PathwaysWeb

PathwaysWeb integrates publicly available gene, pathway, and gene-interaction data to provide pathway-centric biological information for analysis of human genetics and inference of pathways in other species.

Key Features:

• Data integration: Aggregates publicly available biological data relating to genes, pathways, and gene interactions.
• Gene Ontology (GO) terms: Integrates GO annotations linked to genes and pathways.
• Directional interaction networks: Provides directional gene-gene interaction networks.
• PubMed linkage: Links pathway and gene records to relevant PubMed documents.
• API: Exposes an API for retrieval and interrelation of diverse pathway-related data types from multiple original sources.
• Versioned datasets: Provides access to all versions of its datasets to support reproducibility.
• Cross-species inference: Produces inferred pathway data for other species such as mice, reported with high accuracy.
• Human-focused data: Emphasizes comprehensive human genetic information.

Scientific Applications:

• Biological pathway analysis: Enables analyses of pathways using integrated GO terms, interaction networks, and literature linkage.
• Gene function and interaction exploration: Supports investigation of gene functions and directional gene-gene interactions in human data and inferred species data.
• Bioinformatics application development: Supports development of applications that require complex pathway data integration via the API.
• Reproducible research: Facilitates reproducible analyses by providing access to versioned datasets.

Methodology:

Integration of Gene Ontology (GO) terms, directional gene-gene interaction networks, and PubMed document linkage; API-based retrieval and interrelation of pathway-related data from multiple original sources; provision of versioned datasets; and inference of pathway data for non-human species (e.g., mice).