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Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species
2011
Nucleic Acids Research
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Ensembl Genomes (http://www.ensemblgenomes .org) is an integrative resource for genome-scale data from non-vertebrate species. ...
resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. ...
ACKNOWLEDGEMENTS We would also like to acknowledge the contributions of all our collaborators; and of all colleagues working on the Ensembl project at the EBI and the Wellcome Trust Sanger Institute. ...
doi:10.1093/nar/gkr895
pmid:22067447
pmcid:PMC3245118
fatcat:eiin7kxbqvgajkocq7yzyw4xsm
Ensembl Genomes 2020-enabling non-vertebrate genomic research
2019
Nucleic Acids Research
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Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context ...
Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across ...
ACKNOWLEDGEMENTS We would like to acknowledge the following Ensembl developers for developing and maintaining the front-end and back-end software and infrastructure that underpins Ensembl Genomes: Premanand ...
doi:10.1093/nar/gkz890
pmid:31598706
pmcid:PMC6943047
fatcat:vj27adwlbnbq3hzxxei5nj55ji
Ensembl Genomes: Extending Ensembl across the taxonomic space
2009
Nucleic Acids Research
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ACKNOWLEDGEMENTS The authors would like to thank Kim Rutherford for permission to use circular_diagram.pl within EnsemblGenomes. ...
This paper describes 'Ensembl Genomes', a new resource recently launched by the EBI to complement Ensembl by providing access to genome-scale data from non-vertebrate species through the same user interfaces ...
With Ensembl Genomes, we aim to provide an integrated portal to reference sequence and annotation from all species of scientific interest; and thereby to complement, and provide convenient access to, data ...
doi:10.1093/nar/gkp871
pmid:19884133
pmcid:PMC2808935
fatcat:g6q3xclnp5gzrkmdus5mzspssy
Ensembl Genomes 2016: more genomes, more complexity
2015
Nucleic Acids Research
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Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context ...
23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. ...
Vertebrate metazoa are the focus of the Ensembl project (http://www.ensembl.org) (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species. ...
doi:10.1093/nar/gkv1209
pmid:26578574
pmcid:PMC4702859
fatcat:n3oewab7gvei5fbg6wfrx2ydaa
Ensembl comparative genomics resources
2016
Database: The Journal of Biological Databases and Curation
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The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here ...
The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. ...
We also thank the rest of the Ensembl team, especially the members of Ensembl Outreach for supporting the users and helping with the documentation and tutorials. ...
doi:10.1093/database/baw053
pmid:27141089
pmcid:PMC4852398
fatcat:sluvrnnct5dpxmd7grm3z76m3y
Ensembl Genomes 2013: scaling up access to genome-wide data
2013
Nucleic Acids Research
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ACKNOWLEDGEMENTS The authors would also like to acknowledge the contributions of all our collaborators and of all colleagues working on the Ensembl project. ...
Vertebrate metazoa are the focus of the Ensembl project (http://www.ensembl.org) (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species. ...
The overall suite of Ensembl Genomes interfaces mirrors the interfaces provided for vertebrate genomes in Ensembl, and allows users access to genomic data from across the tree of life in a consistent manner ...
doi:10.1093/nar/gkt979
pmid:24163254
pmcid:PMC3965094
fatcat:bzydx6qowvdunnkte5sioqgk5y
Ensembl variation resources
2010
BMC Genomics
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Description: The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. ...
The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. ...
Additional funding for Ensembl's variation resources comes from EMBL, the European Union Framework 6 STAR project, European Union Framework 7 Programme GEN2PHEN project and the UK Medical Research Council ...
doi:10.1186/1471-2164-11-293
pmid:20459805
pmcid:PMC2894800
fatcat:3f65senktbg7tnax5llz4focg4
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
2017
Nucleic Acids Research
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Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl ...
Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate ...
Vertebrate metazoa are the focus of the Ensembl project (1); Ensembl Genomes provides a complementary set of interfaces for non-vertebrate species. ...
doi:10.1093/nar/gkx1011
pmid:29092050
pmcid:PMC5753204
fatcat:mmgammsp3fcrpdfrwprhsxl4g4
Touring Ensembl: A practical guide to genome browsing
2010
BMC Genomics
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This paper offers a practical guide to the integration of gene, comparative genomic, and functional genomics data using the Ensembl website at http://www.ensembl.org. ...
The number of databases in molecular biological fields has rapidly increased to provide a large-scale resource. ...
Genome browsers provide an aid to the researcher by importing biological data from various sources and presenting these data in an integrated way. ...
doi:10.1186/1471-2164-11-295
pmid:20459808
pmcid:PMC2894802
fatcat:avjtzfwzpzhwlelmfl4nei6ray
Ensembl 2019
2018
Nucleic Acids Research
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Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. ...
Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download. ...
ACKNOWLEDGEMENTS We thank all our users for their regular questions and feedback and for those external data generators that make prepublication data available to be incorporated into Ensembl. ...
doi:10.1093/nar/gky1113
pmid:30407521
fatcat:q2roq24hdjaqrlqc6r52kemvzi
The Ensembl Variant Effect Predictor
2016
Genome Biology
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The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. ...
It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. ...
The data files necessary for annotation in 80 vertebrate species and many invertebrates are distributed by Ensembl and Ensembl Genomes [34] , respectively. ...
doi:10.1186/s13059-016-0974-4
pmid:27268795
pmcid:PMC4893825
fatcat:lziduun2xnhpteudwo3utn4nyi
Ensembl 2020
2019
Nucleic Acids Research
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The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. ...
The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key ...
ACKNOWLEDGEMENTS We wish to thank all of our user community and data providers for making their data available for reuse within Ensembl. ...
doi:10.1093/nar/gkz966
pmid:31691826
pmcid:PMC7145704
fatcat:i5tdgfqtd5dn7by55qjej2dade
Ensembl 2014
2013
Nucleic Acids Research
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Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. ...
Finally, we provide updated information about our methods for data access and resources for user training. ...
ACKNOWLEDGEMENTS The authors wish to thank all of their users, the systems teams who maintain their computational infrastructure and those researchers who have provided data to ...
doi:10.1093/nar/gkt1196
pmid:24316576
pmcid:PMC3964975
fatcat:knxp7akjtnbvnm7hlxajhvnzra
Ensembl 2018
2017
Nucleic Acids Research
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The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research ...
Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. ...
For their assistance with the Ensembl infrastructure and hardware mi- ...
doi:10.1093/nar/gkx1098
pmid:29155950
pmcid:PMC5753206
fatcat:g7pg5j5vpfgilgtr2bflfiqyei
Ensembl 2017
2016
Nucleic Acids Research
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Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. ...
We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. ...
ACKNOWLEDGEMENTS Thank you to the Systems Administration teams at the Wellcome Trust Sanger Institute and at EMBL-EBI for ...
doi:10.1093/nar/gkw1104
pmid:27899575
pmcid:PMC5210575
fatcat:hzc4nlutrnfo5obbhqtlljr724
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