biomapper 0.3.0

A unified Python toolkit for biological data harmonization and ontology mapping

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

pip install biomapper

Development Setup

1. Install Python 3.11 with pyenv (if not already installed):

# 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):

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:

git clone https://github.com/yourusername/biomapper.git
cd biomapper

# Install dependencies with Poetry
poetry install

Quick Start

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

# 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

# Run tests
poetry run pytest

# Run tests with coverage
poetry run pytest --cov=biomapper

Code Quality

# 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 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
• RefMet
• RaMP-DB
• UMLS
• OLS
• BioPortal