Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. It contains genomic, development data and community information for Xenopus research. it includes gene expression patterns that incorporates image data from the literature, large scale screens and community submissions.

Prefix

xenbase

Alternative Prefixes

Xenbase

Keywords

anatomy cell biology developmental biology expression functional genomics genetics genome genomics proteomics

Links

Homepage @Xenbase

Contact

Troy Pells   0000-0002-2340-5356   pellst

Pattern for Local Unique Identifiers

Local identifiers in Xenbase should match this regular expression:
^XB\-\w+\-\d+$

Example Local Unique Identifier

XB-GENE-922462   Resolve

Pattern for CURIES

Compact URIs (CURIEs) constructed from Xenbase should match this regular expression:
^xenbase:XB\-\w+\-\d+$

Example CURIE

xenbase:XB-GENE-922462

Publications

• 2022 The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.
• 2020 Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database.
• Xenbase: Facilitating the Use of Xenopus to Model Human Disease.
• 2019 Xenbase: Facilitating the Use of
• Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.
• 2018 Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database.
• 2018 Xenbase: a genomic, epigenomic and transcriptomic model organism database.
• 2016 Xenopus genomic data and browser resources.
• 2014 The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud.
• 2014 Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes.
• 2013 Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase.
• 2009 Xenbase: gene expression and improved integration.

The metaregistry provides mappings between the Bioregistry and other registries. There are 11 mappings to external registries for xenbase with 5 unique external prefixes.

Providers are various services that resolve CURIEs to URLs. The example CURIE xenbase:XB-GENE-922462 is used to demonstrate the provides available for xenbase. Generation of OLS and BioPortal URLs requires additional programmatic logic beyond string formatting.

Additional providers curated in the Bioregistry are listed here.