Xenbase: key features and resources of the Xenopus model organism knowledgebase

Abstract

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.

Keywords: Xenopus; Xenbase; genomics; model organism database; ontology.

Fig. 1.

Xenbase data summary statistics. This infographic shows statistics for several key Xenbase data types.

Fig. 2.

Xenbase landing page. a) Header menu dropdowns. b) Quick search bar. c) Latest news slideshow. d) Sidebar with summary of recently added data and recent community announcements. e) Tiled view of key topic categories and quick access links.

Fig. 3.

Xenbase gene page layout. The top section of the Gene Page shows a brief overview of relevant data and links to both more detailed Xenbase pages and external resources. Tabs switch to further gene-specific data on the relevant topics. The lower sections provide species-specific data for X. tropicalis and X. laevis including graphical summaries of genomic position and gene expression. This example is for the shh gene (https://www.xenbase.org/entry/XB-GENE-488038).

Fig. 4.

Track types available on Xenbase JBrowse. The Xenbase JBrowse instance provides many different track types, such as gene and transcript models, transcription factor binding site data, and RNA-seq data. To the left of the main display is the track selection interface which allows categories of tracks to be navigated and selected, also shown is the “GEO tracks” button which opens an alternative faceted browsing interface for selecting processed GEO tracks.

Fig. 5.

GEO expression data and phenotypes. a) GEO heatmap visualization parameter options as our automated expression pipeline, the values here are the same as those used to derive computational expression phenotypes. b) Heatmaps showing samples from a control brain and a brain from a CRISPR knockdown of dyrk1a. The color map is scaled to the highest absolute value of the maximum and minimum values of the genes displayed. c) An XB-PHENO page displaying part of the corresponding computationally derived expression phenotypes. This differs from the manual XB-PHENO page layout, see Fig. 6c, in the lack of accompanying image and additional links to the Xenbase and NCBI pages for the original GEO series and research article (Willsey et al. 2020). The phenotype data shown here are available at https://www.xenbase.org/entry/XB-PHENO-25206.

Fig. 6.

Phenotype search and XB-PHENO pages. a) The Xenbase Phenotype Search interface takes terms that are genes, anatomical entities, GO terms, and diseases and allows for partial matches. Searches can be filtered either before or after the search is run by selecting one of the categories in the left-hand sidebar. Results are also shown from the Monarch Initiative for humans and mice. In this example, results are shown for the partial DO term “heterotaxy”. b) An example result page for a Disease Ontology term search. This page shows counts for different categories of phenotype data associated with models of “visceral heterotaxy.” The default display shows descriptive information about the disease and a summary of experimental reagents used in models of the disease. c) XB-PHENO page showing anatomical phenotype and disease annotations. The layout has a heading summary with a brief experiment description and the source reference, a description of the experiment and assay details in a table, the phenotype terms and statements, and a thumbnail of the source image to the right-hand side. This example shows phenotype curation for a CRISPR experiment modeling visceral heterotaxy and congenital heart disease (Sempou et al. 2018). The phenotype data shown here are available at https://www.xenbase.org/entry/XB-PHENO-24241.