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The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data

Gautier Koscielny, Gagarine Yaikhom, Vivek Iyer, Terrence F. Meehan, Hugh Morgan, Julian Atienza-Herrero, Andrew Blake, Chao-Kung Chen, Richard Easty, Armida Di Fenza, Tanja Fiegel, Mark Grifiths (+21 others)
2013 Nucleic Acids Research  
They thank Mary Todd Bergman and Spencer Phillips of the EBI for their assistance with figures for this article and Hayley Protheroe and the WTSI Team 109 for providing mouse images.  ...  ACKNOWLEDGEMENTS The authors thank the members of the IMPC consortium, the EMBL-EBI Industry Programme, Staff of MRC Harwell, the Wellcome Trust Sanger Institute, Francis Rowland, Jennifer Cham, Sangya  ...  INTRODUCTION The goal of the International Mouse Phenotyping Consortium (IMPC) is to generate and phenotypically characterize knockout mutant strains for every proteincoding gene in the mouse (1, 2) .  ... 
doi:10.1093/nar/gkt977 pmid:24194600 pmcid:PMC3964955 fatcat:67adsckyo5c3jo65sc7ecercrm

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

M. Ringwald, V. Iyer, J. C. Mason, K. R. Stone, H. D. Tadepally, J. A. Kadin, C. J. Bult, J. T. Eppig, D. J. Oakley, S. Briois, E. Stupka, V. Maselli (+6 others)
2010 Nucleic Acids Research  
We would like to thank the members of the IKMC steering committee and the advisors of the IKMC programs for providing valuable input and feedback on the development of the IKMC web portal.  ...  ACKNOWLEDGEMENTS We would like to thank all our colleagues from the different IKMC programs for making their data available to the IKMC web portal project and for very collegial and productive interactions  ...  THE IKMC WEB PORTAL: ACCESSING IKMC DATA AND RESOURCES The IKMC web site (www.knockoutmouse.org) is a central entry point to IKMC data and resources.  ... 
doi:10.1093/nar/gkq879 pmid:20929875 pmcid:PMC3013768 fatcat:qrhhuo6nxrhgdkfqrdqsoegxwe

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

Ann-Marie Mallon, Vivek Iyer, David Melvin, Hugh Morgan, Helen Parkinson, Steve D. M. Brown, Paul Flicek, William C. Skarnes
2012 Mammalian Genome  
The International Mouse Phenotyping Consortium (IMPC) (http://www.mousephenotype.org) will reveal the pleiotropic functions of every gene in the mouse genome and uncover the wider role of genetic loci  ...  Here we review the existing EuroPhenome and WTSI phenotype informatics systems and the IKMC portal, and present plans for extending these systems and lessons learned to the development of a robust IMPC  ...  Building upon these efforts, a number of newly funded initiatives have begun under the International Mouse Phenotyping Consortium (IMPC) umbrella to phenotype 5,000 knockout mouse lines over the next 5  ... 
doi:10.1007/s00335-012-9428-9 pmid:22991088 pmcid:PMC4106044 fatcat:gk4s2xebgfe5lggaovhzznfxpy

Mouse Genome Informatics (MGI): reflecting on 25 years

Janan T. Eppig, Joel E. Richardson, James A. Kadin, Martin Ringwald, Judith A. Blake, Carol J. Bult
2015 Mammalian Genome  
From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human  ...  Through major paradigm shifts in biological research and computer technologies, MGI has adapted and evolved to become an integral part of the larger global bioinformatics infrastructure and honed its ability  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creative commons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ... 
doi:10.1007/s00335-015-9589-4 pmid:26238262 pmcid:PMC4534491 fatcat:uevvmlmyobagjowk5fuggyflze

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  
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  ...  We report here on recent enhancements to this resource, including improved access to mouse disease model and human phenotype data and enhanced relationships of mouse models to human disease.  ...  The use of Human Phenotype Ontology and Human Phenotype Annotation files from Dr Peter Robinson (The Jackson Laboratory) is gratefully acknowledged.  ... 
doi:10.1093/nar/gkx1006 pmid:29092072 pmcid:PMC5753350 fatcat:vvlq4zpe4jac7ik25sh26qrulq

Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse

Janan T. Eppig
2017 ILAR journal  
Here we describe one slice of MGI relating to the development of community-wide large-scale mutagenesis and phenotyping projects and introduce ways to access and use these MGI data.  ...  This review describes the nexus of the body of growing genetic and biological data and the advances in computer technology in the late 1980s, including the World Wide Web, that together launched the beginnings  ...  Information about the IKMC is also available on the web (International Knockout Mouse Consortium 2016).  ... 
doi:10.1093/ilar/ilx013 pmid:28838066 pmcid:PMC5886341 fatcat:6crth734sjb6hiutnvjqm5r764

Expanding the mammalian phenotype ontology to support automated exchange of high throughput mouse phenotyping data generated by large-scale mouse knockout screens

Cynthia L Smith, Janan T Eppig
2015 Journal of Biomedical Semantics  
A vast array of data is about to emerge from the large scale high-throughput mouse knockout phenotyping projects worldwide.  ...  Results: The IMPC (International Mouse Phenotyping Consortium) is using the Mammalian Phenotype (MP) ontology in the automated annotation of phenodeviant data from high throughput phenotyping screens.  ...  Henrik Westerberg and the data wranglers of the IMPC consortium have made many requests for terms and have suggested revisions.  ... 
doi:10.1186/s13326-015-0009-1 pmid:25825651 pmcid:PMC4378007 fatcat:yxfrcuzhxrf2hae2w4mhd7tamq

Phenobabelomics--mouse phenotype data resources

J. M. Hancock, A.-M. Mallon
2008 Briefings in Functional Genomics & Proteomics  
A wide variety of online sites exist that provide different types of phenotypic information on the laboratory mouse.  ...  An essential aspect to understanding the functional significance of individual genes in the mouse genome is an understanding of the phenotypic consequences of gene mutations.  ...  the work of the MPDIC.  ... 
doi:10.1093/bfgp/elm033 pmid:18192320 fatcat:o37od2s24vbc3i73tnpssupaoa

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

Cynthia L. Smith, Janan T. Eppig
2012 Mammalian Genome  
Finally we discuss future application of the MP in providing standard descriptors of the phenotype pipeline test results from the International Mouse Phenotype Consortium projects.  ...  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  ...  Bello and R. 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

A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals

2018 ILAR journal  
First initiated by the World Health Organization's International Agency for Research on Cancer for rodents, it has evolved to include pathology of the major species (rats, mice, guinea pigs, nonhuman primates  ...  The need for international collaboration in rodent pathology has evolved since the 1970s and was initially driven by the new field of toxicologic pathology.  ...  The IMPC's web portal (http://www.mousephenotype.org) provides a unified single point of access to the production and phenotyping data and enables researchers to formulate hypotheses for biomedical and  ... 
doi:10.1093/ilar/ily005 pmid:30476141 pmcid:PMC6927895 fatcat:lmatrxhlbzbc5dmz43t6e4inve

BioMart Central Portal: an open database network for the biological community

J. M. Guberman, J. Ai, O. Arnaiz, J. Baran, A. Blake, R. Baldock, C. Chelala, D. Croft, A. Cros, R. J. Cutts, A. Di Genova, S. Forbes (+49 others)
2011 Database: The Journal of Biological Databases and Curation  
, UK Data on mutant products (mice, ES cells and vectors) generated and made available by members of the International Knockout Mouse Consotium (22) InterPro EBI, UK Integrated database of predictive  ...  Central Portal can provide an instantly available and automatically updated source of annotations for other projects, as is done in the International Cancer Genome Consortium Data Portal (4) .  ... 
doi:10.1093/database/bar041 pmid:21930507 pmcid:PMC3263598 fatcat:sypgedelfncfbflx4d7skx2v6a

The European Bioinformatics Institute's data resources 2014

Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet Thornton
2013 Nucleic Acids Research  
Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of  ...  The authors are also indebted to hundreds of thousands of scientists who have submitted data and annotation to the shared data collections.  ...  and our industry partners.  ... 
doi:10.1093/nar/gkt1206 pmid:24271396 pmcid:PMC3964968 fatcat:7dgar73rqjhwzci6shbolfpvfq

Meeting report of the 26th International Mammalian Genome Conference

Melissa A. Musser, Steven C. Munger, Teresa M. Gunn
2013 Mammalian Genome  
(Margaret Sherry, Gayle Hodge, and Lotte Kerr) to make this year's meeting a success. The  ...  Acknowledgments The IMGS acknowledges Teresa Gunn and Michelle Southard-Smith for stepping up on short notice to serve as the local organizers for this year's conference.  ...  and data International mouse phenotyping consortium (IMPC) http://mousephenotype.org Systematic phenotype data available for hundreds of mutant mouse lines (O-31, P-5, P-6, P-19, P-46) Sanger  ... 
doi:10.1007/s00335-013-9455-1 pmid:23673682 pmcid:PMC5814252 fatcat:cshzc6zk6nf6dnzu4f5mk7vyrq

An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder

Olivia J. Veatch, Merlin G. Butler, Sarah H. Elsea, Beth A. Malow, James S. Sutcliffe, Jason H. Moore
2020 International Journal of Molecular Sciences  
genes: (1) expressed in the human brain, (2) involved in ASD-relevant biological processes and resulting in analogous phenotypes in mice, (3) whose products are targeted by approved pharmaceutical compounds  ...  Notably, none of the prioritized genes are represented among the 59 genes compiled by the ACMG, and 78% had a pathogenic or likely pathogenic variant in ClinVar.  ...  On-going efforts by groups like the International Mouse Phenotyping Consortium (IMPC) offer web portals which allow for rapid mining of mouse phenotype data from knockout mutant strains for eventually  ... 
doi:10.3390/ijms21239029 pmid:33261099 fatcat:jn6d5rgjhrckxcmjnvrvhftzai

Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques

Martina Rauner, Ines Foessl, Melissa M. Formosa, Erika Kague, Vid Prijatelj, Nerea Alonso Lopez, Bodhisattwa Banerjee, Dylan Bergen, Björn Busse, Ângelo Calado, Eleni Douni, Yankel Gabet (+16 others)
2021 Frontiers in Endocrinology  
The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare  ...  These standards will promote data integration from various -omics technologies and functional dissection of human complex traits.  ...  COST is a funding agency for research and innovation networks.  ... 
doi:10.3389/fendo.2021.731217 pmid:34938269 pmcid:PMC8686830 fatcat:xr3yfs2ukbalbpufas3okbcb64
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