2014 | Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos Garcia Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Nathan Johnson, Thomas Juettemann, Andreas K. Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet S. Riat, Magali Ruffier, Daniel Sheppard, Kieron Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Javier Herrero, Tim J.P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino and Stephen M.J. Searle
Ensembl 2014 is a comprehensive database for genomic analysis in chordate species, with a focus on human, major vertebrates, and farm animals. The database now supports 77 species, including human, mouse, zebrafish, rat, and various farm animals. The Ensembl browser has been significantly updated with a scrollable, zoomable genome browser called Genoverse, replacing the previous overview panel. The search engine has been upgraded to Solr, and new search features such as faceting and auto-completion have been introduced. The variation and phenotype data displays have also been improved, with structural variants now colored by class and additional phenotype data integrated for relevant genes.
Ensembl annotations are based on integration of relevant data sources, including evidence-based gene annotations and comparative genomics analysis. The human gene set is updated with a merge of Ensembl's automatic annotation and Havana's manual annotation. The Ensembl variation annotation integrates all publicly available variation datasets to provide a comprehensive resource for variome interpretation across 217 million variants in 18 species with supported variation resources. The regulatory annotation is available across multiple human and mouse cell lines, with the Ensembl Regulatory Build providing a comprehensive synthesis of functional assays from various consortia.
Comparative genomics resources include whole-genome alignments of vertebrate species, with high-quality genomes aligned using the EPO pipeline. The Ensembl REST service has been extended with additional support for comparative genomics and ontology information. The Ensembl BioMart, APIs, and web displays provide access to all data, which are also available for querying via public MySQL servers, full data downloads, and Amazon public datasets.
Ensembl also provides training and outreach through workshops, online training, and social media. The Ensembl project is funded by the Wellcome Trust and other organizations, and it supports community standards that promote interoperability in genomics. The Ensembl project continues to develop and improve its tools and resources to support genomic research.Ensembl 2014 is a comprehensive database for genomic analysis in chordate species, with a focus on human, major vertebrates, and farm animals. The database now supports 77 species, including human, mouse, zebrafish, rat, and various farm animals. The Ensembl browser has been significantly updated with a scrollable, zoomable genome browser called Genoverse, replacing the previous overview panel. The search engine has been upgraded to Solr, and new search features such as faceting and auto-completion have been introduced. The variation and phenotype data displays have also been improved, with structural variants now colored by class and additional phenotype data integrated for relevant genes.
Ensembl annotations are based on integration of relevant data sources, including evidence-based gene annotations and comparative genomics analysis. The human gene set is updated with a merge of Ensembl's automatic annotation and Havana's manual annotation. The Ensembl variation annotation integrates all publicly available variation datasets to provide a comprehensive resource for variome interpretation across 217 million variants in 18 species with supported variation resources. The regulatory annotation is available across multiple human and mouse cell lines, with the Ensembl Regulatory Build providing a comprehensive synthesis of functional assays from various consortia.
Comparative genomics resources include whole-genome alignments of vertebrate species, with high-quality genomes aligned using the EPO pipeline. The Ensembl REST service has been extended with additional support for comparative genomics and ontology information. The Ensembl BioMart, APIs, and web displays provide access to all data, which are also available for querying via public MySQL servers, full data downloads, and Amazon public datasets.
Ensembl also provides training and outreach through workshops, online training, and social media. The Ensembl project is funded by the Wellcome Trust and other organizations, and it supports community standards that promote interoperability in genomics. The Ensembl project continues to develop and improve its tools and resources to support genomic research.