The ARKdb: genome databases for farmed and other animals

Area of Science:

• Animal Genomics
• Bioinformatics
• Comparative Genomics

Background:

• Genome mapping data for farmed and other animal species are often fragmented across various resources.
• Developing species-specific genome databases can be resource-intensive and prohibitive for many species.
• Existing databases like GDB and MGD serve human and mouse, highlighting a need for broader animal genomic data repositories.

Purpose of the Study:

• To establish ARKdb, a comprehensive and generic genome database for farmed and other animal species.
• To provide a publicly accessible repository for genome mapping data, facilitating research and data sharing.
• To demonstrate the utility of a generic database model for species with limited dedicated resources.

Main Methods:

• Implementation of a generic genome database model.
• Data integration including loci, maps, experimental methods, and references.
• Development of web-based access tools: ARKdb browser and Anubis map viewer.
• Establishment of data curation processes involving active genome research scientists.

Main Results:

• ARKdb has been successfully implemented for 10 species: pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey, and salmon.
• The database provides access to detailed genome mapping information and links to external resources like PubMed and EMBL/GenBank.
• A generic database model proved effective, offering wide utility, especially for species lacking dedicated resources.
• Shared responsibility for data entry and curation ensures data quality and relevance.

Conclusions:

• ARKdb serves as a valuable, comprehensive public repository for animal genome mapping data.
• The generic database approach enhances accessibility and utility for a wide range of animal species.
• ARKdb supports the advancement of genome research in farmed and other animals through shared data and resources.