hbp-knowledge 0.0.4

Knowledge curated in BEL from full text during the Human Brain Pharmacome project

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.