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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
HPD: an online integrated human pathway database enabling systems biology studies.
Sudhir R Chowbina1, Xiaogang Wu, Fan Zhang
1Indiana University School of Informatics, Indianapolis, IN 46202, USA.
BMC Bioinformatics
|October 9, 2009
Summary
The Human Pathway Database (HPD) integrates diverse human pathway data, offering a unified resource for biological pathway research. This comprehensive tool aids in searching, managing, and analyzing complex biological pathways for disease studies.
Area of Science:
- Bioinformatics
- Systems Biology
- Genomics
Background:
- Biological pathway databases suffer from poor data quality and integration challenges due to incompatibilities.
- Existing resources lack comprehensive coverage and interoperability for molecular signaling, gene regulation, and metabolic events.
Purpose of the Study:
- To develop a unified, comprehensive resource for human biological pathways.
- To overcome data heterogeneity and improve accessibility for pathway research.
Main Methods:
- Integrated heterogeneous human pathway data from multiple curated sources (NCI PID, Reactome, BioCarta, KEGG, Protein Lounge).
- Employed a unified data model and data warehousing techniques for syntactic, semantic, and schematic level integration.
- Developed a user-friendly web interface and a relational database backend.
Main Results:
- Created the Human Pathway Database (HPD) with 999 human pathways and over 59,341 molecular entities.
- HPD provides a comprehensive view connecting proteins, genes, RNA, enzymes, and various pathway events.
- Enabled advanced querying, pathway-protein association analysis, pathway similarity studies, and integrated network construction.
Conclusions:
- HPD serves as a valuable new resource for searching, managing, and studying human biological pathways.
- Facilitates the comparison of pathways and molecular compositions, aiding in building disease pathway models.
- Supports diverse pathway-related research questions in human disease biology.
