WormBase: a comprehensive resource for nematode research

By T. Harris, I. Antoshechkin, Tamberlyn Bieri, Darin Blasiar, J. Chan, Wen J. Chen, Norie De La Cruz, Paul Davis, M. Duesbury, Ruihua Fang and 22 more. Nucleic Acids Res., 2009

397 citations recorded by the source corpus.

WormBase (http://www.wormbase.org) is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base.

Subfields: Aging, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/06ebe6293352458bb993123b7bd89c06f57427e9

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In Molecular Biology

Citations in the corpus

A practical guide to linking brain-wide gene expression and neuroimaging data (2018, background): “The development of standardized work ﬂ ows will be essential to ensure reproducibility, particularly as gene expression atlases become more widely available and increase in their sophistication (Lein et al., 2007, Harris et al., 2010, Miller et al., 2014a).”
The BioGRID Interaction Database: 2011 update (2010, background): “For example, a systematic effort to extract interaction data from all C. elegans publications annotated by GO is currently in progress by BioGRID and WormBase curators (11).”
COMPARTMENTS: unification and visualization of protein subcellular localization evidence (2014, methodology): “The first channel, called knowledge, is based on annotations from UniProtKB (1), MGI (2), SGD (3), FlyBase (4) and WormBase (5).”
The case for cloud computing in genome informatics (2010, background): “Most users access the information either through websites created by the archival databases, or through value-added integrators of genomic data, such as Ensembl [7], the University of California at Santa Cruz (UCSC) Genome Browser [8], Galaxy [9], or one of the many model organism databases [10-13].”
The UniProt-GO Annotation database in 2011 (2011, background): “Such integration efforts can be exempliﬁed by work in the last year to include 43 different gene, protein and chemical identiﬁer types [such as WormBase (11), ChEBI (12) and EcoCyc (7) identiﬁers] in the annotation format to provide a more complete display of external manual annotations.”
RBPDB: a database of RNA-binding specificities (2010, background): “Each protein and experiment is assigned a unique internal ID number, and proteins are linked to Ensembl, FlyBase and WormBase gene annotations and RNA-bound protein structures on PDB (14–17).”