Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Area of Science:

• Bioinformatics
• Systems Biology
• Molecular Biology

Background:

• Biological pathways are crucial for understanding cellular functions.
• Integrating diverse pathway data is essential for comprehensive analysis.
• Existing resources often lack integrated, searchable, and downloadable pathway information.

Purpose of the Study:

• To present Pathway Commons as a unified resource for biological pathway data.
• To provide tools and services for accessing, analyzing, and visualizing pathway information.
• To enhance the usability of pathway data for researchers through interactive applications and training.

Main Methods:

• Data integration from 22 public databases using standard formats like BioPAX.
• Development of search tools, bulk data download sites, and software libraries (Java, R, Python, Javascript).
• Implementation of a web service for programmatic data querying and visualization using SBGN.

Main Results:

• Pathway Commons integrates data from 22 databases, containing 4794 human pathways and ~2.3 million interactions.
• Provides multiple access points: interactive web applications, bulk downloads, software libraries, and a web service.
• Supports pathway visualization using Systems Biological Graphical Notation (SBGN).

Conclusions:

• Pathway Commons serves as a valuable, integrated resource for biological pathway data.
• The platform empowers researchers with diverse tools for pathway exploration and advanced analysis.
• Ongoing development focuses on enhancing usability and accessibility for end-users.