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Ontology searching and browsing at the Rat Genome Database
2012
Database: The Journal of Biological Databases and Curation
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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
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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
2016
Disease Models & Mechanisms
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2004
Nucleic Acids Research
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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
2009
Nucleic Acids Research
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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
2015
Genomics, Proteomics & Bioinformatics
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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
2007
Nucleic Acids Research
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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
2011
Nucleic Acids Research
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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
2011
Human Genomics
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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
2008
Nature Genetics
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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
2005
Physiological Genomics
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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
2009
Nucleic Acids Research
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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
2013
Journal of Biomedical Semantics
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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
2009
Nucleic Acids Research
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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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