The Ensembl REST API: Ensembl Data for Any Language

被引：112

作者：

Yates, Andrew ^{[1
]}

Beal, Kathryn ^{[1
]}

Keenan, Stephen ^{[1
]}

McLaren, William ^{[1
]}

Pignatelli, Miguel ^{[1
]}

Ritchie, Graham R. S. ^{[1
,2
]}

Ruffier, Magali ^{[1
]}

Taylor, Kieron ^{[1
]}

Vullo, Alessandro ^{[1
]}

Flicek, Paul ^{[1
,2
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

BIOINFORMATICS | 2015年 / 31卷 / 01期

基金：

英国惠康基金;

关键词：

BIOLOGY;

D O I：

10.1093/bioinformatics/btu613

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language.

引用

页码：143 / 145

页数：3

共 11 条

[1] An integrated map of genetic variation from 1,092 human genomes
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.
Schmidt, Jeanette P.
Sherry, Stephen T.
Wang, Jun
Wilson, Richard K.
Gibbs, Richard A.
Dinh, Huyen
Kovar, Christie
Lee, Sandra
Lewis, Lora
Muzny, Donna
Reid, Jeff
Wang, Min
Wang, Jun
Fang, Xiaodong
Guo, Xiaosen
Jian, Min
Jiang, Hui
Jin, Xin
Li, Guoqing
Li, Jingxiang
Li, Yingrui
Li, Zhuo
Liu, Xiao
Lu, Yao
Ma, Xuedi
Su, Zhe
Tai, Shuaishuai
Tang, Meifang
[J]. NATURE, 2012, 491 (7422) : 56 - 65
[2] RNAcentral: A vision for an international database of RNA sequences
Bateman, Alex
Agrawal, Shipra
Birney, Ewan
Bruford, Elspeth A.
Bujnicki, Janusz M.
Cochrane, Guy
Cole, James R.
Dinger, Marcel E.
Enright, Anton J.
Gardner, Paul P.
Gautheret, Daniel
Griffiths-Jones, Sam
Harrow, Jen
Herrero, Javier
Holmes, Ian H.
Huang, Hsien-Da
Kelly, Krystyna A.
Kersey, Paul
Kozomara, Ana
Lowe, Todd M.
Marz, Manja
Moxon, Simon
Pruitt, Kim D.
Samuelsson, Tore
Stadler, Peter F.
Vilella, Albert J.
Vogel, Jan-Hinnerk
Williams, Kelly P.
Wright, Mathew W.
Zwieb, Christian
[J]. RNA, 2011, 17 (11) : 1941 - 1946
[3] Dalliance: interactive genome viewing on the web
Down, Thomas A.
Piipari, Matias
Hubbard, Tim J. P.
[J]. BIOINFORMATICS, 2011, 27 (06) : 889 - 890
[4] Fielding RaRT, 2000, PhD Dissertation
[5] Ensembl 2014
Flicek, Paul
Amode, M. Ridwan
Barrell, Daniel
Beal, Kathryn
Billis, Konstantinos
Brent, Simon
Carvalho-Silva, Denise
Clapham, Peter
Coates, Guy
Fitzgerald, Stephen
Gil, Laurent
Giron, Carlos Garcia
Gordon, Leo
Hourlier, Thibaut
Hunt, Sarah
Johnson, Nathan
Juettemann, Thomas
Kaehaeri, Andreas K.
Keenan, Stephen
Kulesha, Eugene
Martin, Fergal J.
Maurel, Thomas
McLaren, William M.
Murphy, Daniel N.
Nag, Rishi
Overduin, Bert
Pignatelli, Miguel
Pritchard, Bethan
Pritchard, Emily
Riat, Harpreet S.
Ruffier, Magali
Sheppard, Daniel
Taylor, Kieron
Thormann, Anja
Trevanion, Stephen J.
Vullo, Alessandro
Wilder, Steven P.
Wilson, Mark
Zadissa, Amonida
Aken, Bronwen L.
Birney, Ewan
Cunningham, Fiona
Harrow, Jennifer
Herrero, Javier
Hubbard, Tim J. P.
Kinsella, Rhoda
Muffato, Matthieu
Parker, Anne
Spudich, Giulietta
Yates, Andy
[J]. NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) : D749 - D755
[6] Bioconductor: open software development for computational biology and bioinformatics
Gentleman, RC
Carey, VJ
Bates, DM
Bolstad, B
Dettling, M
Dudoit, S
Ellis, B
Gautier, L
Ge, YC
Gentry, J
Hornik, K
Hothorn, T
Huber, W
Iacus, S
Irizarry, R
Leisch, F
Li, C
Maechler, M
Rossini, AJ
Sawitzki, G
Smith, C
Smyth, G
Tierney, L
Yang, JYH
Zhang, JH
[J]. GENOME BIOLOGY, 2004, 5 (10)
[7] phyloXML: XML for evolutionary biology and comparative genomics
Han, Mira V.
Zmasek, Christian M.
[J]. BMC BIOINFORMATICS, 2009, 10
[8] Integrating biological data -: the Distributed Annotation System
Jenkinson, Andrew M.
Albrecht, Mario
Birney, Ewan
Blankenburg, Hagen
Down, Thomas
Finn, Robert D.
Hermjakob, Henning
Hubbard, Tim J. P.
Jimenez, Rafael C.
Jones, Philip
Kahari, Andreas
Kulesha, Eugene
Macias, Jose R.
Reeves, Gabrielle A.
Prlic, Andreas
[J]. BMC BIOINFORMATICS, 2008, 9 (Suppl 8)
[9] Ensembl BioMarts: a hub for data retrieval across taxonomic space
Kinsella, Rhoda J.
Kaehaeri, Andreas
Haider, Syed
Zamora, Jorge
Proctor, Glenn
Spudich, Giulietta
Almeida-King, Jeff
Staines, Daniel
Derwent, Paul
Kerhornou, Arnaud
Kersey, Paul
Flicek, Paul
[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2011,
[10] Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
McLaren, William
Pritchard, Bethan
Rios, Daniel
Chen, Yuan
Flicek, Paul
Cunningham, Fiona
[J]. BIOINFORMATICS, 2010, 26 (16) : 2069 - 2070

← 1 2 →