Ensembl 2018

被引:1992
作者
Zerbino, Daniel R. [1 ]
Achuthan, Premanand [1 ]
Akanni, Wasiu [1 ]
Amode, M. Ridwan [1 ]
Barrell, Daniel [1 ,2 ]
Bhai, Jyothish [1 ]
Billis, Konstantinos [1 ]
Cummins, Carla [1 ]
Gall, Astrid [1 ]
Giron, Carlos Garcia [1 ]
Gil, Laurent [1 ]
Gordon, Leo [1 ]
Haggerty, Leanne [1 ]
Haskell, Erin [1 ]
Hourlier, Thibaut [1 ]
Izuogu, Osagie G. [1 ]
Janacek, Sophie H. [1 ]
Juettemann, Thomas [1 ]
To, Jimmy Kiang [1 ]
Laird, Matthew R. [1 ]
Lavidas, Ilias [1 ]
Liu, Zhicheng [1 ]
Loveland, Jane E. [1 ]
Maurel, Thomas [1 ]
McLaren, William [1 ]
Moore, Benjamin [1 ]
Mudge, Jonathan [1 ]
Murphy, Daniel N. [1 ]
Newman, Victoria [1 ]
Nuhn, Michael [1 ]
Ogeh, Denye [1 ]
Ong, Chuang Kee [1 ]
Parker, Anne [1 ]
Patricio, Mateus [1 ]
Riat, Harpreet Singh [1 ]
Schuilenburg, Helen [1 ]
Sheppard, Dan [1 ]
Sparrow, Helen [1 ]
Taylor, Kieron [1 ]
Thormann, Anja [1 ]
Vullo, Alessandro [1 ]
Walts, Brandon [1 ]
Zadissa, Amonida [1 ]
Frankish, Adam [1 ]
Hunt, Sarah E. [1 ]
Kostadima, Myrto [1 ]
Langridge, Nicholas [1 ]
Martin, Fergal J. [1 ]
Muffato, Matthieu [1 ]
Perry, Emily [1 ]
机构
[1] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England
[2] Eagle Genom Ltd, Wellcome Genome Campus, Cambridge CB10 1DR, England
[3] Wellcome Trust Sanger Inst, Wellcome Genome Campus, Cambridge CB10 1SA, England
基金
欧盟地平线“2020”; 英国惠康基金; 美国国家卫生研究院; 英国生物技术与生命科学研究理事会;
关键词
DATABASE; PROJECT; VARIANTS; ARCHIVE;
D O I
10.1093/nar/gkx1098
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of rawdata are thus transformed into knowledge, which is made available via amultitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
引用
收藏
页码:D754 / D761
页数:8
相关论文
共 33 条
[1]   BLUEPRINT to decode the epigenetic signature written in blood [J].
Adams, David ;
Altucci, Lucia ;
Antonarakis, Stylianos E. ;
Ballesteros, Juan ;
Beck, Stephan ;
Bird, Adrian ;
Bock, Christoph ;
Boehm, Bernhard ;
Campo, Elias ;
Caricasole, Andrea ;
Dahl, Fredrik ;
Dermitzakis, Emmanouil T. ;
Enver, Tariq ;
Esteller, Manel ;
Estivill, Xavier ;
Ferguson-Smith, Anne ;
Fitzgibbon, Jude ;
Flicek, Paul ;
Giehl, Claudia ;
Graf, Thomas ;
Grosveld, Frank ;
Guigo, Roderic ;
Gut, Ivo ;
Helin, Kristian ;
Jarvius, Jonas ;
Kueppers, Ralf ;
Lehrach, Hans ;
Lengauer, Thomas ;
Lernmark, Ake ;
Leslie, David ;
Loeffler, Markus ;
Macintyre, Elizabeth ;
Mai, Antonello ;
Martens, Joost H. A. ;
Minucci, Saverio ;
Ouwehand, Willem H. ;
Pelicci, Pier Giuseppe ;
Pendeville, Helene ;
Porse, Bo ;
Rakyan, Vardhman ;
Reik, Wolf ;
Schrappe, Martin ;
Schuebeler, Dirk ;
Seifert, Martin ;
Siebert, Reiner ;
Simmons, David ;
Soranzo, Nicole ;
Spicuglia, Salvatore ;
Stratton, Michael ;
Stunnenberg, Hendrik G. .
NATURE BIOTECHNOLOGY, 2012, 30 (03) :224-226
[2]   The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes [J].
Adams, David J. ;
Doran, Anthony G. ;
Lilue, Jingtao ;
Keane, Thomas M. .
MAMMALIAN GENOME, 2015, 26 (9-10) :403-412
[3]   A method and server for predicting damaging missense mutations [J].
Adzhubei, Ivan A. ;
Schmidt, Steffen ;
Peshkin, Leonid ;
Ramensky, Vasily E. ;
Gerasimova, Anna ;
Bork, Peer ;
Kondrashov, Alexey S. ;
Sunyaev, Shamil R. .
NATURE METHODS, 2010, 7 (04) :248-249
[4]   Ensembl 2017 [J].
Aken, Bronwen L. ;
Achuthan, Premanand ;
Akanni, Wasiu ;
Amode, M. Ridwan ;
Bernsdorff, Friederike ;
Bhai, Jyothish ;
Billis, Konstantinos ;
Carvalho-Silva, Denise ;
Cummins, Carla ;
Clapham, Peter ;
Gil, Laurent ;
Giron, Carlos Garcia ;
Gordon, Leo ;
Hourlier, Thibaut ;
Hunt, Sarah E. ;
Janacek, Sophie H. ;
Juettemann, Thomas ;
Keenan, Stephen ;
Laird, Matthew R. ;
Lavidas, Ilias ;
Maurel, Thomas ;
McLaren, William ;
Moore, Benjamin ;
Murphy, Daniel N. ;
Nag, Rishi ;
Newman, Victoria ;
Nuhn, Michael ;
Ong, Chuang Kee ;
Parker, Anne ;
Patricio, Mateus ;
Riat, Harpreet Singh ;
Sheppard, Daniel ;
Sparrow, Helen ;
Taylor, Kieron ;
Thormann, Anja ;
Vullo, Alessandro ;
Walts, Brandon ;
Wilder, Steven P. ;
Zadissa, Amonida ;
Kostadima, Myrto ;
Martin, Fergal J. ;
Muffato, Matthieu ;
Perry, Emily ;
Ruffier, Magali ;
Staines, Daniel M. ;
Trevanion, Stephen J. ;
Cunningham, Fiona ;
Yates, Andrew ;
Zerbino, Daniel R. ;
Flicek, Paul .
NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D635-D642
[5]   The Ensembl gene annotation system [J].
Aken, Bronwen L. ;
Ayling, Sarah ;
Barrell, Daniel ;
Clarke, Laura ;
Curwen, Valery ;
Fairley, Susan ;
Banet, Julio Fernandez ;
Billis, Konstantinos ;
Giron, Carlos Garcia ;
Hourlier, Thibaut ;
Howe, Kevin ;
Kahari, Andreas ;
Kokocinski, Felix ;
Martin, Fergal J. ;
Murphy, Daniel N. ;
Nag, Rishi ;
Ruffier, Magali ;
Schuster, Michael ;
Tang, Y. Amy ;
Vogel, Jan-Hinnerk ;
White, Simon ;
Zadissa, Amonida ;
Flicek, Paul ;
Searle, Stephen M. J. .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2016,
[6]   A global reference for human genetic variation [J].
Altshuler, David M. ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Donnelly, Peter ;
Eichler, Evan E. ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Green, Eric D. ;
Hurles, Matthew E. ;
Knoppers, Bartha M. ;
Korbel, Jan O. ;
Lander, Eric S. ;
Lee, Charles ;
Lehrach, Hans ;
Mardis, Elaine R. ;
Marth, Gabor T. ;
McVean, Gil A. ;
Nickerson, Deborah A. ;
Wang, Jun ;
Wilson, Richard K. ;
Boerwinkle, Eric ;
Doddapaneni, Harsha ;
Han, Yi ;
Korchina, Viktoriya ;
Kovar, Christie ;
Lee, Sandra ;
Muzny, Donna ;
Reid, Jeffrey G. ;
Zhu, Yiming ;
Chang, Yuqi ;
Feng, Qiang ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Lan, Tianming ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Liu, Shengmao ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Tang, Meifang ;
Wang, Bo .
NATURE, 2015, 526 (7571) :68-+
[7]   Integrating common and rare genetic variation in diverse human populations [J].
Altshuler, David M. ;
Gibbs, Richard A. ;
Peltonen, Leena ;
Dermitzakis, Emmanouil ;
Schaffner, Stephen F. ;
Yu, Fuli ;
Bonnen, Penelope E. ;
de Bakker, Paul I. W. ;
Deloukas, Panos ;
Gabriel, Stacey B. ;
Gwilliam, Rhian ;
Hunt, Sarah ;
Inouye, Michael ;
Jia, Xiaoming ;
Palotie, Aarno ;
Parkin, Melissa ;
Whittaker, Pamela ;
Chang, Kyle ;
Hawes, Alicia ;
Lewis, Lora R. ;
Ren, Yanru ;
Wheeler, David ;
Muzny, Donna Marie ;
Barnes, Chris ;
Darvishi, Katayoon ;
Hurles, Matthew ;
Korn, Joshua M. ;
Kristiansson, Kati ;
Lee, Charles ;
McCarroll, Steven A. ;
Nemesh, James ;
Keinan, Alon ;
Montgomery, Stephen B. ;
Pollack, Samuela ;
Price, Alkes L. ;
Soranzo, Nicole ;
Gonzaga-Jauregui, Claudia ;
Anttila, Verneri ;
Brodeur, Wendy ;
Daly, Mark J. ;
Leslie, Stephen ;
McVean, Gil ;
Moutsianas, Loukas ;
Nguyen, Huy ;
Zhang, Qingrun ;
Ghori, Mohammed J. R. ;
McGinnis, Ralph ;
McLaren, William ;
Takeuchi, Fumihiko ;
Grossman, Sharon R. .
NATURE, 2010, 467 (7311) :52-58
[8]   UniProt: the universal protein knowledgebase [J].
Bateman, Alex ;
Martin, Maria Jesus ;
O'Donovan, Claire ;
Magrane, Michele ;
Alpi, Emanuele ;
Antunes, Ricardo ;
Bely, Benoit ;
Bingley, Mark ;
Bonilla, Carlos ;
Britto, Ramona ;
Bursteinas, Borisas ;
Bye-A-Jee, Hema ;
Cowley, Andrew ;
Da Silva, Alan ;
De Giorgi, Maurizio ;
Dogan, Tunca ;
Fazzini, Francesco ;
Castro, Leyla Garcia ;
Figueira, Luis ;
Garmiri, Penelope ;
Georghiou, George ;
Gonzalez, Daniel ;
Hatton-Ellis, Emma ;
Li, Weizhong ;
Liu, Wudong ;
Lopez, Rodrigo ;
Luo, Jie ;
Lussi, Yvonne ;
MacDougall, Alistair ;
Nightingale, Andrew ;
Palka, Barbara ;
Pichler, Klemens ;
Poggioli, Diego ;
Pundir, Sangya ;
Pureza, Luis ;
Qi, Guoying ;
Rosanoff, Steven ;
Saidi, Rabie ;
Sawford, Tony ;
Shypitsyna, Aleksandra ;
Speretta, Elena ;
Turner, Edward ;
Tyagi, Nidhi ;
Volynkin, Vladimir ;
Wardell, Tony ;
Warner, Kate ;
Watkins, Xavier ;
Zaru, Rossana ;
Zellner, Hermann ;
Xenarios, Ioannis .
NUCLEIC ACIDS RESEARCH, 2017, 45 (D1) :D158-D169
[9]   GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species [J].
Challis, Richard J. ;
Kumar, Sujai ;
Stevens, Lewis ;
Blaxter, Mark .
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2017,
[10]   The International Nucleotide Sequence Database Collaboration [J].
Cochrane, Guy ;
Karsch-Mizrachi, Ilene ;
Takagi, Toshihisa .
NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D48-D50