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.
Subject(s)
Caenorhabditis , Nematoda , Animals , Caenorhabditis/genetics , Caenorhabditis elegans/genetics , Databases, Genetic , Genome , Genomics , Humans , Nematoda/geneticsABSTRACT
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.
Subject(s)
Caenorhabditis elegans/genetics , Databases, Genetic , Genes, Helminth , Animals , Data Mining , Genomics , Internet , User-Computer InterfaceABSTRACT
WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.
Subject(s)
Databases, Genetic , Genome , Nematoda/genetics , Animals , Caenorhabditis/genetics , Caenorhabditis elegans/genetics , Data Curation , Data Mining , Datasets as Topic , Disease Models, Animal , Forecasting , Gene Ontology , Humans , Information Storage and Retrieval , Platyhelminths/genetics , Publishing , RNA Interference , Sequence Alignment , User-Computer Interface , Web BrowserABSTRACT
We report a systematic RNA interference (RNAi) screen of 5,690 Caenorhabditis elegans genes for gene inactivations that increase lifespan. We found that genes important for mitochondrial function stand out as a principal group of genes affecting C. elegans lifespan. A classical genetic screen identified a mutation in the mitochondrial leucyl-tRNA synthetase gene (lrs-2) that impaired mitochondrial function and was associated with longer-lifespan. The long-lived worms with impaired mitochondria had lower ATP content and oxygen consumption, but differential responses to free-radical and other stresses. These data suggest that the longer lifespan of C. elegans with compromised mitochrondria cannot simply be assigned to lower free radical production and suggest a more complex coupling of metabolism and longevity.
Subject(s)
Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism , Genes, Helminth/genetics , Longevity/genetics , Mitochondria/metabolism , RNA Interference , Adenosine Triphosphate/metabolism , Animals , Caenorhabditis elegans/cytology , Caenorhabditis elegans/enzymology , Gene Expression Regulation , Genetic Testing , Leucine-tRNA Ligase/genetics , Leucine-tRNA Ligase/metabolism , Mitochondria/enzymology , Mitochondria/genetics , Mitochondria/pathology , Oxygen Consumption , Stress, Physiological/metabolismABSTRACT
We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress.
