Skip to main content
Donate to the Python Software Foundation or Purchase a PyCharm License to Benefit the PSF! Donate Now

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

Project description


HBP Knowledge Travis CI DOI

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

InstallationUsageContributingLicense

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.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
hbp_knowledge-0.0.4-py3-none-any.whl (7.9 MB) Copy SHA256 hash SHA256 Wheel py3
hbp_knowledge-0.0.4.tar.gz (7.7 MB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page