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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #349535

Research Project: Enhancing Plant Genome Function Maps Through Genomic, Genetic, Computational and Collaborative Research

Location: Plant, Soil and Nutrition Research

Title: Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Author
item KERSEY, PAUL - European Bioinformatics Institute
item ALLEN, JAMES - European Bioinformatics Institute
item ALLOT, ALEXIS - European Bioinformatics Institute
item BARBA, MATTHIE - European Bioinformatics Institute
item BODDU, SANJAY - European Bioinformatics Institute
item BOLT, BRUCE - European Bioinformatics Institute
item CARVALHO-SILVA, DENISE - European Bioinformatics Institute
item CHRISTENSEN, MIKKEL - European Bioinformatics Institute
item DAVIS, PAUL - European Bioinformatics Institute
item GRABMUELLER, CHRISTOPH - European Bioinformatics Institute
item KUMAR, NAVIN - European Bioinformatics Institute
item LIU, ZICHENG - European Bioinformatics Institute
item MAUREL, THOMAS - European Bioinformatics Institute
item MOORE, BEN - European Bioinformatics Institute
item MCDOWALL, MARK - European Bioinformatics Institute
item MAHESWARI, UMA - European Bioinformatics Institute
item NAAMATI, GUY - European Bioinformatics Institute
item NEWMAN, VICTORIA - European Bioinformatics Institute
item ONG, CHUANG KEE - European Bioinformatics Institute
item PAULINI, MICHAEL - European Bioinformatics Institute
item PEDRO, HELDER - European Bioinformatics Institute
item PERRY, EMILY - European Bioinformatics Institute
item RUSSELL, MATTHEW - European Bioinformatics Institute
item SPARROW, HELEN - European Bioinformatics Institute
item TAPANARI, ELECTRA - European Bioinformatics Institute
item TAYLOR, KIERON - European Bioinformatics Institute
item VULLO, ALESSANDRO - European Bioinformatics Institute
item WILLIAMS, GARETH - European Bioinformatics Institute
item ZADISSIA, AMONIDA - European Bioinformatics Institute
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item Ware, Doreen
item LUCIANI, AURELIEN - European Bioinformatics Institute
item POTTER, SIMON - European Bioinformatics Institute
item FINN, ROBERT - European Bioinformatics Institute
item URBAN, MARTIN - Rothamsted Research
item HAMMOND-KOSACK, KIM - Rothamsted Research
item BOLSER, DAN - European Bioinformatics Institute
item NISHADI, DE SILVA - European Bioinformatics Institute
item HOWE, KEVIN - European Bioinformatics Institute
item LANGRIDGE, NICHOLAS - European Bioinformatics Institute
item MASLEN, GARETH - European Bioinformatics Institute
item STAINES, DANIEL - European Bioinformatics Institute
item YATES, ANDREW - European Bioinformatics Institute

Submitted to: Nucleic Acids Research
Publication Type: Review Article
Publication Acceptance Date: 10/24/2018
Publication Date: 1/4/2018
Citation: Kersey, P., Allen, J., Allot, A., Barba, M., Boddu, S., Bolt, B., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., Mcdowall, M., Maheswari, U., Naamati, G., Newman, V., Ong, C., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R., Urban, M., Hammond-Kosack, K., Bolser, D., Nishadi, D., Howe, K., Langridge, N., Maslen, G., Staines, D., Yates, A. 2018. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Research. 46(D1):D802-D808. doi: 10.1093/nar/gkx1011.
DOI: https://doi.org/10.1093/nar/gkx1011

Interpretive Summary:

Technical Abstract: Ensembl Genomes is an online resource that integrates genome-scale data for five non-vertebrate groups: plants, bacteria, protists, fungi and invertebrate metazoan. It complements the Ensembl resource Ensembl software tools that were created for comparative analysis, data mining and visualization across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation. The Ensembl group developed a genome annotation system for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. The group brings the integrative power of Ensembl tools for comparative analysis, data mining and visualization across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation. This article is an update of the Ensembl Genomes database reporting over 20,000 new genome assemblies and over 35,000 tracks of RNA-Seq data. Other advances include implementation of a new data format called RDF, increased data curation by the scientific community, a new protein search tool, additional references to other bioinformatics resources and data sources, improved annotation of genes that do not encode proteins, and the establishment of prerelease and archival websites.