WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans

Abstract

WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.

Keywords: Caenorhabditis elegans; annotation; caenorhabditis; community; curation; data; database; gene; health; human; literature; mining; model; nematode; platform; research; resource; software; tools.

Fig. 1.

Examples of RNA-Seq expression data availability in WormBase through custom interfaces. a) FPKM expression over conditions, as determined by different studies; the left panel is a study selector, and the right panel shows data for the selected study; b) a customized plot for the highly-accessed modENCODE RNA-Seq data corpus.

Fig. 2.

For single-cell data, WormBase developed two web apps for easily performing differential gene expression analysis (scdefg app) and visualization of gene expression (wormcells-viz app) in the annotated cell types.

Fig. 3.

Wormicloud creates word clouds from the scientific literature based on the words you input (in this case the input was “WormBase”).

Fig. 4.

Vennter tool allows researchers to visualize available interactions and select the interaction type(s) of interest and retrieve a list of genes that interact with a focused gene.