Skip to content

About

About the chemgraphbuilder Package

The chemgraphbuilder package is a powerful tool designed to facilitate the construction of knowledge graphs that represent complex chemical-gene interactions. This package is ideal for researchers and data scientists working in the fields of bioinformatics, cheminformatics, and computational biology. By providing a structured framework for integrating data on compounds, genes, proteins, and bioassays, chemgraphbuilder helps uncover the intricate relationships between these entities.

Key features include:

  • Node Representation: Incorporates diverse nodes such as compounds, genes, proteins, and bioassays.
  • Comprehensive Relationships: Maps out various interactions, including gene-protein relationships, bioassay-gene relationships, bioassay-compound relationships, compound similarities, compound co-occurrences in literature, and more nuanced interactions like inhibitor, activator, ligand, and other roles between compounds and genes.
  • Data Integration: The knowledge graph schema is designed to support the integration of additional data sources, enhancing the depth and accuracy of the knowledge graph.
  • Command Line and Programmatic Access: Provides flexibility in usage, allowing for integration into larger workflows or standalone analyses.

About the Author

Asmaa Ali Abdelwahab is a research data scientisy and bioinformatician with extensive experience in data science, particularly in the realm of computational drug design and toxicology. Her work is focused on leveraging artificial intelligence and bioinformatics to have valuable contributions in precision medicine and precision toxicology.

With a commitment to open science, Asmaa is passionate about making her work accessible to the broader scientific community, as exemplified by the chemgraphbuilder package. This tool is part of her broader effort to democratize access to advanced data analysis tools in the life sciences, promoting greater collaboration and innovation in the field.

Author LinkedIn Profile: https://www.linkedin.com/in/asmaa-a-abdelwahab/.

ChemGraphBuilder GitHub: https://github.com/asmaa-a-abdelwahab/ChemGraphBuilder.