iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: http://www.ncbi.nlm.nih.gov/pubmed/30407521
Ensembl 2019 - PubMed Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Jan 8;47(D1):D745-D751.
doi: 10.1093/nar/gky1113.

Ensembl 2019

Fiona Cunningham  1 , Premanand Achuthan  1 , Wasiu Akanni  1 , James Allen  1 , M Ridwan Amode  1 , Irina M Armean  1 , Ruth Bennett  1 , Jyothish Bhai  1 , Konstantinos Billis  1 , Sanjay Boddu  1 , Carla Cummins  1 , Claire Davidson  1 , Kamalkumar Jayantilal Dodiya  1 , Astrid Gall  1 , Carlos García Girón  1 , Laurent Gil  1 , Tiago Grego  1 , Leanne Haggerty  1 , Erin Haskell  1 , Thibaut Hourlier  1 , Osagie G Izuogu  1 , Sophie H Janacek  1 , Thomas Juettemann  1 , Mike Kay  1 , Matthew R Laird  1 , Ilias Lavidas  1 , Zhicheng Liu  1 , Jane E Loveland  1 , José C Marugán  1 , Thomas Maurel  1 , Aoife C McMahon  1 , Benjamin Moore  1 , Joannella Morales  1 , Jonathan M Mudge  1 , Michael Nuhn  1 , Denye Ogeh  1 , Anne Parker  1 , Andrew Parton  1 , Mateus Patricio  1 , Ahamed Imran Abdul Salam  1 , Bianca M Schmitt  1 , Helen Schuilenburg  1 , Dan Sheppard  1 , Helen Sparrow  1 , Eloise Stapleton  1 , Marek Szuba  1 , Kieron Taylor  1 , Glen Threadgold  1 , Anja Thormann  1 , Alessandro Vullo  1 , Brandon Walts  1 , Andrea Winterbottom  1 , Amonida Zadissa  1 , Marc Chakiachvili  1 , Adam Frankish  1 , Sarah E Hunt  1 , Myrto Kostadima  1 , Nick Langridge  1 , Fergal J Martin  1 , Matthieu Muffato  1 , Emily Perry  1 , Magali Ruffier  1 , Daniel M Staines  1 , Stephen J Trevanion  1 , Bronwen L Aken  1 , Andrew D Yates  1 , Daniel R Zerbino  1 , Paul Flicek  1
Affiliations

Ensembl 2019

Fiona Cunningham et al. Nucleic Acids Res. .

Abstract

The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support. We have also doubled the number of available human variants and added regulatory regions for many mouse cell types and developmental stages. Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Example of Ensembl's new motif feature visualization, displaying the position weight motif of IRF4, IRF5, IRF8 and IRF9, using height to represent information content.
Figure 2.
Figure 2.
The variant table for a transcript summarizes the annotation across the transcript for each variant, including the global allele frequency, clinical significance, consequence, allele change as well as five different prediction algorithms to assess the variant impact: SIFT (21), PolyPhen-2 (33), CADD (30), REVEL (29), MetaLR (31) and MutationAssessor (32).
See this image and copyright information in PMC

Similar articles

  • Ensembl 2021.
    Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P. Howe KL, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891. doi: 10.1093/nar/gkaa942. Nucleic Acids Res. 2021. PMID: 33137190 Free PMC article.
  • Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
    Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, Flicek P. Yates AD, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D996-D1003. doi: 10.1093/nar/gkab1007. Nucleic Acids Res. 2022. PMID: 34791415 Free PMC article.
  • Ensembl 2022.
    Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez JG, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh DN, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Pérez-Silva JG, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt SE, IIsley GR, Loveland JE, Martin FJ, Moore B, Mudge JM, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Dyer S, Harrison PW, Howe KL, Yates AD, Zerbino DR, Flicek P. Cunningham F, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. doi: 10.1093/nar/gkab1049. Nucleic Acids Res. 2022. PMID: 34791404 Free PMC article.
  • Genome information resources - developments at Ensembl.
    Hammond MP, Birney E. Hammond MP, et al. Trends Genet. 2004 Jun;20(6):268-72. doi: 10.1016/j.tig.2004.04.002. Trends Genet. 2004. PMID: 15145580 Review.
  • An overview of Ensembl.
    Birney E, Andrews TD, Bevan P, Caccamo M, Chen Y, Clarke L, Coates G, Cuff J, Curwen V, Cutts T, Down T, Eyras E, Fernandez-Suarez XM, Gane P, Gibbins B, Gilbert J, Hammond M, Hotz HR, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Lehvaslaiho H, McVicker G, Melsopp C, Meidl P, Mongin E, Pettett R, Potter S, Proctor G, Rae M, Searle S, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Ureta-Vidal A, Woodwark KC, Cameron G, Durbin R, Cox A, Hubbard T, Clamp M. Birney E, et al. Genome Res. 2004 May;14(5):925-8. doi: 10.1101/gr.1860604. Epub 2004 Apr 12. Genome Res. 2004. PMID: 15078858 Free PMC article. Review.
See all similar articles

Cited by

See all "Cited by" articles

References

    1. Ruffier M., Kähäri A., Komorowska M., Keenan S., Laird M.R., Longden I., Proctor G., Searle S., Staines D., Taylor K. et al. . Ensembl Core Software Resources: storage and programmatic access for DNA sequence and genome annotation. Database (Oxford). 2017; 2017:bax20. - PMC - PubMed
    1. Yates A., Beal K., Keenan S., McLaren W., Pignatelli M., Ritchie G.R.S., Ruffier M., Taylor K., Vullo A., Flicek P.. The Ensembl REST API: Ensembl data for any language. Bioinformatics. 2015; 31:143–145. - PMC - PubMed
    1. Rios D., McLaren W.M., Chen Y., Birney E., Stabenau A., Flicek P., Cunningham F.. A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics. 2010; 11:238. - PMC - PubMed
    1. Aken B.L., Ayling S., Barrell D., Clarke L., Curwen V., Fairley S., Fernandez Banet J., Billis K., García Girón C., Hourlier T. et al. . The Ensembl gene annotation system. Database (Oxford). 2016; 2016:baw093. - PMC - PubMed
    1. Chen Y., Cunningham F., Rios D., McLaren W.M., Smith J., Pritchard B., Spudich G.M., Brent S., Kulesha E., Marin-Garcia P. et al. . Ensembl variation resources. BMC Genomics. 2010; 11:293. - PMC - PubMed

Publication types