WormBase: a Modern Model Organism Information Resource

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Oct 24

PMID 31642470

Citations 179

Authors

Todd W Harris

Valerio Arnaboldi

Scott Cain

Juancarlos Chan

Wen J Chen

Jaehyoung Cho

Paul Davis

Sibyl Gao

Christian A Grove

Ranjana Kishore

Raymond Y N Lee

Hans-Michael Muller

Cecilia Nakamura

Paulo Nuin

Michael Paulini

Daniela Raciti

Faye H Rodgers

Matthew Russell

Gary Schindelman

Kimberly V Auken

Qinghua Wang

Gary Williams

Adam J Wright

Karen Yook

Kevin L Howe

Tim Schedl

Lincoln Stein

Paul W Sternberg

Affiliations

Soon will be listed here.

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.

Citing Articles

Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics.

Cinquin O Brief Bioinform. 2025; 26(1).

PMID: 39910777 PMC: 11798674. DOI: 10.1093/bib/bbaf045.

CUL4-Based Ubiquitin Ligases in Chromatin Regulation: An Evolutionary Perspective.

Nakagawa M, Nakagawa T Cells. 2025; 14(2).

PMID: 39851492 PMC: 11763709. DOI: 10.3390/cells14020063.

High-throughput tracking enables systematic phenotyping and drug repurposing in disease models.

OBrien T, Barlow I, Feriani L, Brown A Elife. 2025; 12.

PMID: 39773880 PMC: 11709427. DOI: 10.7554/eLife.92491.

Transcriptomic Sexual Conflict at Two Evolutionary Timescales Revealed by Experimental Evolution in Caenorhabditis elegans.

Kasimatis K, Willis J, Sedore C, Phillips P Genome Biol Evol. 2024; 16(12).

PMID: 39570916 PMC: 11687035. DOI: 10.1093/gbe/evae256.

Loss of the Na+/K+ cation pump CATP-1 suppresses nekl-associated molting defects.

Binti S, Edeen P, Fay D G3 (Bethesda). 2024; .

PMID: 39428996 PMC: 11631496. DOI: 10.1093/g3journal/jkae244.

References

Lee R, Sternberg P . Building a cell and anatomy ontology of Caenorhabditis elegans. Comp Funct Genomics. 2008; 4(1):121-6. PMC: 2447384. DOI: 10.1002/cfg.248. View

Hibbs M, Hess D, Myers C, Huttenhower C, Li K, Troyanskaya O . Exploring the functional landscape of gene expression: directed search of large microarray compendia. Bioinformatics. 2007; 23(20):2692-9. DOI: 10.1093/bioinformatics/btm403. View

Siepel A, Bejerano G, Pedersen J, Hinrichs A, Hou M, Rosenbloom K . Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005; 15(8):1034-50. PMC: 1182216. DOI: 10.1101/gr.3715005. View

Fang R, Schindelman G, Van Auken K, Fernandes J, Chen W, Wang X . Automatic categorization of diverse experimental information in the bioscience literature. BMC Bioinformatics. 2012; 13:16. PMC: 3305665. DOI: 10.1186/1471-2105-13-16. View

Cho J, Grove C, Van Auken K, Chan J, Gao S, Sternberg P . 2018 Update on Protein-Protein Interaction Data in WormBase. MicroPubl Biol. 2020; 2018. PMC: 7255808. DOI: 10.17912/micropub.biology.000074. View

Cook D, Zdraljevic S, Roberts J, Andersen E . CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res. 2016; 45(D1):D650-D657. PMC: 5210618. DOI: 10.1093/nar/gkw893. View

Kohler S, Carmody L, Vasilevsky N, Jacobsen J, Danis D, Gourdine J . Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 2018; 47(D1):D1018-D1027. PMC: 6324074. DOI: 10.1093/nar/gky1105. View

Harris T, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W . WormBase: a cross-species database for comparative genomics. Nucleic Acids Res. 2003; 31(1):133-7. PMC: 165500. DOI: 10.1093/nar/gkg053. View

Smith C, Eppig J . The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med. 2010; 1(3):390-399. PMC: 2801442. DOI: 10.1002/wsbm.44. View

10.

Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J . WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 2000; 29(1):82-6. PMC: 29781. DOI: 10.1093/nar/29.1.82. View

11.

Buels R, Dider S, Diesh C, Robinson J, Holmes I . Cram-JS: reference-based decompression in node and the browser. Bioinformatics. 2019; 35(21):4451-4452. PMC: 6821367. DOI: 10.1093/bioinformatics/btz384. View

12.

Howe K, Bolt B, Cain S, Chan J, Chen W, Davis P . WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 2015; 44(D1):D774-80. PMC: 4702863. DOI: 10.1093/nar/gkv1217. View

13.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

14.

Harris T, Baran J, Bieri T, Cabunoc A, Chan J, Chen W . WormBase 2014: new views of curated biology. Nucleic Acids Res. 2013; 42(Database issue):D789-93. PMC: 3965043. DOI: 10.1093/nar/gkt1063. View

15.

Raciti D, Yook K, Harris T, Schedl T, Sternberg P . Micropublication: incentivizing community curation and placing unpublished data into the public domain. Database (Oxford). 2018; 2018. PMC: 5836261. DOI: 10.1093/database/bay013. View

16.

Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J . InterMine: extensive web services for modern biology. Nucleic Acids Res. 2014; 42(Web Server issue):W468-72. PMC: 4086141. DOI: 10.1093/nar/gku301. View

17.

Gerstein M, Lu Z, Van Nostrand E, Cheng C, Arshinoff B, Liu T . Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010; 330(6012):1775-87. PMC: 3142569. DOI: 10.1126/science.1196914. View

18.

Schindelman G, Fernandes J, Bastiani C, Yook K, Sternberg P . Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics. 2011; 12:32. PMC: 3039574. DOI: 10.1186/1471-2105-12-32. View