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Welcome to ChemGraphBuilder DOI

The chemgraphbuilder package is a specialized tool designed for researchers in bioinformatics, cheminformatics, and computational biology. It enables the construction of detailed knowledge graphs that map the complex interactions between chemical compounds, genes, proteins, and bioassays. These knowledge graphs are critical for visualizing and understanding the multifaceted relationships in biochemical networks.

At its core, chemgraphbuilder integrates data from PubChem and utilize Neo4j, creating nodes that represent key entities such as compounds, genes, proteins, and bioassays. It further enriches these graphs by incorporating various relationships, including:

  • BioAssay-Compound Relationships: Capturing the interactions where bioassays evaluate the effects of specific compounds. This is crucial for understanding the efficacy and mechanism of action of pharmaceuticals.
  • BioAssay-Gene Relationships: Documenting instances where bioassays study specific genes, providing valuable data on gene function and regulation.
  • Gene-Protein Relationships: Mapping the connections where genes encode proteins, providing insights into genetic regulation and protein function.
  • Compound-Gene Interactions: Detailing how compounds interact with genes, categorized into various interaction types such as Inhibitors, Inactivators, Activators, Inducers, Substrates, Ligands, and Inactive compounds. This classification aids in understanding gene regulation, drug mechanisms, and potential therapeutic applications.
  • Compound Similarities: Highlighting chemical similarities between compounds, which can suggest similar biological activities or shared molecular properties.
  • Compound Co-occurrence: Identifying instances where compounds or genes co-occur in scientific literature, indicating potential interactions or co-regulation.

The chemgraphbuilder package is versatile and can be utilized both in Python code and via the command line interface. For practical examples and use cases, please refer to the "Usage Examples" section available in the menu on the left sidebar. For comprehensive documentation of the main classes and their functionalities, visit the Documentation Page.

Installation:

You can visit this page to get the installation command: PyPI Project Page

!pip install chemgraphbuilder

Project layout

chemgraphbuilder/                 # Main source code directory for the chemgraphbuilder package.
build/
    lib/chemgraphbuilder/         # Build artifacts and main package files.
chemgraphbuilder.egg-info/        # Package metadata and distribution information.
dist/                             # Distribution packages (.tar.gz, .whl).
docs/                             # Documentation files for the project.
    index.md                      # Documentation homepage.
    ...                           # Other markdown pages, images, and files.
examples/                         # Example scripts and usage demonstrations.
__pycache__/                      # Compiled Python bytecode files.
.gitignore                        # Specifies files and directories to be ignored by Git.
LICENSE                           # License file detailing the terms of use.
README.md                         # Project overview and instructions.
mkdocs.yml                        # Configuration file for MkDocs.
requirements.txt                  # List of Python dependencies for the project.
setup.py                          # Setup script for packaging and distribution.

Welcome to the gallery. Here are some screenshots from the Knowledge Graph built using this package: