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Adapting Disease Vocabularies for Curation at the Rat Genome Database

Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell
2018 International Conference on Biomedical Ontology  
The Rat Genome Database (RGD) has been annotating genes, QTLs, and strains to disease terms for over 15 years.  ...  During that time the controlled vocabulary used for disease curation has changed a few times.  ...  For at least a few years it was the most publicly accessible, complete, and useful vocabulary to describe diseases and disease processes.  ... 
dblp:conf/icbo/LaulederkindHWB18 fatcat:xxszfjfo5zawlmdzs7jm74fzpa

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  
To generate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding  ...  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.  ...  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

Orthology for comparative genomics in the mouse genome database

Mary E. Dolan, Richard M. Baldarelli, Susan M. Bello, Li Ni, Monica S. McAndrews, Carol J. Bult, James A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Judith A. Blake
2015 Mammalian Genome  
The mouse genome database (MGD) is the model organism database component of the mouse genome informatics system at The Jackson Laboratory.  ...  MGD is the international data resource for the laboratory mouse and facilitates the use of mice in the study of human health and disease.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s00335-015-9588-5 pmid:26223881 pmcid:PMC4534493 fatcat:gsj5nwfyj5b4jkwsku72xkysve

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. ....................................................................................................  ...  The rat genome assembly v3.4 and the human genome assembly GRCH37.p5 were used at the time of analysis.  ...  and metabolic diseases) from genome browsers at RGD.  ... 
doi:10.1093/database/bat046 pmid:23794737 pmcid:PMC3689439 fatcat:jsagknmhjrdnhbzxhoslocid4y

OntoMate: a text-mining tool aiding curation at the Rat Genome Database

Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff De Pons, Melinda R. Dwinell, Mary Shimoyama
2015 Database: The Journal of Biological Databases and Curation  
The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data.  ...  OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD.  ...  Funding for open access charge: National Heart, Lung and Blood Institute on behalf of the National Institutes of Health (HL64541). Conflict of interest. None declared.  ... 
doi:10.1093/database/bau129 pmid:25619558 pmcid:PMC4305386 fatcat:tu5j3s7rujf2ngqe2m4rhwj6rq

The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data

S. J. F. Laulederkind, M. Shimoyama, G. T. Hayman, T. F. Lowry, R. Nigam, V. Petri, J. R. Smith, S.-J. Wang, J. de Pons, G. Kowalski, W. Liu, W. Rood (+4 others)
2011 Database: The Journal of Biological Databases and Curation  
Summary The Rat Genome Database curates many types of data (disease, phenotype, pathway, molecular function, biological process, cellular component and nomenclature) for a variety of objects (genes, QTLs  ...  However, because the curation tool software was designed specifically to fit the RGD database schema, it would not be easily adaptable for use with other databases and so it has not been made publicly  ... 
doi:10.1093/database/bar002 pmid:21321022 pmcid:PMC3041158 fatcat:gzoadgdnsre4vi7samk3flcjwu

The Rat Genome Database Pathway Portal

V. Petri, M. Shimoyama, G. T. Hayman, J. R. Smith, M. Tutaj, J. de Pons, M. R. Dwinell, D. H. Munzenmaier, S. N. Twigger, H. J. Jacob
2011 Database: The Journal of Biological Databases and Curation  
Funding Funding for open access charge: National Heart, Lung and Blood Institute on behalf of the National Institutes of Health [5RO1HL064541]. Conflict of interest. None declared.  ...  Introduction The Rat Genome Database [(RGD) http://rgd.mcw.edu], the model organism database for the laboratory rat, provides a breadth of information ranging from genomic and genetic to molecular and  ...  The Mammalian Phenotype Ontology (MP), developed at the Mouse Genome Informatics (MGI, the Mouse Genome Database)-http://www.informatics.jax.org/ with RGD contributing terms, is used for the annotation  ... 
doi:10.1093/database/bar010 pmid:21478484 pmcid:PMC3072770 fatcat:dj52mas7e5hcbihell3dbrf25e

Mouse Genome Database: From sequence to phenotypes and disease models

Janan T. Eppig, Joel E. Richardson, James A. Kadin, Cynthia L. Smith, Judith A. Blake, Carol J. Bult
2015 Genesis  
The Mouse Genome Database (MGD, www. informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements  ...  annotations for mouse gene functions, a comprehensive catalog of mouse mutations and their phenotypes, and a curated compendium of mouse models of human diseases.  ...  The Mammalian Phenotype (MP) Ontology is essential for the curation of phenotype data. It is a structured vocabulary whose initial development and continued maintenance is centered at MGD.  ... 
doi:10.1002/dvg.22874 pmid:26150326 pmcid:PMC4545690 fatcat:fv3rrn7kk5ccliujtdbbsyzm5a

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
2015 Database: The Journal of Biological Databases and Curation  
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.  ...  In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases.  ...  Acknowledgements We thank Dieter Scheller, whilst at UCB Pharma, for contributions as a disease expert. We are also grateful to Jonathan van Eyll for his inputs.  ... 
doi:10.1093/database/bav099 pmid:26475471 pmcid:PMC4608514 fatcat:r5sachf3wjhqzcgb6lycqo6gre

The MINTAct Archive for Mutations Influencing Molecular Interactions

Pablo Porras Millán, Margaret Duesbury, Maximilian Koch, Sandra Orchard
2017 Genomics and Computational Biology  
The dataset contains data from about 300 different organisms, with a predominance of events related to human proteins, and it is freely available at the IntAct database website using this link: www.ebi.ac.uk  ...  The MINTAct archive for mutations affecting interaction holds results of over 28,000 events on the influence of a change of protein sequence on physical interaction outcome.  ...  The IntAct database at the European Bioinformatics Institute (www.ebi.ac. uk/intact) [1] has, as its primary aim, the collation of highly detailed experimental interaction data to make it available for  ... 
doi:10.18547/gcb.2018.vol4.iss1.e100053 fatcat:djdbtmnm6vdphmr674w4cjw6pq

Mouse Genome Informatics (MGI): latest news from MGD and GXD

Martin Ringwald, Joel E. Richardson, Richard M. Baldarelli, Judith A. Blake, James A. Kadin, Cynthia Smith, Carol J. Bult
2021 Mammalian Genome  
MGI's mission is to facilitate the use of the mouse as an experimental model for understanding the genetic and genomic basis of human health and disease.  ...  The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI's two major knowledgebases.  ...  Acknowledgements We thank all the MGI curators and developers for their dedication and their many contributions to MGI. We are grateful to Dr. Hagit Shatkay (University of Delaware) and Dr.  ... 
doi:10.1007/s00335-021-09921-0 pmid:34698891 pmcid:PMC8913530 fatcat:zwlwn4gb5vhwzfnkx5qszjn7ii

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 Comparative Toxicogenomics Database: update 2017

Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Benjamin L. King, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly
2016 Nucleic Acids Research  
Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate  ...  The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases.  ...  A single, robust, community-accepted disease vocabulary would be valuable for synchronizing the vast arrays of different biological databases.  ... 
doi:10.1093/nar/gkw838 pmid:27651457 pmcid:PMC5210612 fatcat:povogyqyofcebnljc3jnl4fnoq

The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data

Cynthia L. Smith, Janan T. Eppig
2012 Mammalian Genome  
A wealth of phenotype data on mouse mutations and variants annotated to the MP already exists in the Mouse Genome Informatics database.  ...  The Mammalian Phenotype Ontology (MP) is a structured vocabulary for describing mammalian phenotypes and serves as a critical tool for efficient annotation and comprehensive retrieval of phenotype data  ...  Babiuk for helpful comments on the manuscript. This work was funded by the National Institutes of Health, National Human Genome Research Institute (NHGRI) Grant HG000330.  ... 
doi:10.1007/s00335-012-9421-3 pmid:22961259 pmcid:PMC3463787 fatcat:ygcz5rtafnbo7a7exo764r5vsu

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

William J. Bug, Giorgio A. Ascoli, Jeffrey S. Grethe, Amarnath Gupta, Christine Fennema-Notestine, Angela R. Laird, Stephen D. Larson, Daniel Rubin, Gordon M. Shepherd, Jessica A. Turner, Maryann E. Martone
2008 Neuroinformatics  
Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured  ...  A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neurosciencerelevant resources.  ...  the original author(s) and source are credited.  ... 
doi:10.1007/s12021-008-9032-z pmid:18975148 pmcid:PMC2743139 fatcat:5xu3gqt2hndotmmjru4xwnwaqu
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