Skip to content

Welcome to BioEPIC Skills

A Python library designed to simplify various research tasks for users looking to extract and prepare structured data from scientific literature for use with the EcoSIM model.

Features

  • 🔍 API Search: Flexible search and query capabilities
  • 🔐 Authentication: Secure API authentication handling
  • 📊 Data Processing: Utilities for data transformation and analysis
  • 🧪 Testing: Comprehensive test suite
  • 📚 Documentation: Complete API reference and user guides

Overview

BioEPIC Skills provides a collection of general-purpose functions that facilitate easy access, manipulation, and analysis of biological data through APIs.

Key Components

  • APIBase: Base class for API interactions with environment configuration
  • APISearch: Search and retrieve data from API collections
  • BioEPICAuth: Authentication handler with token management
  • DataProcessing: Data transformation and analysis utilities

Installation

Install from source:

git clone https://github.com/bioepic-data/bioepic_skills.git
cd bioepic_skills
pip install -e ".[dev]"

Or via pip (once published):

pip install bioepic_skills

Quick Example

from bioepic_skills.api_search import APISearch
from bioepic_skills.data_processing import DataProcessing

# Create clients
api_client = APISearch(collection_name="samples")
dp = DataProcessing()

# Get records
records = api_client.get_records(max_page_size=10)

# Convert to DataFrame
df = dp.convert_to_df(records)
print(df.head())

Getting Help

License

This project is licensed under the BSD License. See the LICENSE file for details.