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

expression genome organism-specific databases

Links

Homepage

Publications

https://bioregistry.io/pubmed:36755307

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

2019 Xenbase: Facilitating the Use of

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

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

Contact

Troy Pells   0000-0002-2340-5356   pellst

A summary of the relations in the Semantic Farm schema can be found here.

In Collection

Synapse.org external links

The metaregistry provides mappings between the Semantic Farm and other registries. There are 10 mappings to external registries for this resource with 4 unique external prefixes.

A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).

The local unique identifier XB-GENE-922462 is used to demonstrate the providers available for Xenbase. Some providers may use a different example, which is displayed in the table below. A guide for curating additional providers can be found here.

Additional providers curated in the Semantic Farm are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.