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Alliance of Genome Resources Portal: unified model organism research platform

2019 Nucleic Acids Research  
The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human  ...  and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms.  ...  ACKNOWLEDGEMENTS The Alliance platform is designed and implemented by a core group of developers and curators at SGD, Worm-Base, ZFIN, RGD, MGD, FlyBase and the GOC.  ... 
doi:10.1093/nar/gkz813 pmid:31552413 pmcid:PMC6943066 fatcat:kfgyjj7jybclndvfjbk5s53wci

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

The Alliance of Genome Resources Consortium
2019 Genetics  
In 2016, these six MODs and the GOC joined forces as the Alliance of Genome Resources (the Alliance).  ...  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  ...  Acknowledgments We thank all members of the Alliance of Genome Resources, the staff of the MODs and GOC, and the Alliance Scientific Advisory Board for their contributions to developing the vision and  ... 
doi:10.1534/genetics.119.302523 pmid:31796553 pmcid:PMC6893393 fatcat:fxxxo7f62nhhhirqf6rgtz3oaq

The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources

Leyla Ruzicka, Douglas G Howe, Sridhar Ramachandran, Sabrina Toro, Ceri E Van Slyke, Yvonne M Bradford, Anne Eagle, David Fashena, Ken Frazer, Patrick Kalita, Prita Mani, Ryan Martin (+7 others)
2018 Nucleic Acids Research  
ZFIN is also a founding member of the Alliance of Genome Resources, a collaboration of six model organism databases (MODs) and the Gene Ontology Consortium (GO).  ...  The recently launched Alliance portal (https://alliancegenome.org) provides a unified, comparative view of MOD, GO, and human data, and facilitates foundational and translational biomedical research.  ...  The Alliance of Genome Resources The Alliance of Genome Resources (https: //alliancegenome.org) was founded by six model organism databases (MODs: ZFIN, Mouse Genome Informatics Database (http://informatics.jax.org  ... 
doi:10.1093/nar/gky1090 pmid:30407545 pmcid:PMC6323962 fatcat:dhrucy7vmve75jckjuofnine2e

CORBEL Framework in place for launching transnational open user access via the common LS (formerly BMS) cluster web portal and RI specific user community communication channels

Sonja Hansen, Frauke Leitner
2020 Zenodo  
web portal and RI specific user community communication channels."  ...  In D4.3, we observe that the Open Calls have enabled cross-cutting interdisciplinary projects, which allow the users to advance in their research and to open new avenues in science.  ...  ACCESS TO RESOURCES EMBRC provides wild type organisms (sampled on request), culture collections of a wide selection of microorganisms, and marine model organisms grown in the lab with full control of  ... 
doi:10.5281/zenodo.3856040 fatcat:fp3lh6q7mvcj5do5wah3tgexsi

WormBase 2017: molting into a new stage

Raymond Y N Lee, Kevin L Howe, Todd W Harris, Valerio Arnaboldi, Scott Cain, Juancarlos Chan, Wen J Chen, Paul Davis, Sibyl Gao, Christian Grove, Ranjana Kishore, Hans-Michael Muller (+18 others)
2017 Nucleic Acids Research  
To better serve the broader research community, Worm-Base, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources  ...  WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide.  ...  More recently, we joined the Alliance of Genome Resources (AGR) to provide a uniform portal of knowledge for major model organisms for medical research.  ... 
doi:10.1093/nar/gkx998 pmid:29069413 pmcid:PMC5753391 fatcat:5rholx7nqvaurox74fnyrulgs4

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J.P. Gourdine (+14 others)
2016 Nucleic Acids Research  
Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources  ...  Nonhuman organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts.  ...  ACKNOWLEDGEMENTS We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1093/nar/gkw1128 pmid:27899636 pmcid:PMC5210586 fatcat:tbsgmbgu4vfmpiwwsenemxj2cm

Auditland

Andrew Murphie
2014 PORTAL: Journal of Multidisciplinary International Studies  
'"investments," skills sets, temporary alliances,' as Mirowski puts it (2013: 59) .  ...  has one foot in a unifying homogenisation and another in its own generative and differential adaptation to a wide range of events and 'habitats.'  ... 
doi:10.5130/portal.v11i2.3407 fatcat:mrs7kr63vvah7cpcisrohpe3j4

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform

2019 Nucleic Acids Research  
to develop new precision models of disease or to more fully explore emerging details within a system or across multiple systems.  ...  for >150 years, RGD has always been disease-focused and committed to providing data and tools for researchers doing comparative genomics and translational studies.  ...  to form the Alliance of Genome Resources ('Alliance', (55) ).  ... 
doi:10.1093/nar/gkz1041 pmid:31713623 pmcid:PMC7145519 fatcat:4a6ja3vobncmtbp7m2hivrebr4

European Biomedical Research Infrastructures and the Fight against COVID-19 Pandemic

E V Tarasova, P I Makarevich, A Yu Efimenko, M A Kulebyakina, Zh A Akopyan
2021 Sovremennye tehnologii v medicine  
The study aims to assess the role of EU biomedical research infrastructures in the fight against the COVID-19 pandemic and to analyze their response to the challenges associated with the spread of the  ...  Biomedical activities covered by organizations -members of the Alliance for Medical Research Infrastructures [15] Figure 3 . 3 Figure 3.  ...  As part of the global research integration, other international alliances outside Europe are expected to provide access to their resources.  ... 
doi:10.17691/stm2021.13.1.01 pmid:34513061 pmcid:PMC8353692 fatcat:g3cqulc7v5fg7pbe7qb26dgfm4

The Monarch Initiative: Insights across species reveal human disease mechanisms [article]

Christopher Mungall, Julie McMurry, Sebastian Koehler, James Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, TOM CONLIN, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine (+14 others)
2016 bioRxiv   pre-print
analysis, genomic diagnostics, and precision medicine on the basis of a large-scale platform of multimodal data that is deeply integrated across species and covering broad areas of disease.  ...  Applying the range of available knowledge to solve challenging disease problems requires unified data relating genomics, phenotypes, and disease; it also requires computational tools that leverage these  ...  Acknowledgments We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1101/055756 fatcat:26ov5gydkvgmxekc5z7yvcqzly

Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases

Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski (+8 others)
2021 Briefings in Bioinformatics  
Tripal is a mature, open source platform built to meet this need.  ...  Online, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets.  ...  of Agriculture.  ... 
doi:10.1093/bib/bbab238 pmid:34251419 pmcid:PMC8574961 fatcat:khqsm7dedrgupeu7h5iyaoi7wi

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  ...  ACKNOWLEDGEMENTS The EMBL-EBI is indebted to the support of its funders: EMBL's member states, the European Commission, the Wellcome Trust, the UK Research Councils, the US National Institutes of Health  ...  The authors are also indebted to hundreds of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gkt1206 pmid:24271396 pmcid:PMC3964968 fatcat:7dgar73rqjhwzci6shbolfpvfq

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  
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.  ...  , genomics, and biology of the laboratory mouse.  ...  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

33rd international mammalian genome conference: meeting highlights

Lauren J. Tracey, Kelsey E. Noll, Xavier Montagutelli
2020 Mammalian Genome  
Scientists from 12 countries met at the International Mammalian Genome Conference (IMGC) to share advances in mammalian genetics and genomics research.  ...  of 63 oral presentations, 65 posters, and 5 workshops in the fields of epigenetics, system genetics, developmental biology, cancer, human disease modeling, technical advances, and bioinformatics.  ...  The IMGS would also like to thank the members of  ... 
doi:10.1007/s00335-020-09830-8 pmid:32124004 fatcat:wh75ikzwjze43kqacwev4asa5u

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
genomic surveillance.  ...  , data centers, mesocenters and data-producing infrastructures) from 16 research organizations and 160 persons, totaling 40 FTE of involvement in the 4 work packages and 5 thematic implementation studies  ...  >> Detailed report of the survey  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq
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