biomapper 0.3.3

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 and AI-powered techniques
• 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

• RaMP-DB: Integration with the Rapid Mapping Database for metabolites and pathways

Mapping Services

• ChEBI: Chemical Entities of Biological Interest database integration
• UniChem: Cross-referencing of chemical structure identifiers
• UniProt: Protein-focused mapping capabilities
• RefMet: Reference list of metabolite names and identifiers
• RAG-Based Mapping: AI-powered mapping using Retrieval Augmented Generation
• Multi-Provider RAG: Combining multiple data sources for improved mapping accuracy

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.mapping import UniProtFocusedMapper, MetaboliteNameMapper
from biomapper.standardization import RaMPClient

# Example 1: Using UniProt-focused mapping
uniprot_mapper = UniProtFocusedMapper()
protein_mapping = uniprot_mapper.map_identifier("P12345")

# Example 2: Using Metabolite Name Mapping
metabolite_mapper = MetaboliteNameMapper()
metabolite_mapping = metabolite_mapper.map_name("glucose")

# Example 3: 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"])

# Example 4: Using RAG-based mapping
from biomapper.mapping import RagMapper

rag_mapper = RagMapper()
rag_results = rag_mapper.map_name("alpha-D-glucose")

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
• Implement RAG-based mapping capabilities
• Add support for major chemical/biological databases (ChEBI, UniChem, UniProt)
• Add caching layer for improved performance
• Expand RAG capabilities with more specialized models
• Add batch processing capabilities
• Develop REST API interface

Acknowledgments

• RaMP-DB
• ChEBI
• UniChem
• UniProt
• RefMet