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WormBase: new content and better access

Tamberlyn Bieri, Darin Blasiar, Philip Ozersky, Igor Antoshechkin, Carol Bastiani, Payan Canaran, Juancarlos Chan, Nansheng Chen, Wen J. Chen, Paul Davis, Tristan J. Fiedler, Lisa Girard (+22 others)
2006 Nucleic Acids Research  
Access to and searching WormBase has become more dependable and flexible via multiple mirror sites and indexing through Google.  ...  Several existing datasets including phenotype descriptions and RNAi experiments have seen a large increase in new content.  ...  Over the years, WormBase has evolved and expanded through developing and utilizing better software, and providing richer content (3) by bringing in data from classical genetics, cell biology and functional  ... 
doi:10.1093/nar/gkl818 pmid:17099234 pmcid:PMC1669750 fatcat:ldwiaecqcnftrcya7e6ftxm4by

WormBase: better software, richer content

E. M. Schwarz
2006 Nucleic Acids Research  
WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content.  ...  Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known  ...  WormBase is supported by grant P41-HG02223 from the US National Human Genome Research Institute, and by the British Medical Research Council.  ... 
doi:10.1093/nar/gkj061 pmid:16381915 pmcid:PMC1347424 fatcat:t3p5g7dkfbhgrmfm4esppxynse

WormBase 2014: new views of curated biology

Todd W. Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Christian Grove, Kevin Howe, Ranjana Kishore, Raymond Lee (+21 others)
2013 Nucleic Acids Research  
Launched in March 2012, the new site offers users the option to customize the content and arrangement of pages to suit individual needs.  ...  WormMine, a new data mining tool using the Intermine data mining platform, was launched offering new options for querying and interacting with data at WormBase.  ... 
doi:10.1093/nar/gkt1063 pmid:24194605 pmcid:PMC3965043 fatcat:lh2mkgbydvfwrdngdv7nz3icme

WormBase: a modern Model Organism Information Resource

2019 Nucleic Acids Research  
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  ...  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.  ...  ACKNOWLEDGEMENTS The authors wish to thank funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose results form the foundation and purpose of WormBase  ... 
doi:10.1093/nar/gkz920 pmid:31642470 pmcid:PMC7145598 fatcat:6gcdoykkt5fmjji2i67akl3sw4

WormBase 2017: molting into a new stage

Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J Chen, Paul Davis, Sibyl Gao, Christian Grove, Ranjana Kishore, Hans-Michael Muller (+18 others)
2017 Nucleic Acids Research  
Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response  ...  Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query  ...  Many widgets and pages have been extended with new content and new visualization options. The Expression widget has been updated to include faceting of data by anatomy, life stage and localization.  ... 
doi:10.1093/nar/gkx998 pmid:29069413 pmcid:PMC5753391 fatcat:5rholx7nqvaurox74fnyrulgs4

WormBase 2012: more genomes, more data, new website

K. Yook, T. W. Harris, T. Bieri, A. Cabunoc, J. Chan, W. J. Chen, P. Davis, N. de la Cruz, A. Duong, R. Fang, U. Ganesan, C. Grove (+27 others)
2011 Nucleic Acids Research  
To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase.  ...  Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive.  ...  Data availability and releases With the ensuing flood of new genomic data, we have created a data warehouse with highly standardized file names, paths and contents for all species at WormBase as well as  ... 
doi:10.1093/nar/gkr954 pmid:22067452 pmcid:PMC3245152 fatcat:4jkq3undtzc6lporuvo3nteium

WormBase: a comprehensive data resource for Caenorhabditis biology and genomics

N. Chen
2004 Nucleic Acids Research  
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  ...  This paper reviews recent progress in WormBase content and improvements in the user interface, explains how WormBase is evolving and discusses different methods of accessing the data.  ... 
doi:10.1093/nar/gki066 pmid:15608221 pmcid:PMC540020 fatcat:ffmlelkm4zcv3h5al6d7gsbbcq

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes [chapter]

Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris, Kevin L. Howe, Ranjana Kishore, Raymond Lee, Michael Paulini, Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken (+1 others)
2018 Msphere  
This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries.  ...  Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.  ...  SPELL can be accessed from the WormBase "Tools" menu.  ... 
doi:10.1007/978-1-4939-7737-6_14 pmid:29761466 fatcat:pmvjwlblwrf6fkwid5fm272sfq

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase

2020 Database: The Journal of Biological Databases and Curation  
WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline.  ...  In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation.  ...  Acknowledgements We would particularly like to thank all authors who participated in testing and all WB curators who helped validate author submissions.  ... 
doi:10.1093/database/baaa006 pmid:32185395 pmcid:PMC7078066 fatcat:rqgg4d73ufb5xmkusxfyhj6tzi

Toward 959 nematode genomes

Sujai Kumar, Georgios Koutsovoulos, Gaganjot Kaur, Mark Blaxter
2012 Worm  
For all these communities, it is now clear that access to genome scale data will be key to advancing understanding, and in the case of parasites, developing new ways to control or cure diseases.  ...  The sequencing of the complete genome of the nematode Caenorhabditis elegans was a landmark achievement and ushered in a new era of whole-organism, systems analyses of the biology of this powerful model  ...  and the members of the Blaxter Lab for their constant support and advice on bioinformatics analyses.  ... 
doi:10.4161/worm.19046 pmid:24058822 pmcid:PMC3670170 fatcat:bnsl3sgtx5bxnelky6lnvfccui

WikiPathways: capturing the full diversity of pathway knowledge

Martina Kutmon, Anders Riutta, Nuno Nunes, Kristina Hanspers, Egon L. Willighagen, Anwesha Bohler, Jonathan Mélius, Andra Waagmeester, Sravanthi R. Sinha, Ryan Miller, Susan L. Coort, Elisa Cirillo (+3 others)
2015 Nucleic Acids Research  
We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities  ...  New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies.  ...  ACKNOWLEDGEMENTS Thanks to all the people who contributed to WikiPathways content, code and discussions. We are grateful for the support of the Google Summer of Code program.  ... 
doi:10.1093/nar/gkv1024 pmid:26481357 pmcid:PMC4702772 fatcat:4xge7wkrtbajzaoudxgakyc3aa

Meta Analysis of Human AlzGene Database: Benefits and Limitations of Using C. elegans for the Study of Alzheimer's Disease and Co-morbid Conditions

Behrad Vahdati Nia, Christine Kang, Michelle G. Tran, Deborah Lee, Shin Murakami
2017 Frontiers in Genetics  
studied in several model species, orthologs in the nematode, Caenorhabditis elegans, remain incompletely identified, with orthologs to only 17 AD-related genes identified in the C. elegans database, WormBase  ...  (NOTCH signaling) and associated with neural (neurotransmitter clearance) and immune (advanced glycation end-product receptor signaling and TRAF6-NF-kappaB) systems.  ...  AUTHOR CONTRIBUTIONS All authors listed, have made substantial, direct and intellectual contribution to the work, and approved it for publication.  ... 
doi:10.3389/fgene.2017.00055 pmid:28553317 pmcid:PMC5427079 fatcat:dk6xruu2hzg6zaamrsern2ojo4

Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data

J. Martin, S. Abubucker, E. Heizer, C. M. Taylor, M. Mitreva
2011 Nucleic Acids Research  
Two new features for data analysis and comparative genomics have been added to the site.  ...  HelmCoP (Helminth Control and Prevention) as an independent component of Nematode.net provides an integrated resource for storage, annotation and comparative genomics of helminth genomes to aid in learning  ...  We would like to thank Gaia Remerowski for technical advice and John Spieth, who heads the Wormbase efforts at the TGI.  ... 
doi:10.1093/nar/gkr1194 pmid:22139919 pmcid:PMC3245159 fatcat:3cg4tlli5ree3lmiz54chz5ngi

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Daniela Raciti, Karen Yook, Todd W Harris, Tim Schedl, Paul W Sternberg
2018 Database: The Journal of Biological Databases and Curation  
Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community.  ...  Our longterm goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery.  ...  , Phoenix Bioinformatics), Xenbase and ZFIN for their feedback on submission forms and workflow and to the Conflict of interest.  ... 
doi:10.1093/database/bay013 pmid:29688367 pmcid:PMC5836261 fatcat:dhf2ampq4jgjzkpwnb7g63xkh4

Tough Mining

Steven Dickman
2003 PLoS Biology  
Experts in text-searching uniformly cite access as a key obstacle for developing better search tools.  ...  Running the same search three times on three different subsets of content might be better than running it 15 times-but wouldn't it be easier to run it just once?  ... 
doi:10.1371/journal.pbio.0000048 pmid:14624250 pmcid:PMC261887 fatcat:qzd5wnojwjd5zdojprq6rqk2sy
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