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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological
Tadashi Imanishi1, Hajime Nakaoka
1Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. t.imanishi@aist.go.jp
Nucleic Acids Research
|May 21, 2009
Summary
The Hyperlink Management System (HMS) automates the creation and maintenance of hyperlinks between life science databases. This system ensures up-to-date data connections, simplifying biological data retrieval and integration.
Area of Science:
- Bioinformatics
- Life Sciences
- Database Management
Background:
- Maintaining hyperlinks across diverse life science databases is crucial for data integration but is often labor-intensive.
- Existing methods for linking biological data between databases lack automation, leading to outdated or broken hyperlinks.
Purpose of the Study:
- To develop an automated system for managing hyperlinks among major public life science databases.
- To provide researchers with a reliable and up-to-date method for accessing related biological data across different resources.
Main Methods:
- Developed a Hyperlink Management System (HMS) that daily updates data ID correspondence tables for human genes and proteins.
- Implemented a CGI program within HMS to generate correct, current URLs for data across multiple databases based on user-specified IDs.
- Integrated support for various data IDs (e.g., International Nucleotide Sequence Databases accession numbers, HUGO Gene Symbols, UniProt IDs) and database URLs (e.g., H-InvDB, HGNC, NCBI Entrez Gene, UniProt, PDB).
- Developed an associated ID Converter System (ICS) for seamless data ID conversion using HMS tables.
Main Results:
- The HMS successfully automates the laborious task of updating hyperlinks, providing maintenance-free connections.
- It supports a wide range of data IDs and links to numerous major life science databases, enhancing data accessibility.
- Demonstrated example: 23,297 H-InvDB Locus view pages are accessible via HUGO Gene Symbols through the HMS.
- The system includes both a CGI program and a web interface for URL retrieval and database exploration.
Conclusions:
- The Hyperlink Management System (HMS) significantly improves the efficiency and reliability of linking biological data across disparate databases.
- Automated hyperlink maintenance reduces manual effort and ensures data integrity, facilitating more effective biological research.
- The HMS and its companion ID Converter System (ICS) are freely available, promoting wider adoption and accessibility in the life science community.
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