HBP Knowledge

This repository contains knowledge curated in Biological Expression Language (BEL) for the Human Brain Pharmacome (HBP) project.

Installation • Usage • Contributing • License

Content

• hbp_knowledge: This folder contains curated BEL documents. Most have been organized by category (protein of interest, biological process of interest, pathway, etc.). AMost BEL documents correspond to a single publication, but a select few contain content from several due to topic-based curation.
• docs: This folder contains automatically generated HTML summaries of the content that can best be accesed through https://pharmacome.github.io/knowledge.
• notebooks: This folder contains various Jupyter notebooks associated with the repository. Since many of them use PyBEL-Jupyter, they may be best viewed using NBViewer.

Installation

hbp_knowledge can be installed from PyPI with the following command:

$ pip install hbp_knowledge

or the latest version can be installed from GitHub with:

$ pip install git+https://github.com/pharmacome/knowledge.git

Usage

The graph can be loaded with:

from hbp_knowledge import get_graphs
from pybel import union

# Get all graphs
graphs = get_graphs()

# Combine them all using pybel.union
graph = union(graphs.values())

Contributing

Contributions are welcome! Please submit all pull requests to https://github.com/pharmacome/knowledge.

License

• BEL scripts in this repository are licensed under the CC BY 4.0 license.
• Python source code in this repository is licensed under the MIT license.