Installation¶

Requirements¶

Python 3.10 or higher
pip or uv package manager

Basic Installation¶

Install biodbs using pip:

pip install biodbs

Or using uv:

uv add biodbs

Optional Dependencies¶

biodbs has optional dependencies for additional features:

Graph Module¶

For knowledge graph exports (NetworkX, RDF):

pip install biodbs[graph]

Or using uv:

uv add biodbs --optional graph

Development Installation¶

For development, clone the repository and install in editable mode:

git clone https://github.com/qwerty239qwe/biodbs.git
cd biodbs
pip install -e ".[dev]"

Or using uv:

git clone https://github.com/qwerty239qwe/biodbs.git
cd biodbs
uv sync --all-extras

Verifying Installation¶

Verify your installation by running:

import biodbs
print(biodbs.__version__)

# Test a simple API call
from biodbs.fetch import uniprot_get_entry
entry = uniprot_get_entry("P04637")
print(entry.entries[0].protein_name)

Dependencies¶

Core dependencies (installed automatically):

Package	Purpose
`pandas`	DataFrame operations
`polars`	Alternative DataFrame library
`pydantic`	Data validation and models
`requests`	HTTP client for API calls
`scipy`	Statistical functions for ORA

Optional dependencies (graph module):

Package	Purpose
`networkx`	Graph algorithms and NetworkX export
`rdflib`	RDF/Turtle export