This knowledge repository, developed during the Human Brain Pharmacome project, contains documents in Biological Expression Language (BEL) describing neurodegenerative disease phenomena such as tauopathies.
Installation • Usage • Contributing • License
- hbp_knowledge: This folder contains curated BEL documents. Most have been organized by category (protein of interest, biological process of interest, pathway, etc.). Almost 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/conib.
- 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.
Here are a few links for navigating the GitHub issues and pull requests:
hbp_knowledge can be installed from PyPI with the following command:
$ pip install hbp_knowledgeor the latest version can be installed from GitHub with:
$ pip install git+https://github.com/pharmacome/conib.gitThe graph can be loaded with:
import hbp_knowledge
# Get a dictionary of names to graphs
graphs = hbp_knowledge.get_graphs()
# Get all BEL documents as a single graph
graph = hbp_knowledge.get_graph()
# Get all knowledge as INDRA statements
stmts = hbp_knowledge.get_indra_statements()Contributions are welcome! Please submit all pull requests to https://github.com/pharmacome/conib.
- 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.