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Published May 2024 | Published
Journal Article Open

WormBase 2024: status and transitioning to Alliance infrastructure

Sternberg, Paul W.1 ORCID icon
Van Auken, Kimberly ORCID icon
Wang, Qinghua
Wright, Adam ORCID icon
Yook, Karen ORCID icon
Zarowiecki, Magdalena ORCID icon
Arnaboldi, Valerio ORCID icon
Becerra, Andrés ORCID icon
Brown, Stephanie ORCID icon
Cain, Scott ORCID icon
Chan, Juancarlos ORCID icon
Chen, Wen J.
Cho, Jaehyoung
Davis, Paul
Diamantakis, Stavros
Dyer, Sarah
Grigoriadis, Dionysis
Grove, Christian A. ORCID icon
Harris, Todd ORCID icon
Howe, Kevin ORCID icon
Kishore, Ranjana ORCID icon
Lee, Raymond ORCID icon
Longden, Ian
Luypaert, Manuel ORCID icon
Müller, Hans-Michael
Nuin, Paulo
Quinton-Tulloch, Mark ORCID icon
Raciti, Daniela ORCID icon
Schedl, Tim ORCID icon
Schindelman, Gary
Stein, Lincoln ORCID icon
  • 1. ROR icon California Institute of Technology

Abstract

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects.

Copyright and License

© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Acknowledgement

We thank our numerous C. elegans and other nematode colleagues for their continual feedback. We thank the National Human Genome Research Institute (NHGRI) Program Staff (Sandhya Xirasagar, Valentina di Francesco, Sarah Hutchison, and Helen Thompson) for guidance.

Funding

The core funding for WormBase is from the National Human Genome Research Institute (NHGRI) U24HG002223 and Medical Research Council-UK grant MR/L001020/1; funding for the Alliance is from NHGRI and the National Heart, Lung and Blood Institute (U24HG010859). Curation tools are supported in part by the National Library of Medicine (NLM) R01LM013871.

Data Availability

All WormBase and Alliance code and information are freely available. Specifically, WormBase code is freely available at https://github.com/WormBase. WormBase data are available for download and programmatically by API as described at https://wormbase.org/about/userguide/for_developers/api-rest#10–10. Alliance data are at https://www.alliancegenome.org/downloads. Alliance code is available at https://github.com/alliance-genome. Alliance APIs are available at https://www.alliancegenome.org/swagger-ui/.

Acknowledgement

The authors declare no conflict of interest.

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Additional details

Identifiers Funding Caltech Custom Metadata
Created:
May 9, 2024
Modified:
May 9, 2024