Xenbase

Xenbase is the Xenopus model organism knowledgebase, serving as the primary repository for research data on the African clawed frog (Xenopus laevis) and Western clawed frog (Xenopus tropicalis). These amphibian species are widely used as model organisms in developmental biology, cell biology, and biomedical research.

Key Features

• Genome Resources: Complete genome assemblies and gene models for X. laevis v10.1 and X. tropicalis v10.0
• Gene Expression Data: Comprehensive collection of RNA-seq, in situ hybridization, and microarray expression data
• Anatomy & Development: Detailed anatomical atlases, developmental staging information, and fate maps
• Phenotype & Disease Models: Curated phenotype data, mutant lines, and disease model information
• Community Resources: Protocols, reagents, stock centers, and research tools

Data Types

Xenbase provides access to:

• Genomic Data: Genome assemblies, gene annotations, sequences, and BLAST databases
• Expression Data: Temporal and spatial gene expression patterns across development
• Phenotype Data: Morphological and functional phenotypes from experimental studies
• Anatomical Data: Standardized anatomy with developmental staging
• Literature: Curated bibliographic data and community contributions
• Protocols & Reagents: Research methodologies and available biological materials

Supported Species

• Primary: Xenopus laevis (African clawed frog), Xenopus tropicalis (Western clawed frog)
• Additional: Ambystoma mexicanum, Nanorana parkeri, Lithobates catesbeiana, Hymenochirus boettgeri

Ontologies

Xenbase maintains several controlled vocabularies:

• XAO: Xenopus Anatomy Ontology for anatomical structures and development
• XPO: Xenopus Phenotype Ontology for standardized phenotype descriptions
• XSMO: Xenopus Small Molecules Ontology
• XBED: Xenbase Experimental Data Ontology

Citation

If you use Xenbase in your research, please cite:

Karimi, K., et al. Xenbase: key features and resources of the Xenopus model organism knowledgebase. Genetics. 2023;224(1):iyad018. https://doi.org/10.1093/genetics/iyad018

Funding

Major funding for Xenbase is provided by grant P41 HD064556: “Xenbase: The Xenopus Model Organism Knowledgebase” from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD/NIH).

Alliance Membership

Xenbase is a founding member of the Alliance of Genome Resources, collaborating with other model organism databases to provide integrated access to genomic and biological data.