Ensembl 2018

Ensembl 2018

Published online 16 November 2017 | Daniel R. Zerbino, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, Thomas Maurel, William McLaren, Benjamin Moore, Jonathan Mudge, Daniel N. Murphy, Victoria Newman, Michael Nuhn, Denye Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Fiona Cunningham, Andrew Yates and Paul Flicke
The Ensembl project has been providing open access to genomic data since the initial release of the human genome draft, aiming to accelerate genomics research through rapid distribution of public data. Over time, Ensembl has expanded its resources to include multiple fields of genomics, such as gene annotation, comparative genomics, genetics, and epigenomics. The project now covers a growing number of genome assemblies, with Ensembl Release 90 containing exactly 100. Ensembl's databases feed into various services for different use cases, from quick browsing to genome-wide bioinformatic analysis. The latest developments focus on managing an increasing number of assemblies, supporting genome interpretation, and improving the browser. Ensembl's purpose is to accelerate genomic research worldwide by providing an openly-accessible window into the wealth of data produced by the scientific community. Genomic and epigenomic datasets are selected from public archives, downloaded, processed by automated methods, and stored in integrated databases. Ensembl's web-based genome browser is the visible tip of a large underlying infrastructure. Since the first releases of the draft human genome, Ensembl has grown with the field of genomics, developing comparative genomic resources and incorporating data from large variation discovery projects. International epigenomic surveys have provided supporting evidence for genome-wide annotation of regulatory elements. Ensembl collaborates with major bioinformatics databases and resources such as UniProt, GENCODE, UCSC, and NCBI. The project's infrastructure now supports a range of services for different use cases, including a web browser for quick queries and APIs for genome-wide analyses. Ensembl also supports dedicated tools such as BioMart and the Ensembl Variant Effect Predictor (VEP). The project's work is guided by the belief that scientific progress can only be accelerated by making data freely available as early as possible, adhering to the FAIR principles. Ensembl release 90 included 15 new and updated annotated rodent genomes, including two assemblies of the Chinese hamster ovary (CHO) cell line, male and female genome assemblies for the naked mole-rat, and three chromosome-level assemblies. The project also annotated the newest pig reference assembly and updated the GRC10 zebrafish assembly. Ensembl's comparative genomics resources have been updated to include new genomes and assemblies, increasing the number of pairwise-alignments available. Ensembl has significantly updated the VEP code to improve its robustness and functionality, enhancing analysis of RefSeq human transcripts and predicting the impact of missense variants on protein function. The project has also improved support for genome interpretation by enriching variant annotations and providing linkage disequilibrium plots. Ensembl now maps phenotype associations to ontology terms, improving the ability to query results across multiple sources. Ensembl has also improved its browsing experience with a new gallery portal showcasing visual interfaces and a new interface for searching and selecting species. The project has developed a new training website to distribute training materials and has improved the usability of its web interface.The Ensembl project has been providing open access to genomic data since the initial release of the human genome draft, aiming to accelerate genomics research through rapid distribution of public data. Over time, Ensembl has expanded its resources to include multiple fields of genomics, such as gene annotation, comparative genomics, genetics, and epigenomics. The project now covers a growing number of genome assemblies, with Ensembl Release 90 containing exactly 100. Ensembl's databases feed into various services for different use cases, from quick browsing to genome-wide bioinformatic analysis. The latest developments focus on managing an increasing number of assemblies, supporting genome interpretation, and improving the browser. Ensembl's purpose is to accelerate genomic research worldwide by providing an openly-accessible window into the wealth of data produced by the scientific community. Genomic and epigenomic datasets are selected from public archives, downloaded, processed by automated methods, and stored in integrated databases. Ensembl's web-based genome browser is the visible tip of a large underlying infrastructure. Since the first releases of the draft human genome, Ensembl has grown with the field of genomics, developing comparative genomic resources and incorporating data from large variation discovery projects. International epigenomic surveys have provided supporting evidence for genome-wide annotation of regulatory elements. Ensembl collaborates with major bioinformatics databases and resources such as UniProt, GENCODE, UCSC, and NCBI. The project's infrastructure now supports a range of services for different use cases, including a web browser for quick queries and APIs for genome-wide analyses. Ensembl also supports dedicated tools such as BioMart and the Ensembl Variant Effect Predictor (VEP). The project's work is guided by the belief that scientific progress can only be accelerated by making data freely available as early as possible, adhering to the FAIR principles. Ensembl release 90 included 15 new and updated annotated rodent genomes, including two assemblies of the Chinese hamster ovary (CHO) cell line, male and female genome assemblies for the naked mole-rat, and three chromosome-level assemblies. The project also annotated the newest pig reference assembly and updated the GRC10 zebrafish assembly. Ensembl's comparative genomics resources have been updated to include new genomes and assemblies, increasing the number of pairwise-alignments available. Ensembl has significantly updated the VEP code to improve its robustness and functionality, enhancing analysis of RefSeq human transcripts and predicting the impact of missense variants on protein function. The project has also improved support for genome interpretation by enriching variant annotations and providing linkage disequilibrium plots. Ensembl now maps phenotype associations to ontology terms, improving the ability to query results across multiple sources. Ensembl has also improved its browsing experience with a new gallery portal showcasing visual interfaces and a new interface for searching and selecting species. The project has developed a new training website to distribute training materials and has improved the usability of its web interface.
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