WormBase: a Comprehensive Data Resource for Caenorhabditis Biology and Genomics

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Dec 21

PMID 15608221

Citations 94

Authors

Nansheng Chen

Todd W Harris

Igor Antoshechkin

Carol Bastiani

Tamberlyn Bieri

Darin Blasiar

Keith Bradnam

Payan Canaran

Juancarlos Chan

Chao-Kung Chen

Wen J Chen

Fiona Cunningham

Paul Davis

Eimear Kenny

Ranjana Kishore

Daniel Lawson

Raymond Lee

Hans-Michael Muller

Cecilia Nakamura

Shraddha Pai

Philip Ozersky

Andrei Petcherski

Anthony Rogers

Aniko Sabo

Erich M Schwarz

Kimberly Van Auken

Qinghua Wang

Richard Durbin

John Spieth

Paul W Sternberg

Lincoln D Stein

Affiliations

Soon will be listed here.

Abstract

WormBase (http://www.wormbase.org), the model organism database for information about Caenorhabditis elegans and related nematodes, continues to expand in breadth and depth. Over the past year, WormBase has added multiple large-scale datasets including SAGE, interactome, 3D protein structure datasets and NCBI KOGs. To accommodate this growth, the International WormBase Consortium has improved the user interface by adding new features to aid in navigation, visualization of large-scale datasets, advanced searching and data mining. Internally, we have restructured the database models to rationalize the representation of genes and to prepare the system to accept the genome sequences of three additional Caenorhabditis species over the coming year.

Citing Articles

ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection.

Eliad B, Schneider N, Ben-Naim Zgayer O, Amichan Y, Glaser F, Erdmann E Nucleic Acids Res. 2024; 52(16):9501-9518.

PMID: 39036970 PMC: 11381337. DOI: 10.1093/nar/gkae641.

WormBase 2024: status and transitioning to Alliance infrastructure.

Sternberg P, Van Auken K, Wang Q, Wright A, Yook K, Zarowiecki M Genetics. 2024; 227(1).

PMID: 38573366 PMC: 11075546. DOI: 10.1093/genetics/iyae050.

A bioinformatics approach to elucidate conserved genes and pathways in C. elegans as an animal model for cardiovascular research.

Ray A, Priya A, Malik M, Thanaraj T, Singh A, Mago P Sci Rep. 2024; 14(1):7471.

PMID: 38553458 PMC: 10980734. DOI: 10.1038/s41598-024-56562-9.

Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro.

Dube F, Hinas A, Roy S, Martin F, Abrink M, Svard S Parasit Vectors. 2022; 15(1):158.

PMID: 35513885 PMC: 9074254. DOI: 10.1186/s13071-022-05260-4.

Towards a reporting guideline for developmental and reproductive toxicology testing in and other nematodes.

van der Voet M, Teunis M, Louter-van de Haar J, Stigter N, Bhalla D, Rooseboom M Toxicol Res (Camb). 2021; 10(6):1202-1210.

PMID: 34950447 PMC: 8692742. DOI: 10.1093/toxres/tfab109.

References

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

Muller H, Kenny E, Sternberg P . Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2004; 2(11):e309. PMC: 517822. DOI: 10.1371/journal.pbio.0020309. View

Kim S, Lund J, Kiraly M, Duke K, Jiang M, Stuart J . A gene expression map for Caenorhabditis elegans. Science. 2001; 293(5537):2087-92. DOI: 10.1126/science.1061603. View

Twigger S, Lu J, Shimoyama M, Chen D, Pasko D, Long H . Rat Genome Database (RGD): mapping disease onto the genome. Nucleic Acids Res. 2001; 30(1):125-8. PMC: 99132. DOI: 10.1093/nar/30.1.125. View

Kent W . BLAT--the BLAST-like alignment tool. Genome Res. 2002; 12(4):656-64. PMC: 187518. DOI: 10.1101/gr.229202. View

Berman H, Battistuz T, Bhat T, Bluhm W, Bourne P, Burkhardt K . The Protein Data Bank. Acta Crystallogr D Biol Crystallogr. 2002; 58(Pt 6 No 1):899-907. DOI: 10.1107/s0907444902003451. View

Stein L, Mungall C, Shu S, Caudy M, Mangone M, Day A . The generic genome browser: a building block for a model organism system database. Genome Res. 2002; 12(10):1599-610. PMC: 187535. DOI: 10.1101/gr.403602. View

Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C . The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002; 12(10):1611-8. PMC: 187536. DOI: 10.1101/gr.361602. 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

10.

. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 2003; 31(1):172-5. PMC: 165541. DOI: 10.1093/nar/gkg094. View

11.

Kamath R, Fraser A, Dong Y, Poulin G, Durbin R, Gotta M . Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature. 2003; 421(6920):231-7. DOI: 10.1038/nature01278. View

12.

Lewis S, Searle S, Harris N, Gibson M, Lyer V, Richter J . Apollo: a sequence annotation editor. Genome Biol. 2003; 3(12):RESEARCH0082. PMC: 151184. DOI: 10.1186/gb-2002-3-12-research0082. View

13.

Lopez R, Silventoinen V, Robinson S, Kibria A, Gish W . WU-Blast2 server at the European Bioinformatics Institute. Nucleic Acids Res. 2003; 31(13):3795-8. PMC: 168979. DOI: 10.1093/nar/gkg573. View

14.

Dowell R, Jokerst R, Day A, Eddy S, Stein L . The distributed annotation system. BMC Bioinformatics. 2001; 2:7. PMC: 58584. DOI: 10.1186/1471-2105-2-7. View

15.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

16.

Gupta B, Sternberg P . The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Genome Biol. 2003; 4(12):238. PMC: 329410. DOI: 10.1186/gb-2003-4-12-238. View

17.

Christie K, Weng S, Balakrishnan R, Costanzo M, Dolinski K, Dwight S . Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res. 2003; 32(Database issue):D311-4. PMC: 308767. DOI: 10.1093/nar/gkh033. View

18.

Harris T, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C . WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 2003; 32(Database issue):D411-7. PMC: 308800. DOI: 10.1093/nar/gkh066. View

19.

Krieger C, Zhang P, Mueller L, Wang A, Paley S, Arnaud M . MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2003; 32(Database issue):D438-42. PMC: 308834. DOI: 10.1093/nar/gkh100. View

20.

Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y . Ensembl 2004. Nucleic Acids Res. 2003; 32(Database issue):D468-70. PMC: 308772. DOI: 10.1093/nar/gkh038. View