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

Content

conib: 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.

Curation Planning

Here are a few links for navigating the GitHub issues and pull requests:

Installation

conib can be installed from PyPI with the following command:

$ pip install conib

or the latest version can be installed from GitHub with:

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

Usage

The graph can be loaded with:

import conib
# Get a dictionary of names to graphs
graphs = conib.get_graphs()
# Get all BEL documents as a single graph
graph = conib.get_graph()
# Get all knowledge as INDRA statements
stmts = conib.get_indra_statements()

The latest compiled version of the graph can be retrieved remotely with:

import requests
import pybel
URL = 'https://github.com/pharmacome/conib/raw/master/conib/_cache.bel.nodelink.json'
res_json = requests.get(URL).json()
graph = pybel.from_nodelink(res_json)
# Get INDRA statements
from indra.sources.bel import process_pybel_graph
pbp = process_pybel_graph(graph)
pbp.get_statements()
stmts = pbp.statements
# Quick version
stmts = pybel.to_indra_statements(graph)

Contributing

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

License