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

Project description


Curation of Neurodegeneration in BEL (CONIB) Travis CI DOI

This knowledge repository, developed during the Human Brain Pharmacome project, contains documents in Biological Expression Language (BEL) describing neurodegenerative disease phenomena such as tauopathies.

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.). 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()

Contributing

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

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


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Files for hbp-knowledge, version 0.0.7
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Filename, size hbp_knowledge-0.0.7-py3-none-any.whl (11.9 MB) File type Wheel Python version py3 Upload date Hashes View
Filename, size hbp_knowledge-0.0.7.tar.gz (9.2 MB) File type Source Python version None Upload date Hashes View

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