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. 2020 Jan 8;48(D1):D762-D767.
doi: 10.1093/nar/gkz920.

WormBase: a modern Model Organism Information Resource

Todd W Harris  1 , Valerio Arnaboldi  2 , Scott Cain  1 , Juancarlos Chan  2 , Wen J Chen  2 , Jaehyoung Cho  2 , Paul Davis  3 , Sibyl Gao  1 , Christian A Grove  2 , Ranjana Kishore  2 , Raymond Y N Lee  2 , Hans-Michael Muller  2 , Cecilia Nakamura  2 , Paulo Nuin  1 , Michael Paulini  3 , Daniela Raciti  2 , Faye H Rodgers  4 , Matthew Russell  3 , Gary Schindelman  2 , Kimberly V Auken  2 , Qinghua Wang  2 , Gary Williams  3 , Adam J Wright  1 , Karen Yook  2 , Kevin L Howe  3 , Tim Schedl  5 , Lincoln Stein  1 , Paul W Sternberg  2
Affiliations

WormBase: a modern Model Organism Information Resource

Todd W Harris et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1.
Figure 1.
The gene description of cpn-1 is an example of a description informed by the function of the orthologous human gene and the predicted protein domain signatures.
Figure 2.
Figure 2.
The Swagger (https://swagger.io) REST API interface at WormBase (http://rest.wormbase.org) makes it trivial to identify and test REST endpoints for creating programmatic data mining workflows. (A) A list of all endpoints. (B) A typical response.
See this image and copyright information in PMC

References

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