WormBase is the major publicly available database of information related to Caenorhabditis elegans, an important organism for basic biomedical research, and other nematodes of medical and agricultural signficance. Although a crucial daily resource for members of the C. elegans research field, our users extend to the larger parasitology, biomedical, and bioinformatics research communities. WormBase acts as a central forum through which every research group can contribute to the global effort to comprehend nematode genomes and biology. Most users access WormBase via the Internet (www.wormbase.org); some install the database locally. WormBase offers extensive coverage of C. elegans core genomic, genetic, anatomical and functional information, allowing the biomedical community to fully utilize the results of intensive molecular genetic analyses and functional genomic studies of this organism in the study of human disease. These data include all available nematode genomic data (such as genome sequence, transcripts and cis-regulatory sites prioritized by species), large-scale functional genomic datasets, the function and interactions of genes and gene products as they relate to development, physiology and behavior, and biological reagents and their source information. WormBase comprises a set of databases storing a wide range of biological information; a website that allows users to access stored information and precomputed analyses based on these data; and tools for programmatic access such as an application programming interface, a data mining platform, and bulk downloads. Curation activities include extraction and integration of information from the literature (assisted by the use of information retrieval tools), incorporation of large-scale datasets from a range of research projects, and gene model verification from experimental data. We will curate many nematode genome sequences, along with their annotations and core genetic information, as well as data on gene function, pathways and transcriptional regulatory networks for C. elegans and select other species. We will expand tools available for data mining, workflow management, visualization, and community annotation, and integrate, store and distribute data in a maintainable, interoperable and scalable system. The project team involves three sites: Caltech primarily curates functional information and develops ontologies; EBI carries out sequence-based curation and builds databases for public release; and OICR develops and supports the web presence and visualization. The three sites work closely together and share tasks to ensure timely incorporation, storage and display of information, as well as user outreach and education.
Nematodes (roundworms) are major parasites of humans, livestock and crops, and understanding how to control them is a major world health and economic challenge. One species of nematode, C. elegans, is extensively used for basic biomedical research to elucidate how networks of genes affect cells, organs, and whole anima development, physiology and behavior to understand human disease. WormBase collects, stores and displays information about the genomes and genes of C. elegans and other nematodes to facilitate research about this diverse and important group of animals.
| Van Auken, Kimberly; Fey, Petra; Berardini, Tanya Z et al. (2012) Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database (Oxford) 2012:bas040 |
