# biomapper
A unified Python toolkit for biological data harmonization and ontology mapping. `biomapper` provides a single interface for standardizing identifiers and mapping between various biological ontologies, making multi-omic data integration more accessible and reproducible.
## Features
### Core Functionality
- **ID Standardization**: Unified interface for standardizing biological identifiers
- **Ontology Mapping**: Comprehensive ontology mapping using major biological databases
- **Data Validation**: Robust validation of input data and mappings
- **Extensible Architecture**: Easy integration of new data sources and mapping services
### Supported Systems
#### ID Standardization Tools
- BridgeDb
- RefMet
- RaMP-DB
#### Ontology Mapping Services
- UMLS Metathesaurus
- Ontology Lookup Service (OLS)
- BioPortal
## Installation
### Using pip
```bash
pip install biomapper
```
### Development Setup
1. Install Python 3.11 with pyenv (if not already installed):
```bash
# Install pyenv dependencies
sudo apt-get update
sudo apt-get install -y make build-essential libssl-dev zlib1g-dev \
libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev \
libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev python3-openssl
# Install pyenv
curl https://pyenv.run | bash
# Add to your shell configuration
echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc
echo 'command -v pyenv >/dev/null || export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc
echo 'eval "$(pyenv init -)"' >> ~/.bashrc
# Reload shell configuration
source ~/.bashrc
# Install Python 3.11
pyenv install 3.11.7
pyenv local 3.11.7
```
2. Install Poetry (if not already installed):
```bash
curl -sSL https://install.python-poetry.org | python3 -
# Add Poetry to your PATH
echo 'export PATH="$HOME/.local/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc
```
3. Clone and set up the project:
```bash
git clone https://github.com/yourusername/biomapper.git
cd biomapper
# Install dependencies with Poetry
poetry install
```
## Quick Start
```python
from biomapper import AnalyteMetadata
from biomapper.standardization import BridgeDBHandler, RaMPClient
# Example 1: Using BridgeDB
# Initialize metadata handler
metadata = AnalyteMetadata()
# Create standardization handler
bridge_handler = BridgeDBHandler()
# Process identifiers
results = bridge_handler.standardize(["P12345", "Q67890"])
# Example 2: Using RaMP-DB
# Initialize the RaMP client
ramp_client = RaMPClient()
# Get database versions
versions = ramp_client.get_source_versions()
# Get pathways for metabolites
# Example: Get pathways for Creatine (HMDB0000064)
pathways = ramp_client.get_pathways_from_analytes(["hmdb:HMDB0000064"])
```
## Development
### Using Poetry
```bash
# Activate virtual environment
poetry shell
# Run a command in the virtual environment
poetry run python script.py
# Add a new dependency
poetry add package-name
# Add a development dependency
poetry add --group dev package-name
# Update dependencies
poetry update
# Show currently installed packages
poetry show
# Build the package
poetry build
```
### Running Tests
```bash
# Run tests
poetry run pytest
# Run tests with coverage
poetry run pytest --cov=biomapper
```
### Code Quality
```bash
# Format code with black
poetry run black .
# Run linting
poetry run flake8 .
# Type checking
poetry run mypy .
```
## Project Structure
```
biomapper/
├── biomapper/ # Main package directory
│ ├── core/ # Core functionality
│ │ ├── metadata.py # Metadata handling
│ │ └── validators.py # Data validation
│ ├── standardization/# ID standardization components
│ ├── mapping/ # Ontology mapping components
│ ├── utils/ # Utility functions
│ └── schemas/ # Data schemas and models
├── tests/ # Test files
├── docs/ # Documentation
├── scripts/ # Utility scripts
├── pyproject.toml # Poetry configuration and dependencies
└── poetry.lock # Lock file for dependencies
```
## License
This project is licensed under the Apache 2.0 License - see the [LICENSE](LICENSE) file for details.
## Support
For support, please open an issue in the GitHub issue tracker.
## Roadmap
- [ ] Initial release with core functionality
- [ ] Add support for additional ontology services
- [ ] Implement caching layer
- [ ] Add batch processing capabilities
- [ ] Develop REST API interface
## Acknowledgments
- [BridgeDb](https://www.bridgedb.org/)
- [RefMet](https://refmet.metabolomicsworkbench.org/)
- [RaMP-DB](http://rampdb.org/)
- [UMLS](https://www.nlm.nih.gov/research/umls/index.html)
- [OLS](https://www.ebi.ac.uk/ols/index)
- [BioPortal](https://bioportal.bioontology.org/)
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"description": "# biomapper\n\nA unified Python toolkit for biological data harmonization and ontology mapping. `biomapper` provides a single interface for standardizing identifiers and mapping between various biological ontologies, making multi-omic data integration more accessible and reproducible.\n\n## Features\n\n### Core Functionality\n- **ID Standardization**: Unified interface for standardizing biological identifiers\n- **Ontology Mapping**: Comprehensive ontology mapping using major biological databases\n- **Data Validation**: Robust validation of input data and mappings\n- **Extensible Architecture**: Easy integration of new data sources and mapping services\n\n### Supported Systems\n\n#### ID Standardization Tools\n- BridgeDb\n- RefMet\n- RaMP-DB\n\n#### Ontology Mapping Services\n- UMLS Metathesaurus\n- Ontology Lookup Service (OLS)\n- BioPortal\n\n## Installation\n\n### Using pip\n```bash\npip install biomapper\n```\n\n### Development Setup\n\n1. 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Clone and set up the project:\n```bash\ngit clone https://github.com/yourusername/biomapper.git\ncd biomapper\n\n# Install dependencies with Poetry\npoetry install\n```\n\n## Quick Start\n\n```python\nfrom biomapper import AnalyteMetadata\nfrom biomapper.standardization import BridgeDBHandler, RaMPClient\n\n# Example 1: Using BridgeDB\n# Initialize metadata handler\nmetadata = AnalyteMetadata()\n\n# Create standardization handler\nbridge_handler = BridgeDBHandler()\n\n# Process identifiers\nresults = bridge_handler.standardize([\"P12345\", \"Q67890\"])\n\n# Example 2: Using RaMP-DB\n# Initialize the RaMP client\nramp_client = RaMPClient()\n\n# Get database versions\nversions = ramp_client.get_source_versions()\n\n# Get pathways for metabolites\n# Example: Get pathways for Creatine (HMDB0000064)\npathways = ramp_client.get_pathways_from_analytes([\"hmdb:HMDB0000064\"])\n```\n\n## Development\n\n### Using Poetry\n\n```bash\n# Activate virtual environment\npoetry shell\n\n# Run a command in the virtual environment\npoetry run python script.py\n\n# Add a new dependency\npoetry add package-name\n\n# Add a development dependency\npoetry add --group dev package-name\n\n# Update dependencies\npoetry update\n\n# Show currently installed packages\npoetry show\n\n# Build the package\npoetry build\n```\n\n### Running Tests\n```bash\n# Run tests\npoetry run pytest\n\n# Run tests with coverage\npoetry run pytest --cov=biomapper\n```\n\n### Code Quality\n```bash\n# Format code with black\npoetry run black .\n\n# Run linting\npoetry run flake8 .\n\n# Type checking\npoetry run mypy .\n```\n\n## Project Structure\n\n```\nbiomapper/\n\u251c\u2500\u2500 biomapper/ # Main package directory\n\u2502 \u251c\u2500\u2500 core/ # Core functionality\n\u2502 \u2502 \u251c\u2500\u2500 metadata.py # Metadata handling\n\u2502 \u2502 \u2514\u2500\u2500 validators.py # Data validation\n\u2502 \u251c\u2500\u2500 standardization/# ID standardization components\n\u2502 \u251c\u2500\u2500 mapping/ # Ontology mapping components\n\u2502 \u251c\u2500\u2500 utils/ # Utility functions\n\u2502 \u2514\u2500\u2500 schemas/ # Data schemas and models\n\u251c\u2500\u2500 tests/ # Test files\n\u251c\u2500\u2500 docs/ # Documentation\n\u251c\u2500\u2500 scripts/ # Utility scripts\n\u251c\u2500\u2500 pyproject.toml # Poetry configuration and dependencies\n\u2514\u2500\u2500 poetry.lock # Lock file for dependencies\n```\n\n## License\n\nThis project is licensed under the Apache 2.0 License - see the [LICENSE](LICENSE) file for details.\n\n## Support\n\nFor support, please open an issue in the GitHub issue tracker.\n\n## Roadmap\n\n- [ ] Initial release with core functionality\n- [ ] Add support for additional ontology services\n- [ ] Implement caching layer\n- [ ] Add batch processing capabilities\n- [ ] Develop REST API interface\n\n## Acknowledgments\n\n- [BridgeDb](https://www.bridgedb.org/)\n- [RefMet](https://refmet.metabolomicsworkbench.org/)\n- [RaMP-DB](http://rampdb.org/)\n- [UMLS](https://www.nlm.nih.gov/research/umls/index.html)\n- [OLS](https://www.ebi.ac.uk/ols/index)\n- [BioPortal](https://bioportal.bioontology.org/)",
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