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The Rat Genome Database 2013--data, tools and users

S. J. F. Laulederkind, G. T. Hayman, S.-J. Wang, J. R. Smith, T. F. Lowry, R. Nigam, V. Petri, J. de Pons, M. R. Dwinell, M. Shimoyama, D. H. Munzenmaier, E. A. Worthey (+1 others)
2013 Briefings in Bioinformatics  
The Rat Genome Database (RGD) was started >10 years ago to provide a core genomic resource for rat researchers.  ...  The value of RGD continues to grow as more types of data and more tools are added, while reaching more types of end users.  ...  Key points RGD is a global resource of biomedical data and analysis tools. RGD serves a diverse user base. RGD data support translational research.  ... 
doi:10.1093/bib/bbt007 pmid:23434633 pmcid:PMC3713714 fatcat:vyyqvyuexrckhnvjrnbtpmilxy

PhenoMiner: quantitative phenotype curation at the rat genome database

Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy F. Lowry, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama
2013 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) PhenoMiner project endeavors to present, extend and expand the quantitative phenotypic data presented by those two large-scale projects.  ...  Technical aspects of the phenominer curation tool, database and user interface PhenoMiner originally started as a stand-alone project with a goal to visualize the existing rat phenotype data collected  ... 
doi:10.1093/database/bat015 pmid:23603846 pmcid:PMC3630803 fatcat:ig4o5af6hrbxbaftzwrgd4dnbi

Analysis of disease-associated objects at the Rat Genome Database

Shur-Jen Wang, Stanley J. F. Laulederkind, G. T. Hayman, Jennifer R. Smith, Victoria Petri, Timothy F. Lowry, Rajni Nigam, Melinda R. Dwinell, Elizabeth A. Worthey, Diane H. Munzenmaier, Mary Shimoyama, Howard J. Jacob
2013 Database: The Journal of Biological Databases and Curation  
Acknowledgement The authors thank Mr Andrew Vallejos for technical assistance on the RatMine tool. ....................................................................................................  ...  These two rat syntenic blocks house 93 cardiovascular and obesity disease genes [data accessed January 2013, from the Rat Genome Browser (http://rgd.mcw.edu/ fgb2/gbrowse/rgd_904/)].  ...  Introduction The Rat Genome Database (RGD; http://rgd.mcw.edu) provides a comprehensive catalogue of genes, quantitative trait loci (QTL) and strains, with associated biological data for the laboratory  ... 
doi:10.1093/database/bat046 pmid:23794737 pmcid:PMC3689439 fatcat:jsagknmhjrdnhbzxhoslocid4y

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs

Izabella Krystkowiak, Jakub Lenart, Konrad Debski, Piotr Kuterba, Michal Petas, Bozena Kaminska, Michal Dabrowski
2013 Database: The Journal of Biological Databases and Curation  
We present the Nencki Genomics Database, which extends the functionality of Ensembl Regulatory Build (funcgen) for the three species: human, mouse and rat.  ...  The intersections and mapping to the genes are pre-computed for the public data, and the result of any procedure run on the data added by the users is stored back into the database, thus incrementally  ...  Database, Vol. 2013, Article ID bat069, doi:10.1093/database/bat069 Page 6 of 7 Database tool  ... 
doi:10.1093/database/bat069 pmid:24089456 pmcid:PMC3788330 fatcat:w2zvtpi67jfh7godawcbi6apwu

metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research

Mike Lyne, Richard N Smith, Rachel Lyne, Jelena Aleksic, Fengyuan Hu, Alex Kalderimis, Radek Stepan, Gos Micklem
2013 Database: The Journal of Biological Databases and Curation  
These are complemented by interoperation with the RatMine rat genomics database, with a corresponding mouse version under development by the Mouse Genome Informatics (MGI) group.  ...  Although the emphasis is on human data, key data sets from mouse and rat are included.  ...  Acknowledgements We would like to thank Felicity Payne, Giles Yeo and Robert Semple for contributing use cases that have helped shape metabolicMine's functionality.  ... 
doi:10.1093/database/bat060 pmid:23935057 pmcid:PMC4438919 fatcat:7eixajlfzbbchifkuqswnlloiu

Ensembl 2014

Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García Girón (+40 others)
2013 Nucleic Acids Research  
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals.  ...  Finally, we provide updated information about our methods for data access and resources for user training.  ...  ACKNOWLEDGEMENTS The authors wish to thank all of their users, the systems teams who maintain their computational infrastructure and those researchers who have provided data to  ... 
doi:10.1093/nar/gkt1196 pmid:24316576 pmcid:PMC3964975 fatcat:knxp7akjtnbvnm7hlxajhvnzra

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform

2019 Nucleic Acids Research  
Formed in late 1999, the Rat Genome Database (RGD, https://rgd.mcw.edu) will be 20 in 2020, the Year of the Rat.  ...  At its inception, before the sequencing of the rat genome, RGD started with only a few data types localized on genetic and radiation hybrid (RH) maps and offered only a few tools for querying and consolidating  ...  SUPPLEMENTARY DATA Supplementary Data are available at NAR Online.  ... 
doi:10.1093/nar/gkz1041 pmid:31713623 pmcid:PMC7145519 fatcat:4a6ja3vobncmtbp7m2hivrebr4

The UCSC Genome Browser database: update 2011

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome  ...  As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data  ...  Other tools The UCSC Genome Browser website provides additional tools to access the database and complement the Genome Browser.  ... 
doi:10.1093/nar/gkq963 pmid:20959295 pmcid:PMC3242726 fatcat:fnemefhmkbc65bmwbfxqlp7lpm

Rat Genome and Model Resources

Mary Shimoyama, Jennifer R. Smith, Elizabeth Bryda, Takashi Kuramoto, Laura Saba, Melinda Dwinell
2017 ILAR journal  
Those profiled here include the Rat Genome Database, PhenoGen, Gene Editing Rat Resource Center, Rat Resource and Research Center, and the National BioResource Project for the Rat in Japan.  ...  This explosion in genomic data has been accompanied by the ability to selectively edit the rat genome, leading to hundreds of new strains through multiple technologies.  ...  Department of Health and Human Services, National Institutes of Health, NIH Office of the Director, grant #P40OD011062 (RRRC); and the Ministry of Education, Culture, Sports, Science and Technology (MEXT  ... 
doi:10.1093/ilar/ilw041 pmid:28838068 pmcid:PMC6057551 fatcat:35ugntkgzzc6jl3o546n7cidhy

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse

Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson
2013 Nucleic Acids Research  
The Mouse Genome Database (MGD) (http://www. informatics.jax.org) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic  ...  vertebrate genomes and new loads of phenotype data from high-throughput phenotyping projects.  ...  INTRODUCTION The Mouse Genome Database (MGD) is the community model organism database resource for the laboratory mouse, a premier animal model for the study of genetic and genomic systems relevant to  ... 
doi:10.1093/nar/gkt1225 pmid:24285300 pmcid:PMC3964950 fatcat:iszlulio2zaw3kc7qmd3t22jmy

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community

Thomas A. Darde, Olivier Sallou, Emmanuelle Becker, Bertrand Evrard, Cyril Monjeaud, Yvan Le Bras, Bernard Jégou, Olivier Collin, Antoine D. Rolland, Frédéric Chalmel
2015 Nucleic Acids Research  
RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner.  ...  We report the development of the ReproGenomics Viewer (RGV), a multi-and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive  ...  We acknowledge the GenOuest bioinformatics facility for hosting the software. We also thank Dominique Mahe Poiron, Nathalie Dejucq-Rainsford and Nathalie Rioux-Leclerq for providing the human samples.  ... 
doi:10.1093/nar/gkv345 pmid:25883147 pmcid:PMC4489245 fatcat:zmoatmbgszddtepilcytxsv3my

InterMOD: integrated data and tools for the unification of model organism research

Julie Sullivan, Kalpana Karra, Sierra A. T. Moxon, Andrew Vallejos, Howie Motenko, J. D. Wong, Jelena Aleksic, Rama Balakrishnan, Gail Binkley, Todd Harris, Benjamin Hitz, Pushkala Jayaraman (+12 others)
2013 Scientific Reports  
So far including budding yeast, nematode worm, fruit fly, zebrafish, rat and mouse, the project has set up data warehouses, synchronized data models, and created analysis tools and links between data from  ...  The InterMOD consortium is developing an infrastructure based around the InterMine data warehouse system to integrate genomic and functional data from a number of key model organisms, leading the way to  ...  Acknowledgments The InterMOD project has been undertaken with support from the National Human Genome Research Institute, National Institutes of Health [RG51958 and RG60870], and the Wellcome Trust [090297  ... 
doi:10.1038/srep01802 pmid:23652793 pmcid:PMC3647165 fatcat:ylyyacmxdbeclgtk6u5jzqsizy

The UCSC Genome Browser database: 2014 update

Donna Karolchik, Galt P. Barber, Jonathan Casper, Hiram Clawson, Melissa S. Cline, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner (+13 others)
2013 Nucleic Acids Research  
As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for 90 organisms.  ...  The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets.  ...  ACKNOWLEDGEMENTS The authors would like to thank the many data contributors and collaborators whose work makes the Genome Browser possible, our Scientific Advisory Board for guiding our efforts, our users  ... 
doi:10.1093/nar/gkt1168 pmid:24270787 pmcid:PMC3964947 fatcat:nqcltynd7zdgrml2ntspdj3v74

The UCSC Genome Browser database: extensions and updates 2013

Laurence R. Meyer, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Robert M. Kuhn, Matthew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Brian J. Raney, Andy Pohl (+20 others)
2012 Nucleic Acids Research  
The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets.  ...  In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013.  ...  ACKNOWLEDGEMENTS The authors would like to thank the many data contributors whose work makes the Genome Browser possible, our Scientific Advisory Board for steering our efforts, our users for their consistent  ... 
doi:10.1093/nar/gks1048 pmid:23155063 pmcid:PMC3531082 fatcat:pernizd77fdijcyqc56eicrqzq

The updated RGD Pathway Portal utilizes increased curation efficiency and provides expanded pathway information

G Thomas Hayman, Pushkala Jayaraman, Victoria Petri, Marek Tutaj, Weisong Liu, Jeff De Pons, Melinda R Dwinell, Mary Shimoyama
2013 Human Genomics  
The application combines these with tables of rat, human and mouse pathway genes, including genetic information, analysis tool and reference links, and disease, phenotype and other pathway annotations  ...  The RGD Pathway Portal provides pathway annotations for rat, human and mouse genes and pathway diagrams and suites, all interconnected via the pathway ontology.  ...  Smith for assistance with preparation of the figures, and the RGD Team.  ... 
doi:10.1186/1479-7364-7-4 pmid:23379628 pmcid:PMC3598722 fatcat:zru4t2k57zbfvcz2ecagj6faz4
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