pyBioDataFuse Documentation

Current version: 1.3.1-dev

💪 Getting Started

We introduce BioDataFuse, a query-based Python tool for seamless integration of biomedical databases. BioDataFuse establishes a modular framework for efficient data wrangling, enabling context-specific knowledge graph creation and supporting graph-based analyses. With a user-friendly interface, it enables users to dynamically create knowledge graphs from their input data. Supported by a robust Python package, pyBiodatafuse, this tool excels in data harmonization, aggregating diverse sources through modular queries. Moreover, BioDataFuse provides plugin capabilities for Cytoscape and Neo4j, allowing local graph hosting. Ongoing refinements enhance the graph utility through tasks like link prediction, making BioDataFuse a versatile solution for efficient and effective biological data integration.

Getting Started

• Installation
• Core Utilities
  • Data Loaders
  • ID Mapping
  • Homologs
  • Annotation Orchestrator
  • Utility Functions
• Data sources
  • Bgee
  • DisGeNET
  • MolMeDB
  • OpenTargets
  • StringDB
  • Wikidata
  • WikiPathways
  • MINERVA
  • AOP-Wiki
  • IntAct
  • KEGG
  • PubChem
  • CompoundWiki
  • gProfiler
  • TFLink
  • MitoCarta
• Data Analysis & Visualization
  • Visualization Utilities
  • Literature Explorer
  • Patent Explorer
  • Graph Summary
• Graph Plotters
  • Graph Generator
  • Graph Savers
  • Cytoscape
  • Neo4J
  • RDF and GraphDB
  • RDF Utilities

Indices and Tables

• Index

• Module Index

• Search Page

⚖️ License

The code in this package is licensed under the MIT License.

📖 Citation

The work was started as part of the Elixir BioHackathon 2023 integrating and bringing together multiple Core Data Resources together.

Gadiya, Y., Ammar, A., Willighagen, E., Martinat, D., Sima, A. C., Balci, H., & Abbassi Daloii, T. (2023). BioHackEU23 report: Extending interoperability of experimental data using modular queries across biomedical resources. BioHackrXiv Preprints. https://doi.org/10.37044/osf.io/mhsqp

📜 Disclaimer

This package was created with @audreyfeldroy’s cookiecutter package using @cthoyt’s cookiecutter-snekpack template.