Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes

Area of Science:

• Amphibian model organism databases
• Bioinformatics
• Comparative genomics

Background:

• Xenopus frogs (Xenopus laevis and Xenopus tropicalis) are vital biomedical research models.
• A centralized database is crucial for managing and accessing diverse data for these species.
• Existing resources may lack comprehensive integration or updated genomic information.

Purpose of the Study:

• To enhance Xenbase as a comprehensive resource for Xenopus research.
• To integrate new genomic data and support for novel reagents.
• To improve data accessibility and usability for the research community.

Main Methods:

• Data integration and curation from Xenopus laevis and Xenopus tropicalis.
• Implementation of cloud infrastructure for improved performance.
• Incorporation of new genome assemblies and support for morpholino reagents.
• Development of enhanced navigation and search functionalities.

Main Results:

• Xenbase now provides integrated data for both Xenopus species with species-specific and agnostic querying.
• New JGI-assembled genomes for both species are available, with BLAST search capabilities.
• Full support for morpholino reagents has been added.
• Expanded image content and improved navigation enhance data discovery.

Conclusions:

• Xenbase serves as a comprehensive and updated resource for Xenopus research.
• The database facilitates efficient retrieval and analysis of diverse research data.
• Enhancements in Xenbase support current and future research endeavors in amphibian models.