Ensembl 2018

Ensembl 2018

2018 | Daniel R. Zerbino, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Daniel Barrel, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos Garcia Girón, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskett, Thibaut Hourlier, Osagie I. 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 Flicek
The Ensembl project has been aggregating, processing, integrating, and redistributing genomic datasets since the initial releases of the draft human genome, aiming to accelerate genomics research through rapid open distribution of public data. Over time, Ensembl has expanded its resources to cover multiple fields of genomics, including gene annotation, comparative genomics, genetics, and epigenomics. It now includes 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. 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. Ensembl has grown alongside the field of genomics, starting with the first releases of the draft human genome. It has expanded to include comparative genomic resources, variation storage and annotation, and international epigenomic surveys. Ensembl collaborates with major bioinformatics databases and resources such as UniProt, GENCODE, UCSC, and NCBI. Ensembl is used in increasingly sophisticated ways, with its infrastructure supporting a range of services for different use cases. The web browser is the tool of choice for quick queries, while genome-wide analyses can be performed with a few lines of code using Ensembl's APIs. Dedicated tools such as BioMart and the Ensembl Variant Effect Predictor (VEP) support common data analysis workflows. Ensembl's work is guided by the belief that scientific progress can only be accelerated by making data freely available as early as possible. This philosophy led to the adoption of the FAIR principles of Findable, Accessible, Interoperable, and Reusable. Ensembl defines globally unique identifiers for genes and genomic features, ensures data is freely and programmatically available, adheres to international naming standards, and tracks the provenance of annotations. Ensembl has expanded to cover more genomes, including 15 new and updated rodent genomes in Release 90. It has also annotated the newest pig reference assembly and updated the zebrafish assembly. Ensembl has also annotated two different assemblies of the Chinese hamster ovary cell line, CHOK1. Ensembl's comparative genomics resources have been updated to include new genomes and assemblies, increasing the number of pairwise-alignments available. Ensembl has also updated its gene homology resource to increase the sensitivity of orthology-calling methods. Ensembl supports genome interpretation by providing updated REST server archives, allele frequency data from large sequencing projects, and improved VEP code for variant analysis. Ensembl also maps phenotype associations from various sources, improving the ability to query results across many sources. Ensembl has also improved its infrastructure to supportThe Ensembl project has been aggregating, processing, integrating, and redistributing genomic datasets since the initial releases of the draft human genome, aiming to accelerate genomics research through rapid open distribution of public data. Over time, Ensembl has expanded its resources to cover multiple fields of genomics, including gene annotation, comparative genomics, genetics, and epigenomics. It now includes 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. 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. Ensembl has grown alongside the field of genomics, starting with the first releases of the draft human genome. It has expanded to include comparative genomic resources, variation storage and annotation, and international epigenomic surveys. Ensembl collaborates with major bioinformatics databases and resources such as UniProt, GENCODE, UCSC, and NCBI. Ensembl is used in increasingly sophisticated ways, with its infrastructure supporting a range of services for different use cases. The web browser is the tool of choice for quick queries, while genome-wide analyses can be performed with a few lines of code using Ensembl's APIs. Dedicated tools such as BioMart and the Ensembl Variant Effect Predictor (VEP) support common data analysis workflows. Ensembl's work is guided by the belief that scientific progress can only be accelerated by making data freely available as early as possible. This philosophy led to the adoption of the FAIR principles of Findable, Accessible, Interoperable, and Reusable. Ensembl defines globally unique identifiers for genes and genomic features, ensures data is freely and programmatically available, adheres to international naming standards, and tracks the provenance of annotations. Ensembl has expanded to cover more genomes, including 15 new and updated rodent genomes in Release 90. It has also annotated the newest pig reference assembly and updated the zebrafish assembly. Ensembl has also annotated two different assemblies of the Chinese hamster ovary cell line, CHOK1. Ensembl's comparative genomics resources have been updated to include new genomes and assemblies, increasing the number of pairwise-alignments available. Ensembl has also updated its gene homology resource to increase the sensitivity of orthology-calling methods. Ensembl supports genome interpretation by providing updated REST server archives, allele frequency data from large sequencing projects, and improved VEP code for variant analysis. Ensembl also maps phenotype associations from various sources, improving the ability to query results across many sources. Ensembl has also improved its infrastructure to support
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