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WormBase: new content and better access
2006
Nucleic Acids Research
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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
2006
Nucleic Acids Research
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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
2013
Nucleic Acids Research
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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
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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
2017
Nucleic Acids Research
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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
2011
Nucleic Acids Research
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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
2004
Nucleic Acids Research
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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]
2018
Msphere
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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
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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
2012
Worm
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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
2015
Nucleic Acids Research
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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
2017
Frontiers in Genetics
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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
2011
Nucleic Acids Research
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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
2018
Database: The Journal of Biological Databases and Curation
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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
2003
PLoS Biology
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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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