IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data...

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Microbiome Research

Background:

• Inflammatory bowel diseases (IBD) are complex conditions involving genetic, environmental, immune, and microbial factors.
• Understanding IBD pathogenesis is challenging due to the intricate interplay of these factors.
• Existing literature lacks a unified, accessible resource for biomolecular data on IBD and gut microbiota.

Purpose of the Study:

• To develop a comprehensive, integrated online resource for IBD-related biomolecular data.
• To facilitate the analysis of 'omics' data in the context of IBD.
• To provide a knowledge base for hypothesis generation and understanding IBD mechanisms.

Main Methods:

• Manual curation of human genes associated with IBD, focusing on immune system alterations and microbiome interactions.
• Automated formatting and integration of heterogeneous metadata to enrich gene information.
• Development of a user-friendly web interface and data analysis tools (e.g., shortest path calculations), integrated with the Galaxy framework for high-throughput analysis.

Main Results:

• Introduction of IBDsite (http://www.itb.cnr.it/ibd), a disease-oriented platform for IBD biomolecular data.
• IBDsite offers queryable, visualized data on altered human genes and relevant gut microbiota.
• The platform is Galaxy-compliant, enabling seamless integration with high-throughput bioinformatics analyses.

Conclusions:

• IBDsite addresses the need for a unified resource by integrating sparse IBD-related information on genes and microbes.
• The platform serves as a knowledge base for filtering, annotating, and understanding experimental data.
• IBDsite facilitates hypothesis generation and discovery of non-trivial knowledge from existing and novel data.