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

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