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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.  ...  The quantitative phenotype annotations greatly increase the depth of the phenotype data available to the database user.  ... 
doi:10.1093/database/bat015 pmid:23603846 pmcid:PMC3630803 fatcat:ig4o5af6hrbxbaftzwrgd4dnbi

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus . Application in hypertension and renal disease

Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama
2015 Database: The Journal of Biological Databases and Curation  
Recently, the Rat Genome Database (http://rgd.mcw.edu) has initiated the PhenoMiner project to integrate quantitative phenotype data from the PhysGen Program for Genomic Applications and the National BioResource  ...  PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease.  ...  To better facilitate data mining across multiple projects, the Rat Genome Database (RGD) has initiated the PhenoMiner project to integrate quantitative phenotype data from PhysGen projects (http:// pga.mcw.edu  ... 
doi:10.1093/database/bau128 pmid:25632109 pmcid:PMC4309021 fatcat:3j7b6o67qjd73bim4d3rwsz4k4

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

2019 Database: The Journal of Biological Databases and Curation  
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  ...  From the curated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred rat strains in control conditions.  ...  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

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.  ...  genome browsers.  ...  Introduction The Rat Genome Database (RGD) (http://rgd. mcw.edu) is recognised as the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus.  ... 
doi:10.1186/1479-7364-5-2-124 pmid:21296746 pmcid:PMC3222152 fatcat:72ew4ndmqbbfpihllv3jmccmce

Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data

Rajni Nigam, Stanley J. F. Laulederkind, G. Thomas Hayman, Jennifer R. Smith, Shur-Jen Wang, Timothy F. Lowry, Victoria Petri, Jeff De Pons, Marek Tutaj, Weisong Liu, Pushkala Jayaraman, Diane H. Munzenmaier (+4 others)
2013 Physiological Genomics  
Rat Genome Database: a unique resource for rat, human, and mouse quantitative trait locus data.  ...  QTL Traits A wide variety of traits associated with multiple physiological systems are represented by the QTLs at Rat Genome Database (RGD).  ...  The strain pages contain links to the quantitative phenotype values cu- rated from this paper and can be accessed through the section on the strain report page "Phenotype Values via PhenoMiner" (8, 9  ... 
doi:10.1152/physiolgenomics.00065.2013 pmid:23881287 pmcid:PMC3783816 fatcat:jsz5bnta7rdbplf5xjawziqiym

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

Mary Shimoyama, Jeff De Pons, G. Thomas Hayman, Stanley J.F. Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth Worthey, Melinda Dwinell (+1 others)
2014 Nucleic Acids Research  
The Rat Genome Database (RGD, http://rgd.mcw.edu) provides the most comprehensive data repository and informatics platform related to the laboratory rat, one of the most important model organisms for disease  ...  Complementing the genomic data catalogs are those associated with phenotypes and disease, including strains, QTL and experimental phenotype measurements across hundreds of strains.  ...  INTRODUCTION The Rat Genome Database (RGD) has been the premier resource for rat genetic, genomic and phenotypic data since its creation in 1999.  ... 
doi:10.1093/nar/gku1026 pmid:25355511 pmcid:PMC4383884 fatcat:2wlnpqd725hazik7iphaxaifk4

OUP accepted manuscript

2019 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) PhenoMiner tool has provided the first step in this effort by standardizing and integrating data from individual studies as well as NBRP and PhysGen. iii Methods Our work  ...  Current resources such as NBRP and PhysGen provided some preliminary work in rat phenotype databases.  ...  Genome Database PhenoMiner Project.  ... 
doi:10.1093/database/baz037 fatcat:ifj26ad6grh2vcqvbtnxoevdwq

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications

Jennifer R Smith, Carissa A Park, Rajni Nigam, Stanley JF Laulederkind, G Hayman, Shur-Jen Wang, Timothy F Lowry, Victoria Petri, Jeff Pons, Marek Tutaj, Weisong Liu, Elizabeth A Worthey (+2 others)
2013 Journal of Biomedical Semantics  
rat phenotype data in order to integrate results from multiple studies into the PhenoMiner database and data mining tool.  ...  The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative  ...  Acknowledgements This project was supported by grants HL064541 (RGD) and HL094271 (PhenoMiner) from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health.  ... 
doi:10.1186/2041-1480-4-26 pmid:24103152 pmcid:PMC3882879 fatcat:nszdruvaffer5mms66nucddxpe

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database

Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Rajni Nigam, Melinda R. Dwinell, Mary Shimoyama
2016 Physiological Genomics  
To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases  ...  The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases.  ...  One of the tabs "Phenotype Values via Phenominer" leads to the quantitative database Phenominer, where numerical values of physiological measurements from rat strains are available (11, 23) . QTLs.  ... 
doi:10.1152/physiolgenomics.00046.2016 pmid:27287925 pmcid:PMC5005459 fatcat:rcxcvzeumva6rfhzhm6uvc5k7i

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

Combined C&D Group Publication on INFRAFRONTIER and IMPC Globally Available and Shared Resources

Asrar Ali Khan, Michael Raess
2020 Zenodo  
At the time of submission of this deliverable, the article was not published.  ...  In standardized pipelines, GMC contributes phenotyping data to the comprehensive databases of the IMPC.  ...  , genotypic/phenotypic data curation and disease model annotation, as well as related training activities.  ... 
doi:10.5281/zenodo.5833762 fatcat:dep7yddhmjfz5dv5ci5t5w63ki

Three Ontologies to Define Phenotype Measurement Data

Mary Shimoyama, Rajni Nigam, Leslie Sanders McIntosh, Rakesh Nagarajan, Treva Rice, D. C. Rao, Melinda R. Dwinell
2012 Frontiers in Genetics  
These ontologies provided the framework for integration of rat phenotype data from multiple studies into a single resource as well as facilitated data integration from multiple human epidemiological studies  ...  Conclusion: An ontology based framework for phenotype measurement data affords the ability to successfully integrate vital phenotype data into critical resources, regardless of underlying technological  ...  ACKNOWLEDGMENTS The authors would like to acknowledge the contributions of the RGD curation team at the Medical College of Wisconsin and the staff and informatics team at Washington University.  ... 
doi:10.3389/fgene.2012.00087 pmid:22654893 pmcid:PMC3361058 fatcat:3zl75bhe7fdf3hbmnef7ptr5ay

The Disease Portals, disease–gene annotation and the RGD disease ontology at the Rat Genome Database

G. Thomas Hayman, Stanley J. F. Laulederkind, Jennifer R. Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff De Pons, Melinda R. Dwinell, Mary Shimoyama
2016 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD; http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide.  ...  The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals.  ...  Introduction In response to the observation that rat researchers, unlike researchers using other model organism databases, tend to be more disease oriented (1) , the Rat Genome Database (RGD) has directed  ... 
doi:10.1093/database/baw034 pmid:27009807 pmcid:PMC4805243 fatcat:ich5qiet3vbobpmbeod2cotkhm

Disease, Models, Variants and Altered Pathways—Journeying RGD Through the Magnifying Glass

Victoria Petri, G. Thomas Hayman, Marek Tutaj, Jennifer R. Smith, Stan Laulederkind, Shur-Jen Wang, Rajni Nigam, Jeff De Pons, Mary Shimoyama, Melinda R. Dwinell
2016 Computational and Structural Biotechnology Journal  
The Rat Genome Database (RGD-http://rgd.mcw.edu) has been established to house rat genetic, genomic and phenotypic data.  ...  The vocabularies/ontologies allow the capture of disease and phenotype associations of rat strains and QTLs, as well as disease and pathway associations of rat, human and mouse genes.  ...  Acknowledgments The RGD project is funded by Grant HL064541 from the National Heart, Lung, and Blood Institute on behalf of the National Institutes of Health.  ... 
doi:10.1016/j.csbj.2015.11.006 pmid:27602200 pmcid:PMC4700298 fatcat:mtz3rsiqp5esxf6qbfgygrzgyy

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  ...  quantitative trait loci (QTLs) and 2347 rat strains.  ...  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
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