Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development, and some information about each of its ~22,000 genes. Five years of funding is requested to maintain and expand WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this and other nematodes. Such a database is necessary to allow the entire biomedical research community to make full use of nematode genomic sequences. The two top priorities will be intensive data curation and user interface improvement. WormBase will include up-to-date annotation of the genomic data, the current genetic and physical maps and many experimental data such as genome-scale datasets connected to the function and interactions of cells and genes, as well as development, physiology and behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication, WormBase will use technology, terminology and style concordant with other databases wherever possible. WormBase will maintain ontologies for nematode anatomy and phenotypes. WormBase will be Web-based and easy to use. Multiple relational databases will be used for data management;the object-based Acedb database system will be used for integration, and this integrated database plus "slave" relational databases will be used to drive the website. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the centers - the Sanger Institute and Washington University - that generated the entire genome sequence. Oxford University will maintain genetic nomenclature. Nematodes (roundworms) are major parasites of humans, livestock and crops, and extension of WormBase to broader coverage of nematode genomics will facilitate research into the diagnosis and treatment of nematode-based disease. Studies of C. elegans have informed us of basic principles of normal development and the molecular basis of aging, cancer, nicotine addiction, as well as a variety of fundamental biological processes such as cell migration, cell differentiation and cell death.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Biotechnology Resource Grants (P41)
Project #
5P41HG002223-13
Application #
8325682
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Bonazzi, Vivien
Project Start
2000-07-20
Project End
2013-07-31
Budget Start
2012-08-01
Budget End
2013-07-31
Support Year
13
Fiscal Year
2012
Total Cost
$2,815,263
Indirect Cost
$645,401
Name
California Institute of Technology
Department
None
Type
Schools of Arts and Sciences
DUNS #
009584210
City
Pasadena
State
CA
Country
United States
Zip Code
91125
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Spieth, John; Lawson, Daniel; Davis, Paul et al. (2014) Overview of gene structure in C. elegans. WormBook :1-18
Wang, Liya; Stein, Lincoln D (2013) Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process. BMC Evol Biol 13:57
Yook, Karen; Harris, Todd W; Bieri, Tamberlyn et al. (2012) WormBase 2012: more genomes, more data, new website. Nucleic Acids Res 40:D735-41
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Stark, Chris; Breitkreutz, Bobby-Joe; Chatr-Aryamontri, Andrew et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39:D698-704
Williams, G W; Davis, P A; Rogers, A S et al. (2011) Methods and strategies for gene structure curation in WormBase. Database (Oxford) 2011:baq039
Rangarajan, Arun; Schedl, Tim; Yook, Karen et al. (2011) Toward an interactive article: integrating journals and biological databases. BMC Bioinformatics 12:175
Gene Ontology Consortium (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38:D331-5
McKay, Sheldon J; Vergara, Ismael A; Stajich, Jason E (2010) Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics Chapter 9:Unit 9.12

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