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PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.

James M Melott1, John N Weinstein2, Bradley M Broom1

  • 1Department of Bioinformatics and Computational Biology and.

Bioinformatics (Oxford, England)
|September 25, 2015
PubMed
Summary

PathwaysWeb offers integrated biological pathway data, including gene interactions and Gene Ontology terms, via a web system and API for reproducible research. It focuses on human data but allows inference for other species.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • Biological pathway information is fragmented across various databases.
  • Integrating diverse data types like genes, pathways, and networks is crucial for comprehensive analysis.
  • Reproducible research requires access to versioned, integrated datasets.

Purpose of the Study:

  • To present PathwaysWeb, a unified resource for biological pathway data.
  • To introduce the PathwaysWeb API for application development.
  • To provide PathwaysBrowser for data exploration.

Main Methods:

  • Developed a resource-based web system integrating data on genes, pathways, Gene Ontology (GO) terms, and gene-gene interaction networks.
  • Implemented an API for retrieving and interrelating pathway-related data from multiple sources.
  • Created a companion website, PathwaysBrowser, for data visualization and exploration.
  • Ensured data reproducibility by providing access to all integrated dataset versions.

Main Results:

  • PathwaysWeb offers integrated data including directional gene-gene interactions and links to PubMed.
  • The PathwaysWeb API facilitates the development of applications for cross-data type retrieval.
  • PathwaysBrowser enables interactive exploration of integrated pathway data.
  • The system supports reproducible analyses through versioned datasets.

Conclusions:

  • PathwaysWeb provides a valuable, integrated resource for biological pathway research.
  • The system and its API simplify access to and analysis of complex biological data.
  • While focused on human data, it enables pathway inference for other species.