.9.0,<4.0.0)
+Requires-Dist: backoff (>=2.2.0,<3.0.0)
+Requires-Dist: bioservices (>=1.16.0,<2.0.0)
+Requires-Dist: chembl-webresource-client (>=0.10.9,<0.11.0)
+Requires-Dist: pandas (>=2.0.0,<3.0.0)
+Requires-Dist: pydantic (>=2.0.0,<3.0.0)
+Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
+Requires-Dist: rdflib (>=7.0.0,<8.0.0)
+Requires-Dist: requests (>=2.31.0,<3.0.0)
+Requires-Dist: rich (>=13.0.0,<14.0.0)
+Requires-Dist: setuptools (>=82.0.1,<83.0.0)
+Requires-Dist: tenacity (>=8.2.0,<9.0.0)
+Requires-Dist: typer (>=0.12.0,<1.0.0)
+Requires-Dist: tyto (>=1.4,<2.0)
+Project-URL: Changelog, https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/blob/main/CHANGELOG.md
+Project-URL: Documentation, https://jonasheinickeBio.github.io/biomedical-knowledge-lookup/
+Project-URL: Homepage, https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup
+Project-URL: Issue Tracker, https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/issues
+Project-URL: Repository, https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup
+Description-Content-Type: text/markdown
+
+# 🧬 Biomedical Knowledge Lookup
+
+[![PyPI version](https://badge.fury.io/py/biomedical-knowledge-lookup.svg)](https://pypi.org/project/biomedical-knowledge-lookup/)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Tests](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/actions/workflows/tests.yml/badge.svg)](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/actions/workflows/tests.yml)
+[![Coverage](https://img.shields.io/codecov/c/github/JonasHeinickeBio/biomedical-knowledge-lookup)](https://codecov.io/gh/JonasHeinickeBio/biomedical-knowledge-lookup)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
+[![Documentation](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://jonasheinickeBio.github.io/biomedical-knowledge-lookup/)
+[![PyPI downloads](https://img.shields.io/pypi/dm/biomedical-knowledge-lookup?color=blue)](https://pypi.org/project/biomedical-knowledge-lookup/)
+[![GitHub last commit](https://img.shields.io/github/last-commit/JonasHeinickeBio/biomedical-knowledge-lookup)](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/commits/main)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1234567.svg)](https://doi.org/10.5281/zenodo.1234567)
+
+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.
+
+## ✨ Features
+
+- **🔍 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
+
+## 🚀 Quick Start
+
+### Installation
+
+```bash
+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
+```
+
+### Basic Usage
+
+```python
+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)
+```
+
+### Advanced Usage with Multi-source Annotation
+
+```python
+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)
+```
+
+## 📋 Supported Knowledge Sources
+
+| Source | Description | API Key Required |
+|--------|-------------|------------------|
+| **BioPortal** | NCBI BioPortal ontology repository | Yes |
+| **OLS** | Ontology Lookup Service | No |
+| **UMLS** | Unified Medical Language System | Yes |
+| **ChEMBL** | Chemical database | No |
+| **DisGeNET** | Disease-gene associations | No |
+| **DrugBank** | Drug information database | No |
+| **Ensembl** | Genome annotation database | No |
+| **Gene Ontology** | Molecular function/process/component | No |
+| **HPO** | Human Phenotype Ontology | No |
+| **Mondo** | Mondo Disease Ontology | No |
+| **OpenTargets** | Target-disease associations | No |
+| **PubChem** | Chemical information | No |
+| **Reactome** | Pathway database | No |
+| **UniProt** | Protein sequence database | No |
+| **WikiData** | Structured knowledge base | No |
+| **ZOOMA** | Ontology mapping service | No |
+| **And 13+ more...** | See full list in documentation | Varies |
+
+## 🏗️ Architecture
+
+```
+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
+```
+
+## 📖 Documentation
+
+- **[Getting Started Guide](docs/getting_started.md)**
+- **[API Reference](docs/api_reference.md)**
+- **[Adapter Documentation](docs/adapters/)**
+- **[Examples](examples/)**
+- **[Contributing Guide](CONTRIBUTING.md)**
+
+### Additional Resources
+
+- **[Documentation Improvement Summary](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/wiki/Documentation-Improvement-Summary)**
+- **[Project Overview](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/wiki/Project-Overview)**
+
+### Example Notebooks
+
+Explore interactive examples in the `examples/` directory:
+- Basic concept lookup
+- Multi-source annotation
+- RDF export and knowledge graph construction
+- Performance benchmarking
+
+## 🔧 Configuration
+
+### API Keys
+
+Some sources require API keys. Set them as environment variables:
+
+```bash
+export BIOPORTAL_API_KEY="your_key_here"
+export UMLS_API_KEY="your_key_here"
+# ... etc
+```
+
+Or create a `.env` file:
+
+```env
+BIOPORTAL_API_KEY=your_key_here
+UMLS_API_KEY=your_key_here
+```
+
+### Advanced Configuration
+
+```python
+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)
+```
+
+## 🧪 Testing
+
+```bash
+# 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
+```
+
+## 🤝 Contributing
+
+We welcome contributions! Please see our [Contributing Guide](CONTRIBUTING.md) for details.
+
+### Adding New Adapters
+
+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
+
+### Development Setup
+
+```bash
+git clone https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup.git
+cd biomedical-knowledge-lookup
+poetry install
+poetry run pre-commit install
+```
+
+## 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+- 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
+
+## 📞 Support
+
+- **Issues**: [GitHub Issues](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/JonasHeinickeBio/biomedical-knowledge-lookup/discussions)
+- **Email**: jonas.heinicke@helmholtz-hzi.de
+
+## 🔬 Citation
+
+If you use this library in your research, please cite:
+
+```bibtex
+@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}
+}
+```
+
+---
+
+<p align="center">
+  <img src="https://img.shields.io/github/stars/JonasHeinickeBio/biomedical-knowledge-lookup?style=social" alt="GitHub stars">
+  <img src="https://img.shields.io/github/forks/JonasHeinickeBio/biomedical-knowledge-lookup?style=social" alt="GitHub forks">
+</p>
+
+<p align="center">
+  <em>⭐ Star this repository if you find it useful!</em>
+</p>
+

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+biomedical_knowledge_lookup-1.0.0.dist-info/licenses/LICENSE,sha256=06lTfw5Gb-5nmTaDki-x3jNeqWym5G0jrk-yr8WONEs,1071
+biomedical_knowledge_lookup-1.0.0.dist-info/RECORD,,

biomedical_knowledge_lookup-1.0.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: poetry-core 2.4.0
+Root-Is-Purelib: true
+Tag: py3-none-any

biomedical_knowledge_lookup-1.0.0.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+knowledge-lookup=knowledge_lookup.__main__:app
+

biomedical_knowledge_lookup-1.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Jonas Heinicke
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

knowledge_lookup/__init__.py

@@ -0,0 +1,112 @@
+"""
+Knowledge Lookup Package Initialization
+
+Central lookup system for biological concept integration across multiple knowledge sources.
+"""
+
+from .adapters import (
+    ADAPTER_CLASSES,
+    BioLinkerAdapter,
+    BioOntologyAdapter,
+    BioPortalAdapter,
+    DBpediaAdapter,
+    DisGeNETAdapter,
+    DrugBankAdapter,
+    EBIOLSAdapter,
+    EnsemblAdapter,
+    EUtilsAdapter,
+    GeneOntologyAdapter,
+    HPOAdapter,
+    KEGGAdapter,
+    MondoAdapter,
+    OBOFoundryAdapter,
+    OLSAdapter,
+    OpenTargetsAdapter,
+    OxOAdapter,
+    PubChemAdapter,
+    QuickGOAdapter,
+    ReactomeAdapter,
+    TytoAdapter,
+    UMLSAdapter,
+    UniChemAdapter,
+    UniProtAdapter,
+    WikidataAdapter,
+    ZoomaAdapter,
+)
+from .cache import KnowledgeLookupCache, get_cache, init_cache
+from .central_lookup import CentralKnowledgeLookup
+from .factory import create_knowledge_lookup
+from .models import (
+    ConceptIdentifier,
+    ConceptMapping,
+    ConceptType,
+    KnowledgeSource,
+    LookupConfig,
+    LookupResult,
+    UnifiedConcept,
+)
+from .multi_source_annotator import (
+    AnnotationConfidence,
+    ConceptAgreement,
+    MultiSourceAnnotationResult,
+    MultiSourceAnnotator,
+    SourceAnnotation,
+)
+
+# Make key classes available at package level
+__all__ = [
+    # Main classes
+    "CentralKnowledgeLookup",
+    "create_knowledge_lookup",
+    "MultiSourceAnnotator",
+    # Caching system
+    "KnowledgeLookupCache",
+    "get_cache",
+    "init_cache",
+    # Data models
+    "KnowledgeSource",
+    "ConceptType",
+    "ConceptIdentifier",
+    "ConceptMapping",
+    "UnifiedConcept",
+    "LookupResult",
+    "LookupConfig",
+    # Multi-source annotation
+    "AnnotationConfidence",
+    "SourceAnnotation",
+    "ConceptAgreement",
+    "MultiSourceAnnotationResult",
+    # Adapters
+    "ADAPTER_CLASSES",
+    "UMLSAdapter",
+    "UniChemAdapter",
+    "BioPortalAdapter",
+    "OLSAdapter",
+    "WikidataAdapter",
+    "BioLinkerAdapter",
+    "DBpediaAdapter",
+    "OxOAdapter",
+    "BioOntologyAdapter",
+    "MondoAdapter",
+    "UniProtAdapter",
+    "DisGeNETAdapter",
+    "OpenTargetsAdapter",
+    "ReactomeAdapter",
+    "PubChemAdapter",
+    "DrugBankAdapter",
+    "GeneOntologyAdapter",
+    "HPOAdapter",
+    "OBOFoundryAdapter",
+    "EBIOLSAdapter",
+    "EnsemblAdapter",
+    "KEGGAdapter",
+    "QuickGOAdapter",
+    "ZoomaAdapter",
+    "TytoAdapter",
+    "EUtilsAdapter",
+]
+
+# Package metadata
+__version__ = "1.0.0"
+__author__ = "AID-PAIS Knowledge Graph Team"
+__description__ = "Unified biological concept lookup across multiple knowledge sources"