WormBase: a modern Model Organism Information Resource.

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.

Development and piloting of 'When Cancer Comes Along': A cancer awareness program for Australian secondary school students.

ISSUE ADDRESSED: Given the increasing prevalence of cancer, there is a growing need for health interventions educating individuals about the disease and its impacts, risk-reduction strategies and how to support others who are affected. School-based programs are a promising medium addressing these issues in adolescents, yet no comprehensive cancer education program exists in Australia. This paper reports on the piloting of a cancer awareness program for Australian students. METHODS: When Cancer Comes Along is a 90-minute interactive presentation covering cancer's impacts, risk-reduction strategies and how to support those affected. The program was piloted in four Australian secondary schools, with students (N = 113, 13-16 years) and teachers (N = 2) providing feedback via postprogram survey. RESULTS: Participants reported high satisfaction overall (92%-97%) and with each program component (71%-95%), and agreed that the program achieved learning outcomes (72%-95%). CONCLUSIONS: Results indicate that When Cancer Comes Along is relevant, engaging and age-appropriate. Participants reported improved understanding of cancer, its impacts, risk-reduction strategies and how to support those affected. A larger-scale evaluation is underway to more comprehensively evaluate program outcomes. SO WHAT?: The program has potential in educating students about various aspects of the cancer experience. It further demonstrates the feasibility and value of addressing psychosocial impacts and support strategies as well as information about cancer risks, elements which have not previously been combined in educational interventions. Equipping adolescents with the knowledge and skills to reduce their cancer risk and support others who are affected has significant health promotion implications for cancer prevention and support provision.

Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase.

ABSTRACT: Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturbations, we compared predictions of perturbation effects based on Reactome pathways against published empirical observations. Ten cancer-relevant Reactome pathways, representing diverse biological processes such as signal transduction, cell division, DNA repair and transcriptional regulation, were selected for testing. For each pathway, root input nodes and key pathway outputs were defined. We then used pathway-diagram-derived logic graphs to predict, either by inspection by biocurators or using a novel algorithm MP-BioPath, the effects of bidirectional perturbations (upregulation/activation or downregulation/inhibition) of single root inputs on the status of key outputs. These predictions were then compared to published empirical tests. In total, 4968 test cases were analyzed across 10 pathways, of which 847 were supported by published empirical findings. Out of the 847 test cases, curators' predictions agreed with the experimental evidence in 670 and disagreed in 177 cases, resulting in ∼81% overall accuracy. MP-BioPath predictions agreed with experimental evidence for 625 and disagreed for 222 test cases, resulting in ∼75% overall accuracy. The expected accuracy of random guessing was 33%. Per-pathway accuracy did not correlate with the number of pathway edges nor the number of pathway nodes but varied across pathways, ranging from 56% (curator)/44% (MP-BioPath) for 'Mitotic G1 phase and G1/S transition' to 100% (curator)/94% (MP-BioPath) for 'RAF/MAP kinase cascade'. This study highlights the potential of pathway databases such as Reactome in modeling genetic perturbations, promoting standardization of experimental pathway activity readout and supporting hypothesis-driven research by revealing relationships between pathway inputs and outputs that have not yet been directly experimentally tested. DATABASE URL: www.reactome.org.

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

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.