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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  
Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing.  ...  To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase.  ...  Over the past 2 years, we have enhanced our database by adding new graphics, more data types, more data overall and new curation tools to increase the efficiency of capturing and annotating all these new  ... 
doi:10.1093/nar/gkr954 pmid:22067452 pmcid:PMC3245152 fatcat:4jkq3undtzc6lporuvo3nteium

WormBase

Kevin Howe, Paul Davis, Michael Paulini, Mary Ann Tuli, Gary Williams, Karen Yook, Richard Durbin, Paul Kersey, Paul W. Sternberg
2012 Worm  
WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans.  ...  In this article, we focus on WormBase's role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains.  ...  ., the update of a gene name, correction of an error, or the import of a new data set) and its availability on the WormBase website.  ... 
doi:10.4161/worm.19574 pmid:24058818 pmcid:PMC3670165 fatcat:2q474cfv7vg3lbzszuzizdocsm

WormBase 2016: expanding to enable helminth genomic research

Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas Down, Sibyl Gao, Christian Grove, Todd W. Harris, Ranjana Kishore (+22 others)
2015 Nucleic Acids Research  
To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations.  ...  WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes.  ...  ACKNOWLEDGEMENTS After many years working closely with WormBase as the guardian and authority for C. elegans genetic nomenclature, Jonathan Hodgkin has now stepped down from this role.  ... 
doi:10.1093/nar/gkv1217 pmid:26578572 pmcid:PMC4702863 fatcat:h3yxwojkojgszivof7ahs6fprq

Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR

K. Van Auken, P. Fey, T. Z. Berardini, R. Dodson, L. Cooper, D. Li, J. Chan, Y. Li, S. Basu, H.-M. Muller, R. Chisholm, E. Huala (+1 others)
2012 Database: The Journal of Biological Databases and Curation  
The members of the WormBase Consortium are M. Berriman and R. Durbin  ...  Acknowledgements We would like to thank the BioCreative Workshop 2012 Steering Committee for the opportunity to participate in the workshop and, in particular, C.  ...  Prior to each build of the WormBase database, data are exported from the PostgreSQL database in file formats conforming to the acedb database, which underlies much of the WormBase website.  ... 
doi:10.1093/database/bas040 pmid:23160413 pmcid:PMC3500519 fatcat:xm263mzjpferrgyn4augokxkgm

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  
The new user interface also links out to specific structured data submission forms, e.g. for phenotype or expression pattern data, giving the authors the opportunity to contribute a more detailed 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 the new system, we included many more data types, ultimately providing more comprehensive data to WB.  ... 
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  ...  At the University of Edinburgh, we especially want to thank Karim Gharbi and colleagues at the GenePool Genomics and Bioinformatics Facility for their expertise and advice on de novo genome sequencing  ... 
doi:10.4161/worm.19046 pmid:24058822 pmcid:PMC3670170 fatcat:bnsl3sgtx5bxnelky6lnvfccui

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

M. Y. Galperin, X. M. Fernandez-Suarez
2011 Nucleic Acids Research  
The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases  ...  The case of TAIR is even more troubling.  ...  The same news release in February 2011 announced the closure of Peptidome, the NCBI resource for tandem mass spectrometry peptide and protein identification data (29) .  ... 
doi:10.1093/nar/gkr1196 pmid:22144685 pmcid:PMC3245068 fatcat:ez36c3s6nbdsbdtrp4lucw2rwq

Large-Scale Screening for Targeted Knockouts in the Caenorhabditis elegans Genome

2012 G3: Genes, Genomes, Genetics  
More recently, we have used array comparative genome hybridization (aCGH) to detect deletions across the entire coding part of the genome and massively parallel short-read sequencing to identify nonsense  ...  This knowledge will usher in a new age of metazoan genetics in which the contribution to any biological process can be assessed for all genes.  ...  ACKNOWLEDGMENTS We thank the staff of WormBase, and especially Mary Ann Tuli, for posting and hosting the deletion and strain descriptions.  ... 
doi:10.1534/g3.112.003830 pmid:23173093 pmcid:PMC3484672 fatcat:mnzvu7lnfrcenknlfeldrvc6de

Opportunities for text mining in the FlyBase genetic literature curation workflow

P. McQuilton
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements The author thanks the BioCreative group for the invitation to give a talk at the BioCreative Workshop 2012 on the FlyBase genetic literature curation workflow, from which this article  ...  The website contains over 2.5 million pages covering 19 different data classes and 20 Drosophila-sequenced genomes.  ...  Data-type flags Data presented in an article Drosophila reagents New allele or aberration Generation of a new classical allele or chromosomal aberration in a Drosophilid genome New transgene  ... 
doi:10.1093/database/bas039 pmid:23160412 pmcid:PMC3500518 fatcat:6yptxqk7x5hcfpedsyjju2jixe

Tetrahymena genome database Wiki: a community-maintained model organism database

N. A. Stover, R. S. Punia, M. S. Bowen, S. B. Dolins, T. G. Clark
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors would like to thank Mike Cherry, Stuart Miyasato, Gail Binkley and the staff at Saccharomyces Genome Database for maintaining TGD service during the transition to Bradley University  ...  to more easily integrate new tools developed by contributors to GMOD.  ...  This number is supported by more recent data based on publication rates in Pubmed.  ... 
doi:10.1093/database/bas007 pmid:22434841 pmcid:PMC3308163 fatcat:jdswubl2wzdh3fvccyulhiwkpm

Automatic categorization of diverse experimental information in the bioscience literature

Ruihua Fang, Gary Schindelman, Kimberly Auken, Jolene Fernandes, Wen Chen, Xiaodong Wang, Paul Davis, Mary Tuli, Steven J Marygold, Gillian Millburn, Beverley Matthews, Haiyan Zhang (+3 others)
2012 BMC Bioinformatics  
Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI).  ...  in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD).  ...  We gratefully acknowledge Karen Yook for making the WormBase data type definition available on the WormBase Wiki page; Juancarlos Chan for help with getting WormBase training data from the WormBase curation  ... 
doi:10.1186/1471-2105-13-16 pmid:22280404 pmcid:PMC3305665 fatcat:pgt5hyh44rdzhlfxdn2tc5hvfa

A Genome-Wide Collection of Mos1 Transposon Insertion Mutants for the C. elegans Research Community

Elodie Vallin, Joseph Gallagher, Laure Granger, Edwige Martin, Jérôme Belougne, Julien Maurizio, Yohann Duverger, Sarah Scaglione, Caroline Borrel, Elisabeth Cortier, Karima Abouzid, Maité Carre-Pierrat (+5 others)
2012 PLoS ONE  
Methods that use homologous recombination to engineer the genome of C. elegans commonly use strains carrying specific insertions of the heterologous transposon Mos1.  ...  At peak production, more than 5,000 strains were generated per month. These strains were then subject to molecular analysis, and more than 13,300 Mos1 insertions characterized.  ...  support, advice and critical reading of the manuscript, Nektarios Tavernarakis for coordination of the NEMAGENTAG consortium, Frederic Montanana-Sanchis, the CIML bioinformatics platform and the staff at Wormbase  ... 
doi:10.1371/journal.pone.0030482 pmid:22347378 pmcid:PMC3275553 fatcat:au7mo2df65bgnc3qo6r4ljsdn4

A brief introduction to web-based genome browsers

J. Wang, L. Kong, G. Gao, J. Luo
2012 Briefings in Bioinformatics  
Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data.  ...  In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization.  ...  The Ensembl and UCSC genome browser are the two most popular general genome browsers.  ... 
doi:10.1093/bib/bbs029 pmid:22764121 fatcat:6q2kz2t3wrbj3l3sfamsyec7g4

Community gene annotation in practice

J. E. Loveland, J. G. R. Gilbert, E. Griffiths, J. L. Harrow
2012 Database: The Journal of Biological Databases and Curation  
It has a very flexible data model allowing the incorporation of new data sources (e.g. short reads) as they become available.  ...  We routinely transfer annotation over to new genome builds when they are available.  ... 
doi:10.1093/database/bas009 pmid:22434843 pmcid:PMC3308165 fatcat:lbqygrvrwjgsjkxjov6eafakbe

One Stop Shop for Everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012 [chapter]

Petra Fey, Robert J. Dodson, Siddhartha Basu, Rex L. Chisholm
2013 Msphere  
dictyBase (http:// dictybase.org), the model organism database for Dictyostelium discoideum, includes the complete genome sequence and expression data for this organism.  ...  In this chapter, we will describe how to navigate the website and highlight some of our newer improvements.  ...  Acknowledgments We thank Kerry Sheppard for her expert technical work at the Dicty Stock Center, Yulia Bushmanova for her contributions to the new gene page layout and the gene model curation tool, and  ... 
doi:10.1007/978-1-62703-302-2_4 pmid:23494302 pmcid:PMC3762881 fatcat:kfcs6cpezfh5lgdnazm5klzkum
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