WormBase 2016: expanding to enable helminth genomic research

By Kevin Lee Howe, B. J. Bolt, S. Cain, J. Chan, Wen J. Chen, Paul Davis, J. Done, Thomas A. Down, Sibyl Gao, Christian A. Grove and 24 more. 2015

339 citations recorded by the source corpus.

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research.

Subfields: Aging, Genetics, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

UniProt: the universal protein knowledgebase (2016, background): “The majority of these proteomes are based on the translation of genome sequence submissions to the International Nucleotide Sequence Database Consortium (INSDC) but also include predictions from Ensembl, RefSeq reference genomes and vector/parasitespecific databases like VectorBase (5) and WormBase ”
WormBase ParaSite − a comprehensive resource for helminth genomics (2017, methodology): “Flicek, The Ensembl REST API: ensembl data for any language, Bioinformatics 31 (1) (2015) 143–145.”
The BioGRID interaction database: 2017 update (2016, methodology): “…to more precisely describe genetic interactions, and reconcile the different terminologies used within the various model organism research communities, BioGRID has collaborated with WormBase (26) to develop a new Genetic Interactions Structured Terminology (GIST) (Grove et al. , in preparation).”
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse (2016, background): “In 2016, MGD joined FlyBase (15), Saccharomyces Genome Database (SGD) (16), WormBase (17), Zebrafish Information Network (ZFIN) (18), Rat Genome Database (RGD) (19) and the Gene Ontology Consortium (GOC) to form the Alliance of Genome Resources D ow naded rom http/academ ic.”
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation (2016, background): “The flexibility of the Ensembl Core infrastructure is most clearly displayed by the many large-scale projects that reuse it, including Ensembl Genomes, Gramene (45), WormBase and WormBase ParaSite (46), VectorBase (47), PomBase (48) and AvianBase (49).”
Lepbase: the Lepidopteran genome database (2016, background): “All results and datafiles are available at http://download.lepase.org”
Expression Atlas: gene and protein expression across multiple studies and organisms (2017, methodology): “Since the last update, the baseline expression widget is also available through WormBase (26), the Complex Portal (27) and the Target Validation Platform by Open Targets (28).”
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs (2016, methodology): “We also explicitly present more detailed annotation records for important model organisms such as: Caenorhabditis elegans from WormBase (29), Danio rerio from the Zebrafish Model Organism Database (30), Drosophila melanogaster from FlyBase (17), Mus musculus from the Mouse Genome Database (31) and S”