WormBase 2024: status and transitioning to Alliance infrastructure

Abstract

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.

Keywords: Caenorhabditis elegans; Global Core Biodata Resources; bioinformatics tools; disease models; genome annotation; knowledgebase; model organism; software.

Fig. 1.

JBrowse with sequence features. A partial view of the lin-3 sequence in the JBrowse viewer. “Classical alleles” (amusingly including CRISPR gene edits) shown in purple provide evidence for the lin-3 vulval enhancer (WBsf919657) shown in green. The top shows the displayed coordinates and allows navigation with left and right arrows as well as the ability to zoom in or out. Users can choose the tracks that are displayed, with many choices hidden in the menu at the upper left. Here, curated exons are shown (magenta) (lin-3 has alternative 5′ exons, one of which is shown here) in the intron of majority transcription unit. Protein motifs are shown next (purple), followed by mutant alleles and finally an enhancer (green).

Fig. 2.

Example of a C. elegans genetic pathway at the Alliance. This pathway diagram for PMK-1 signaling is generated automatically from a curated GO-CAM pathway. In this example, only direct positive and negative regulation occur, but the underlying model can handle indirect inputs as well as biochemical pathways using chemicals as reaction inputs and outputs. The rectangles on the right side show the standard GO annotations associated with the GO-CAM, including molecular function, cell component, and biological processes.

Fig. 3.

A home for C. elegans at the Alliance. a) MOD icons at the bottom of the Alliance homepage. b) WormBase homepage at the Alliance.

Fig. 4.

Comparison of WormBase and Alliance gene pages. Shown is pezo-1 with the WormBase view on the left and Alliance view on the right.

Fig. 5.

Linear genome and synteny views in JBrowse 2. JBrowse 2 showing multiple views: the top panel is a linear genome view showing the region around the C. elegans  lin-2 gene with multiple synteny tracks showing the sequence similarity as determined by minimap2 analysis between the N2 assembly and the assemblies of multiple related genomes. The middle panel is the result of right clicking one of the regions showing synteny between C. elegans and Caenorhabditis inopinata and zooming out slightly to show the entire lin-2 in both assemblies. The lower panel is the same but with the similar region in C. remanei.

Fig. 6.

Mockup of an Anatomy Term page for “intestine”.

Fig. 7.

Community curation. The authors' response rate increased from 20% in 2019 to 31% in 2023, indicating that our efforts in community engagement are increasing participation.