Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

Xenbase

General information

URL: https://www.xenbase.org
Full name:
Description: Xenbase, the Xenopus model organism knowledgebase, is a web-accessible resource that integrates the diverse genomic and biological data from research on the laboratory frogs Xenopus laevis and Xenopus tropicalis.
Year founded: 2023
Last update: 2023
Version: v1.0
Accessibility:
Accessible
Country/Region: United States

Classification & Tag

Data type:
DNA
Data object:
Database category:
Major species:
Keywords:

Contact information

University/Institution: Cincinnati Children’s Hospital Medical Center
Address: Malcolm Fisher, Xenbase, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
City:
Province/State:
Country/Region: United States
Contact name (PI/Team): Malcolm Fisher
Contact email (PI/Helpdesk): malcolm.fisher@cchmc.org

Publications

36755307
Xenbase: key features and resources of the Xenopus model organism knowledgebase. [PMID: 36755307]
Malcolm Fisher, Christina James-Zorn, Virgilio Ponferrada, Andrew J Bell, Nivitha Sundararaj, Erik Segerdell, Praneet Chaturvedi, Nadia Bayyari, Stanley Chu, Troy Pells, Vaneet Lotay, Sergei Agalakov, Dong Zhuo Wang, Bradley I Arshinoff, Saoirse Foley, Kamran Karimi, Peter D Vize, Aaron M Zorn

Xenbase (https://www.xenbase.org/), the Xenopus model organism knowledgebase, is a web-accessible resource that integrates the diverse genomic and biological data from research on the laboratory frogs Xenopus laevis and Xenopus tropicalis. The goal of Xenbase is to accelerate discovery and empower Xenopus research, to enhance the impact of Xenopus research data, and to facilitate the dissemination of these data. Xenbase also enhances the value of Xenopus data through high-quality curation, data integration, providing bioinformatics tools optimized for Xenopus experiments, and linking Xenopus data to human data, and other model organisms. Xenbase also plays an indispensable role in making Xenopus data interoperable and accessible to the broader biomedical community in accordance with FAIR principles. Xenbase provides annotated data updates to organizations such as NCBI, UniProtKB, Ensembl, the Gene Ontology consortium, and most recently, the Alliance of Genomic Resources, a common clearing house for data from humans and model organisms. This article provides a brief overview of key and recently added features of Xenbase. New features include processing of Xenopus high-throughput sequencing data from the NCBI Gene Expression Omnibus; curation of anatomical, physiological, and expression phenotypes with the newly created Xenopus Phenotype Ontology; Xenopus Gene Ontology annotations; new anatomical drawings of the Normal Table of Xenopus development; and integration of the latest Xenopus laevis v10.1 genome annotations. Finally, we highlight areas for future development at Xenbase as we continue to support the Xenopus research community.

Genetics. 2023:224(1) | 67 Citations (from Europe PMC, 2025-12-13)

Ranking

All databases:
519/6895 (92.487%)
Raw bio-data:
40/582 (93.299%)
Gene genome and annotation:
191/2021 (90.599%)
Standard ontology and nomenclature:
35/238 (85.714%)
519
Total Rank
58
Citations
29
z-index

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Record metadata

Created on: 2023-08-28
Curated by:
Yue Qi [2023-09-12]
Yuanyuan Cheng [2023-09-06]
Xinyu Zhou [2023-08-28]