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Curation of Neurodegeneration in BEL (CONIB)

License: Creative Commons Attribution 4.0 International

Python 0.18% Jupyter Notebook 99.82%

conib's Introduction

Curation of Neurodegeneration in BEL (CONIB)

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

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.

Curation Planning

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

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/conib.git

Usage

The 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()