Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.
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DOI：
10.1093/nar/gkx1011
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发表时间：
2018-01-04
影响因子：
14.9
通讯作者：
Yates A
中科院分区：
文献类型：
--
作者：
Kersey PJ;Allen JE;Allot A;Barba M;Boddu S;Bolt BJ;Carvalho-Silva D;Christensen M;Davis P;Grabmueller C;Kumar N;Liu Z;Maurel T;Moore B;McDowall MD;Maheswari U;Naamati G;Newman V;Ong CK;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 RD;Urban M;Hammond-Kosack KE;Bolser DM;De Silva N;Howe KL;Langridge N;Maslen G;Staines DM;Yates A
Ensembl genomics （http://www.ensemblgenomes.org）是一个整合非脊椎动物物种基因组规模数据的资源，补充了Ensembl项目（http://www.ensembl.org）中开发的脊椎动物基因组学资源。这两种资源一起为丰富的数据提供了一套一致的编程和交互界面，包括基因组序列、基因模型、转录序列、遗传变异和比较分析。本文提供了关于该资源的先前出版物的更新，重点是最近的发展和扩展。其中包括合并近20,000个额外的基因组序列和超过35,000个RNA-Seq数据轨道，这些数据已与基因组序列对齐并可用于可视化。自2015年以来的其他进展包括以资源描述框架（RDF）格式发布数据库，社区衍生的管理的大量增加，新的高性能蛋白质序列搜索，额外的交叉参考，改进的非蛋白质编码基因注释，以及发布预发布和存档网站的启动。总的来说，这些变化是对公共基因组规模数据数量不断增加的持续响应的一部分，随之而来的是使用自动化、可扩展的方法对这些数据进行归档、整合、注释和传播的需求。
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.
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影响因子：
14.9
作者：
Smedley D;Haider S;Durinck S;Pandini L;Provero P;Allen J;Arnaiz O;Awedh MH;Baldock R;Barbiera G;Bardou P;Beck T;Blake A;Bonierbale M;Brookes AJ;Bucci G;Buetti I;Burge S;Cabau C;Carlson JW;Chelala C;Chrysostomou C;Cittaro D;Collin O;Cordova R;Cutts RJ;Dassi E;Di Genova A;Djari A;Esposito A;Estrella H;Eyras E;Fernandez-Banet J;Forbes S;Free RC;Fujisawa T;Gadaleta E;Garcia-Manteiga JM;Goodstein D;Gray K;Guerra-Assunção JA;Haggarty B;Han DJ;Han BW;Harris T;Harshbarger J;Hastings RK;Hayes RD;Hoede C;Hu S;Hu ZL;Hutchins L;Kan Z;Kawaji H;Keliet A;Kerhornou A;Kim S;Kinsella R;Klopp C;Kong L;Lawson D;Lazarevic D;Lee JH;Letellier T;Li CY;Lio P;Liu CJ;Luo J;Maass A;Mariette J;Maurel T;Merella S;Mohamed AM;Moreews F;Nabihoudine I;Ndegwa N;Noirot C;Perez-Llamas C;Primig M;Quattrone A;Quesneville H;Rambaldi D;Reecy J;Riba M;Rosanoff S;Saddiq AA;Salas E;Sallou O;Shepherd R;Simon R;Sperling L;Spooner W;Staines DM;Steinbach D;Stone K;Stupka E;Teague JW;Dayem Ullah AZ;Wang J;Ware D;Wong-Erasmus M;Youens-Clark K;Zadissa A;Zhang SJ;Kasprzyk A
通讯作者：
Kasprzyk A
影响因子：
14.9
作者：
Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
14.9
作者：
Finn RD;Clements J;Arndt W;Miller BL;Wheeler TJ;Schreiber F;Bateman A;Eddy SR
通讯作者：
Eddy SR
影响因子：
14.9
作者：
Howe KL;Bolt BJ;Cain S;Chan J;Chen WJ;Davis P;Done J;Down T;Gao S;Grove C;Harris TW;Kishore R;Lee R;Lomax J;Li Y;Muller HM;Nakamura C;Nuin P;Paulini M;Raciti D;Schindelman G;Stanley E;Tuli MA;Van Auken K;Wang D;Wang X;Williams G;Wright A;Yook K;Berriman M;Kersey P;Schedl T;Stein L;Sternberg PW
通讯作者：
Sternberg PW
DOI：
10.1093/bioinformatics/btt637
发表时间：
2014-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Raney BJ;Dreszer TR;Barber GP;Clawson H;Fujita PA;Wang T;Nguyen N;Paten B;Zweig AS;Karolchik D;Kent WJ
通讯作者：
Kent WJ