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Ontology searching and browsing at the Rat Genome Database

S. J. F. Laulederkind, M. Tutaj, M. Shimoyama, G. T. Hayman, T. F. Lowry, R. Nigam, V. Petri, J. R. Smith, S.-J. Wang, J. de Pons, M. R. Dwinell, H. J. Jacob
2012 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) is the premier repository of rat genomic and genetic data and currently houses over 40 000 rat gene records, as well as human and mouse orthologs, 1857 rat and 1912 human  ...  That means a lot of time can be spent searching and browsing ontologies for the appropriate terms needed both for curating and mining the data.  ...  Biocuration at the Rat Genome Database (RGD) involves the use of many different ontologies for annotating biological information to data objects [genes, strains and quantitative trait loci (QTLs)].  ... 
doi:10.1093/database/bas016 pmid:22434847 pmcid:PMC3308169 fatcat:l4yb3lwjajaqxcf7drlbkx5fkm

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database

2019 Database: The Journal of Biological Databases and Curation  
Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search.  ...  To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well  ...  Funding This work was supported by the National Heart, Lung and Blood Institute on behalf of the National Institutes of Health (HL64541).  ... 
doi:10.1093/database/baz014 pmid:30753478 pmcid:PMC6369425 fatcat:qwyuqyxtpzcu5hyom3tedoxoni

Exploring human disease using the Rat Genome Database

Mary Shimoyama, Stanley J. F. Laulederkind, Jeff De Pons, Rajni Nigam, Jennifer R. Smith, Marek Tutaj, Victoria Petri, G. Thomas Hayman, Shur-Jen Wang, Omid Ghiasvand, Jyothi Thota, Melinda R. Dwinell
2016 Disease Models & Mechanisms  
Since 1999, the Rat Genome Database (RGD; http://rgd.mcw.edu) has been the premier resource for genomic, genetic, phenotype and strain data for the laboratory rat.  ...  The primary role of RGD is to curate rat data and validate orthologous relationships with human and mouse genes, and make these data available for incorporation into other major databases such as NCBI,  ...  Because of the recognized value of existing and emerging rat datasets, the Rat Genome Database (RGD; http://rgd.mcw.edu) was created in 1999 and has evolved into the leading resource for rat genomic, genetic  ... 
doi:10.1242/dmm.026021 pmid:27736745 pmcid:PMC5087824 fatcat:vdsgvhtmfne7vp5ddubf3bp3hy

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

Mary Shimoyama, Jennifer R. Smith, Jeff De Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich, Lauren O. Bakaletz, Joseph E. Kerschner
2016 Database: The Journal of Biological Databases and Curation  
Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool.  ...  The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu  ...  CRRD was built on existing software architecture previously developed at the Rat Genome Database (15) .  ... 
doi:10.1093/database/baw073 pmid:27173523 pmcid:PMC4865329 fatcat:fqvpe2zq2vc4lbnieakuwphquy

The Rat Genome Database (RGD): developments towards a phenome database

N. de la Cruz
2004 Nucleic Acids Research  
The Rat Genome Database (RGD) (http://rgd.mcw. edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry  ...  to efficiently browse and survey research data.  ...  Unlike most search engines, RGD searches both ontology annotations and synonyms, and free text notes.  ... 
doi:10.1093/nar/gki050 pmid:15608243 pmcid:PMC540004 fatcat:gnzke5nrlfbmnikqraddcnazea

ERGR: An ethanol-related gene resource

A.-Y. Guo, B. T. Webb, M. F. Miles, M. P. Zimmerman, K. S. Kendler, Z. Zhao
2009 Nucleic Acids Research  
The ERGR database is evolving with new data releases. More functions will also be added. ERGR has a user-friendly web interface with browse and search functions at multiple levels.  ...  At present, the ERGR deposits ethanol-related information of 7000 genes from five organisms: human (3311), mouse (2129), rat (679), fly (614) and worm (228) .  ...  ACKNOWLEDGEMENTS We regret that numerous ethanol studies, from which the ERGR data were extracted through literature search, have not been cited in this paper because of our focus on data curation and  ... 
doi:10.1093/nar/gkn816 pmid:18978021 pmcid:PMC2686553 fatcat:oaubdnp6uvc2zm33mj4z5a5a2e

Web Resources for Model Organism Studies

Bixia Tang, Yanqing Wang, Junwei Zhu, Wenming Zhao
2015 Genomics, Proteomics & Bioinformatics  
Significantly, the organism databases instituted in the early 1990s--such as the Mouse Genome Database (MGD), Saccharomyces Genome Database (SGD), and FlyBase--have developed into what are now comprehensive  ...  Furthermore, all of the databases mentioned here update continually according to user feedback and with advancing technologies.  ...  Supplementary material Supplementary material associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j. gpb.2015.01.003.  ... 
doi:10.1016/j.gpb.2015.01.003 pmid:25707592 pmcid:PMC4411489 fatcat:s56qk3jnx5eq7baciz25exjsaq

The Rat Genome Database, update 2007--Easing the path from disease to data and back again

S. N. Twigger, M. Shimoyama, S. Bromberg, A. E. Kwitek, H. J. Jacob
2007 Nucleic Acids Research  
The Rat Genome Database (RGD, http://rgd.mcw. edu) is one of the core resources for rat genomics and recent developments have focused on providing support for disease-based research using the rat model  ...  We have published a number of papers that provide additional information on the ontology annotations and the tools at RGD for data mining and analysis to better enable researchers to fully utilize the  ...  ACKNOWLEDGEMENTS In addition to the listed authors RGD is built and maintained by the following group of dedicated people: Jiali Chen, Weihong Jin, Nataliya Nenasheva, Rajni Nigam, Andrew Patzer, Victoria  ... 
doi:10.1093/nar/gkl988 pmid:17151068 pmcid:PMC1761441 fatcat:2zdfnka2dfh7fgggb5ulwxznti

AnimalTFDB: a comprehensive animal transcription factor database

H.-M. Zhang, H. Chen, W. Liu, H. Liu, J. Gong, H. Wang, A.-Y. Guo
2011 Nucleic Acids Research  
AnimalTFDB has a user-friendly web interface with multiple browse and search functions, as well as data downloading. It is freely available at http://www.bioguo.org/AnimalTFDB/.  ...  Then, we systematically characterized all the TFs in 50 animal species and constructed a comprehensive animal TF database, AnimalTFDB.  ...  ACKNOWLEDGEMENTS The authors would like to thank Zhaowu Ma, Huashan Ye, Mi Zhou, Jun Yan, Shuzhen Kuang, Yifang Liao and Yuliang Wu for their valuable advices to improve the database.  ... 
doi:10.1093/nar/gkr965 pmid:22080564 pmcid:PMC3245155 fatcat:kpdk2oocf5gytjly6gd2zxjazq

RGD: A comparative genomics platform

Mary Shimoyama, Jennifer R Smith, Tom Hayman, Stan Laulederkind, Tim Lowry, Rajni Nigam, Victoria Petri, Shur-Jen Wang, Melinda Dwinell, Howard Jacob
2011 Human Genomics  
The Rat Genome Database (RGD) (http://rgd.mcw.edu) provides a comprehensive platform for comparative genomics and genetics research.  ...  RGD houses gene, QTL and polymorphic marker data for rat, mouse and human and provides easy access to data through sophisticated searches, disease portals, interactive pathway diagrams and rat and human  ...  GViewer provides users with a genome-wide view of rat genes and QTL retrieved from ontology-based searches.  ... 
doi:10.1186/1479-7364-5-2-124 pmid:21296746 pmcid:PMC3222152 fatcat:72ew4ndmqbbfpihllv3jmccmce

What everybody should know about the rat genome and its online resources

Simon N Twigger, Kim D Pruitt, Xosé M Fernández-Suárez, Donna Karolchik, Kim C Worley, Donna R Maglott, Garth Brown, George Weinstock, Richard A Gibbs, Jim Kent, Ewan Birney, Howard J Jacob
2008 Nature Genetics  
We then cover the key online resources providing access to the rat genome, including the new SNP views at Ensembl, the RefSeq and Genes databases at the US  ...  In this commentary, we describe the current status of the rat genome sequence and the plans for its impending 'upgrade'.  ...  The Phase 2 genome project and SNP discovery at Baylor College of Medicine Human Genome Sequencing Center is funded by NHGRI HG-003273.  ... 
doi:10.1038/ng0508-523 pmid:18443589 pmcid:PMC2505193 fatcat:k5rnfgkj6ngzpkieh27xgwkgpa

Tools and strategies for physiological genomics: the Rat Genome Database

Simon N. Twigger, Dean Pasko, Jeff Nie, Mary Shimoyama, Susan Bromberg, Dan Campbell, Jiali Chen, Norberto dela Cruz, Chunyu Fan, Cindy Foote, Glenn Harris, Brian Hickmann (+20 others)
2005 Physiological Genomics  
The Rat Genome Database (RGD; http://rgd. mcw.edu) has developed computational tools and strategies specifically supporting the goal of linking genes to their functional roles in rat and, using comparative  ...  We present an overview of the database with a focus on these unique computational tools and describe strategies for the use of these resources in the area of physiological genomics.  ...  ACKNOWLEDGMENTS We thank Carol Moreno-Quinn for critical review of this manuscript and Brian Halligan for invaluable help with Acrobat.  ... 
doi:10.1152/physiolgenomics.00040.2005 pmid:16106031 pmcid:PMC4505745 fatcat:a5aranpv5feflcbwjqeddqxg4m

dbDEPC: a database of Differentially Expressed Proteins in human Cancers

Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, Yixue Li
2009 Nucleic Acids Research  
Years of effort from scientists and doctors worldwide have generated large amounts of data at the genome, transcriptome, proteome and even metabolome level, and DNA and RNA cancer signature databases have  ...  dbDEPC is expected to be a reference database for cancer signatures at the protein level.  ...  ACKNOWLEDGEMENT The authors acknowledge Lynne Berry from the Vanderbilt Cancer Biostatistics Center for her editing work.  ... 
doi:10.1093/nar/gkp933 pmid:19900968 pmcid:PMC2808941 fatcat:hnppd37igbbtpgubmc6ky3rtb4

The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species

Carissa A Park, Susan M Bello, Cynthia L Smith, Zhi-Liang Hu, Diane H Munzenmaier, Rajni Nigam, Jennifer R Smith, Mary Shimoyama, Janan T Eppig, James M Reecy
2013 Journal of Biomedical Semantics  
It is being used in the Rat Genome Database and Animal QTL Database for annotation of QTL data for rat, cattle, chicken, swine, sheep, and rainbow trout, and in the Mouse Phenome Database to annotate strain  ...  The ontology is available at http://bioportal.bioontology.org/ontologies/50138.  ...  We would also like to thank the teams at RGD, MGI, and Animal QTL Database for providing ongoing assistance and support.  ... 
doi:10.1186/2041-1480-4-13 pmid:23937709 pmcid:PMC3851175 fatcat:zb7vxbpq2rfj7iysuxnbwa2nme

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs

T. Mituyama, K. Yamada, E. Hattori, H. Okida, Y. Ono, G. Terai, A. Yoshizawa, T. Komori, K. Asai
2009 Nucleic Acids Research  
The former is a sequence database equipped with a powerful search function and hosts a large collection of known/predicted non-coding RNA sequences acquired from existing databases as well as novel/ predicted  ...  The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC Geno-meBrowser  ...  ACKNOWLEDGEMENTS The authors thank everyone in the bioinformatics group of the Functional RNA Project for constructive criticisms and fruitful discussions.  ... 
doi:10.1093/nar/gkn805 pmid:18948287 pmcid:PMC2686472 fatcat:5ap3uo42qnflbheznx65vhj2ge
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