EnrichKit DB

Introduction

This repo contains codes for the data curation pipeline for EnrichKit (Web App implementation & Python implementation). We collected publicly available data set to form a portable sqlite object. Following is the database schema:

The sqlite object is available to download via Zenodo.

The DOI of this sqlite object is - doi.org/10.5281/zenodo.10257552

Usage

• Direct download from Zenodo and establish connections with SQLite

• In addition to download the sqlite object, you may replicate such a sqlite database by following:

1. Clone this repo and create an conda virtual environment using conda env create -f environment.yml
2. Adjust the content in config.py and create_db.py to fit your purpose.
3. run python3 create_db.py

Note:

1. The current version is created with python3.12
2. There is a step in the process where gene ID will be compare to online information in a web-scraping style, this is an I/O bound task which are potentially time-consuming, e.g., this current version used 12 hours with 64 cores.

Update Info & Citation

Last updated on 01/15/2024.

Citation: Liu, L., & Peñagaricano, F. (2024). EnrichKit: a multi-omics tool for livestock research (0.1.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10535657