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Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology

Judith A Blake, Richard Baldarelli, James A Kadin, Joel E Richardson, Cynthia L Smith, Carol J Bult, Anna V Anagnostopoulos, Jon S Beal, Susan M Bello, Olin Blodgett, Nancy E Butler, Jeffry Campbell (+26 others)
2020 Nucleic Acids Research  
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic  ...  and genomic basis for human health and disease.  ...  MOUSE GENOME DATABASE GROUP ACKNOWLEDGEMENTS We thank the members of the MGD Scientific Advisory Board and members of our user community for their feedback and suggestions on the enhancements and new  ... 
doi:10.1093/nar/gkaa1083 pmid:33231642 fatcat:wlxmguufevcnvjsffgxlqxhg7e

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

Cynthia L Smith, Judith A Blake, James A Kadin, Joel E Richardson, Carol J Bult
2017 Nucleic Acids Research  
, genomics, and biology of the laboratory mouse.  ...  MGD serves as the source for biological reference data sets related to mouse genes, gene functions, phenotypes and disease models with an increasing emphasis on the association of these data to human biology  ...  ACKNOWLEDGEMENTS We are grateful to our collaborators at Disease Ontology (DO) and Rat Genome Database (RGD) for providing updated disease ontology files and help with revisions and additions to the ontology  ... 
doi:10.1093/nar/gkx1006 pmid:29092072 pmcid:PMC5753350 fatcat:vvlq4zpe4jac7ik25sh26qrulq

The Mouse Genome Database (MGD): mouse biology and model systems

C. J. Bult, J. T. Eppig, J. A. Kadin, J. E. Richardson, J. A. Blake
2007 Nucleic Acids Research  
The Mouse Genome Database, (MGD, http:// www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology  ...  representation of genome and genome variant information including comparative data on mammalian genes.  ...  ACKNOWLEDGEMENTS The Mouse Genome Database is supported by NIH/ NHGRI grant HG000330. Funding to pay the Open Access publication charges for this article was provided by HG000330.  ... 
doi:10.1093/nar/gkm961 pmid:18158299 pmcid:PMC2238849 fatcat:pmebitz5ura4pmusobr7cfxbuy

The Mouse Genome Database (MGD): integrating biology with the genome

C. J. Bult
2004 Nucleic Acids Research  
The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse.  ...  MGD collaborates with other bioinformatics groups to curate a de®nitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative  ...  ACKNOWLEDGEMENTS MGD is supported by NIH/NHGRI grant HG00330.  ... 
doi:10.1093/nar/gkh125 pmid:14681461 pmcid:PMC308859 fatcat:uprwazyvfndahp6bojvp5rxqo4

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult
2016 Nucleic Acids Research  
The Mouse Genome Database (MGD: http://www. informatics.jax.org) is the primary community data resource for the laboratory mouse.  ...  features with sequence, phenotypes, functional and comparative information, and their relationships to human diseases.  ...  ACKNOWLEDGEMENTS The authors thank David Shaw for his contributions and leadership in providing User Support services to the community of scientists who use MGD and all MGI data resources.  ... 
doi:10.1093/nar/gkw1040 pmid:27899570 pmcid:PMC5210536 fatcat:t7apqsxrl5h7zbjn4bo47zejhu

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

J. A. Blake, C. J. Bult, J. A. Kadin, J. E. Richardson, J. T. Eppig
2010 Nucleic Acids Research  
The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the authoritative source for phenotype and functional annotations of mouse genes.  ...  studying human biology and disease.  ...  INTRODUCTION The Mouse Genome Database (MGD) is an integrated database of genetic, genomic and phenotypic data for the laboratory mouse (1) (2) (3) .  ... 
doi:10.1093/nar/gkq1008 pmid:21051359 pmcid:PMC3013640 fatcat:lvzlsqzkuzg2nhthgtlm7f4mdm

The Mouse Genome Database genotypes::phenotypes

J. A. Blake, C. J. Bult, J. T. Eppig, J. A. Kadin, J. E. Richardson
2009 Nucleic Acids Research  
The Mouse Genome Database (MGD, http://www. informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and  ...  Recent improvements in MGD described here include the unified mouse gene catalog for NCBI Build 37 of the reference genome assembly, and improved representation of mouse mutants and phenotypes.  ...  system for studying human biology.  ... 
doi:10.1093/nar/gkn886 pmid:18981050 pmcid:PMC2686566 fatcat:2ipclifxdnbljet6f65fu4i52y

The Mouse Genome Database: enhancements and updates

Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T Eppig
2009 Nucleic Acids Research  
The Mouse Genome Database (MGD) is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) database resource and serves as the primary community model organism database  ...  representation of genome and genome variant information including comparative data on mammalian genes.  ...  INTRODUCTION The Mouse Genome Database (MGD) is an integrated database of genetic, genomic and phenotypic data for the laboratory mouse (1) (2) (3) .  ... 
doi:10.1093/nar/gkp880 pmid:19864252 pmcid:PMC2808942 fatcat:4azrklowubgqxfc7fogb5644ei

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  ...  Among the key data sets MGD supports are: the complete catalog of mouse genes and genome features, comparative homology data for mouse and vertebrate genes, the authoritative set of Gene Ontology (GO)  ...  myriad genomic tools available for comparative and experimental manipulation.  ... 
doi:10.1002/dvg.22874 pmid:26150326 pmcid:PMC4545690 fatcat:fv3rrn7kk5ccliujtdbbsyzm5a

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  
The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are MGI's two major knowledgebases.  ...  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.  ...  Xiangying Jiang (Amazon) for discussions about machine learning approaches to MGI's literature curation processes.  ... 
doi:10.1007/s00335-021-09921-0 pmid:34698891 pmcid:PMC8913530 fatcat:zwlwn4gb5vhwzfnkx5qszjn7ii

PhenoHM: human–mouse comparative phenome–genome server

Divya Sardana, Suresh Vasa, Nishanth Vepachedu, Jing Chen, Ranga Chandra Gudivada, Bruce J. Aronow, Anil G. Jegga
2010 Nucleic Acids Research  
The MPO (6) from Mouse Genome Database (MGD) (12) enables robust annotation of mammalian phenotypes in the context of mutations, quantitative trait loci and strains that are used as models of human biology  ...  human-mouse comparative phenomics.  ... 
doi:10.1093/nar/gkq472 pmid:20507906 pmcid:PMC2896149 fatcat:trb2tkybvvedrasjh6ob6j7a4e

Protein Bioinformatics Databases and Resources [chapter]

Chuming Chen, Hongzhan Huang, Cathy H. Wu
2017 Msphere  
, gene expression databases, genome annotation databases, organism specific databases, phylogenomic databases, polymorphism and mutation databases, protein-protein interaction databases, proteomic databases  ...  For each category of databases listed in Table 1 , we select some representatives and describe them briefly in section 2.  ...  Table MGD-The Mouse Genome Database (MGD) [84] is a database of integrated genomic, genetic and biological data on the laboratory mouse that is a model for translational research.  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy

The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

The Alliance of Genome Resources Consortium
2019 Genetics  
For decades, researchers who use model organisms have relied on Model Organism Databases (MODs) and the Gene Ontology Consortium (GOC) for expertly curated annotations, and for access to integrated genomic  ...  Model organisms are essential experimental platforms for discovering gene functions, defining protein and genetic networks, uncovering functional consequences of human genome variation, and for modeling  ...  V.D.F. and R.F. contributed to this manuscript in their official roles as program coordinators for the National Institutes of Health National Human Genome Research Institute.  ... 
doi:10.1534/genetics.119.302523 pmid:31796553 pmcid:PMC6893393 fatcat:fxxxo7f62nhhhirqf6rgtz3oaq

Computational resources associating diseases with genotypes, phenotypes and exposures

Wenliang Zhang, Haiyue Zhang, Huan Yang, Miaoxin Li, Zhi Xie, Weizhong Li
2018 Briefings in Bioinformatics  
He is interested in discovering novel genomic variations associated with human diseases. Zhi Xie (MD, PhD) is a professor of Bioinformatics in Zhongshan Ophthalmic Center at Sun Yat-sen University.  ...  Her research is focused on building and applying ontologies for phenotypes and diseases. Huan Yang is a PhD student in Zhongshan School of Medicine at Sun Yat-sen University.  ...  Mouse Genome Database (MGD) [22] and MouseNet [23] , Rat Genome Database (RGD) [24] and Zebrafish Model Organism Database (ZFIN) [25] .  ... 
doi:10.1093/bib/bby071 pmid:30102366 fatcat:63ijmbhgxbf6pousquyuhl3s3a

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

Mary E. Dolan, David P. Hill, Gaurab Mukherjee, Monica S. McAndrews, Elissa J. Chesler, Judith A. Blake
2020 Scientific Reports  
Phenotypic analysis of shared genes revealed significant enrichment for immune system phenotypes and for cardiovascular-related phenotypes, which might point to alleles and phenotypes in mouse models that  ...  We performed our analysis using GeneWeaver (GW), Reactome, and several biomedical ontologies to represent and compare common COVID-19 comorbidities.  ...  Acknowledgements This work was funded by NIH grants to the Mouse Genome Database (NHGRI U41 HG000330), the Jackson Laboratory Center for Precision Genetics (OD U54 OD020351) and GeneWeaver (NIAID RO1 AA18776  ... 
doi:10.1038/s41598-020-77632-8 pmid:33257774 fatcat:cvtj5cyrnrhbxbvqp4gbfc56py
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