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Ensembl creates, integrates and distributes reference datasets and analysis tools that enable genomics. Ensembl is a genome browser that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.


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How to cite this record FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: July 21, 2020, 9:10 p.m.; Last accessed: Dec 02 2020 7:24 p.m.

Publication for citation  Ensembl 2020. Yates AD, et al; Nucleic Acids Res ; 2019; 10.1093/nar/gkz966;


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Record updated: July 21, 2020, 3:20 p.m. by ensembl_fair.

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Access / Retrieve Data

Conditions of Use

Applies to: Data use Applies to: Database software

Data Release

Data Access


REST Web Services



Publications

The Ensembl REST API: Ensembl Data for Any Language.

Yates A,Beal K,Keenan S,McLaren W,Pignatelli M,Ritchie GR,Ruffier M,Taylor K,Vullo A,Flicek P
Bioinformatics 2014

View Paper (PubMed) View Publication

The Ensembl Variant Effect Predictor.

McLaren W,Gil L,Hunt SE,Riat HS,Ritchie GR,Thormann A,Flicek P,Cunningham F
Genome Biol 2016

View Paper (PubMed) View Publication

Incorporating RNA-seq data into the zebrafish Ensembl genebuild.

Collins JE,White S,Searle SM,Stemple DL
Genome Res 2012

View Paper (PubMed) View Publication

Ensembl comparative genomics resources.

Herrero J,Muffato M,Beal K,Fitzgerald S,Gordon L,Pignatelli M,Vilella AJ,Searle SM,Amode R,Brent S,Spooner W,Kulesha E,Yates A,Flicek P
Database (Oxford) 2016

View Paper (PubMed) View Publication

The Ensembl Web site: mechanics of a genome browser.

Stalker J,Gibbins B,Meidl P,Smith J,Spooner W,Hotz HR,Cox AV
Genome Res 2004

View Paper (PubMed) View Publication

The Ensembl core software libraries.

Stabenau A,McVicker G,Melsopp C,Proctor G,Clamp M,Birney E
Genome Res 2004

View Paper (PubMed) View Publication

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, et al.
Genome Res 2012

View Paper (PubMed) View Publication

Disease and phenotype data at Ensembl.

Spudich GM,Fernandez-Suarez XM
Curr Protoc Hum Genet 2011

View Paper (PubMed) View Publication

Genome information resources - developments at Ensembl.

Hammond MP,Birney E
Trends Genet 2004

View Paper (PubMed) View Publication

Ensembl BioMarts: a hub for data retrieval across taxonomic space.

Kinsella RJ,Kahari A,Haider S,Zamora J,Proctor G,Spudich G,Almeida-King J,Staines D,Derwent P,Kerhornou A,Kersey P,Flicek P
Database (Oxford) 2011

View Paper (PubMed) View Publication

Ensembl 2015

Cunningham F et al.
Nucleic Acids Res. 2015

View Paper (PubMed) View Publication

Ensembl 2006.

Birney E et al.
Nucleic Acids Res 2005

View Paper (PubMed) View Publication

The Ensembl REST API: Ensembl Data for Any Language.

Yates A,Beal K,Keenan S,McLaren W,Pignatelli M,Ritchie GR,Ruffier M,Taylor K,Vullo A,Flicek P
Bioinformatics 2014

View Paper (PubMed) View Publication

Ensembl 2014.

Flicek P et al.
Nucleic Acids Res 2013

View Paper (PubMed) View Publication

Ensembl 2006.

Birney E et al.
Nucleic Acids Res 2005

View Paper (PubMed) View Publication

ncRNA orthologies in the vertebrate lineage.

Pignatelli M,Vilella AJ,Muffato M,Gordon L,White S,Flicek P,Herrero J
Database (Oxford) 2016

View Paper (PubMed) View Publication

Ensembl comparative genomics resources.

Herrero J,Muffato M,Beal K,Fitzgerald S,Gordon L,Pignatelli M,Vilella AJ,Searle SM,Amode R,Brent S,Spooner W,Kulesha E,Yates A,Flicek P
Database (Oxford) 2016

View Paper (PubMed) View Publication

The Ensembl computing architecture.

Cuff JA,Coates GM,Cutts TJ,Rae M
Genome Res 2004

View Paper (PubMed) View Publication

Ensembl 2005.

Hubbard T et al.
Nucleic Acids Res 2004

View Paper (PubMed) View Publication

ESTGenes: alternative splicing from ESTs in Ensembl.

Eyras E,Caccamo M,Curwen V,Clamp M
Genome Res 2004

View Paper (PubMed) View Publication

The ensembl regulatory build.

Zerbino DR,Wilder SP,Johnson N,Juettemann T,Flicek PR
Genome Biol 2015

View Paper (PubMed) View Publication

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.

Zerbino DR,Johnson N,Juettemann T,Wilder SP,Flicek P
Bioinformatics 2013

View Paper (PubMed) View Publication

Ensembl 2017.

Aken BL et al.
Nucleic Acids Res 2016

View Paper (PubMed) View Publication

TranscriptSNPView: a genome-wide catalog of mouse coding variation.

Cunningham F,Rios D,Griffiths M,Smith J,Ning Z,Cox T,Flicek P,Marin-Garcin P,Herrero J,Rogers J,van der Weyden L,Bradley A,Birney E,Adams DJ
Nat Genet 2006

View Paper (PubMed) View Publication

Ensembl 2016.

Yates A et al.
Nucleic Acids Res 2015

View Paper (PubMed) View Publication

Genome-wide nucleotide-level mammalian ancestor reconstruction.

Paten B,Herrero J,Fitzgerald S,Beal K,Flicek P,Holmes I,Birney E
Genome Res 2008

View Paper (PubMed) View Publication

Ensembl 2008.

Flicek P et al.
Nucleic Acids Res 2007

View Paper (PubMed) View Publication

Ensembl 2002: accommodating comparative genomics.

Clamp M et al.
Nucleic Acids Res 2003

View Paper (PubMed)

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Vilella AJ,Severin J,Ureta-Vidal A,Heng L,Durbin R,Birney E
Genome Res 2008

View Paper (PubMed) View Publication

Ensembl 2002: accommodating comparative genomics.

Clamp M et al.
Nucleic Acids Res 2003

View Paper (PubMed)

Ensembl variation resources.

Chen Y,Cunningham F,Rios D,McLaren WM,Smith J,Pritchard B,Spudich GM,Brent S,Kulesha E,Marin-Garcia P,Smedley D,Birney E,Flicek P
BMC Genomics 2010

View Paper (PubMed) View Publication

The ensembl regulatory build.

Zerbino DR,Wilder SP,Johnson N,Juettemann T,Flicek PR
Genome Biol 2015

View Paper (PubMed) View Publication

The Ensembl genome database project.

Hubbard T et al.
Nucleic Acids Res 2001

View Paper (PubMed)

Ensembl 2007.

Hubbard TJ et al.
Nucleic Acids Res 2006

View Paper (PubMed) View Publication

A database and API for variation, dense genotyping and resequencing data.

Rios D,McLaren WM,Chen Y,Birney E,Stabenau A,Flicek P,Cunningham F
BMC Bioinformatics 2010

View Paper (PubMed) View Publication

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.

McLaren W,Pritchard B,Rios D,Chen Y,Flicek P,Cunningham F
Bioinformatics 2010

View Paper (PubMed) View Publication

Ensembl 2009.

Hubbard TJ et al.
Nucleic Acids Res 2008

View Paper (PubMed) View Publication

Ensembl's 10th year.

Flicek P et al.
Nucleic Acids Res 2009

View Paper (PubMed) View Publication

The Ensembl gene annotation system.

Aken BL,Ayling S,Barrell D,Clarke L,Curwen V,Fairley S,Fernandez Banet J,Billis K,Garcia Giron C,Hourlier T,Howe K,Kahari A,Kokocinski F,Martin FJ,Murphy DN,Nag R,Ruffier M,Schuster M,Tang YA,Vogel JH,White S,Zadissa A,Flicek P,Searle SM
Database (Oxford) 2016

View Paper (PubMed) View Publication

eHive: an artificial intelligence workflow system for genomic analysis.

Severin J,Beal K,Vilella AJ,Fitzgerald S,Schuster M,Gordon L,Ureta-Vidal A,Flicek P,Herrero J
BMC Bioinformatics 2010

View Paper (PubMed) View Publication

Ensembl regulation resources.

Zerbino DR,Johnson N,Juetteman T,Sheppard D,Wilder SP,Lavidas I,Nuhn M,Perry E,Raffaillac-Desfosses Q,Sobral D,Keefe D,Graf S,Ahmed I,Kinsella R,Pritchard B,Brent S,Amode R,Parker A,Trevanion S,Birney E,Dunham I,Flicek P
Database (Oxford) 2016

View Paper (PubMed) View Publication

Touring Ensembl: a practical guide to genome browsing.

Spudich GM,Fernandez-Suarez XM
BMC Genomics 2010

View Paper (PubMed) View Publication

Genome browsing with Ensembl: a practical overview.

Spudich G,Fernandez-Suarez XM,Birney E
Brief Funct Genomic Proteomic 2007

View Paper (PubMed) View Publication

Ensembl 2011.

Flicek P et al.
Nucleic Acids Res 2010

View Paper (PubMed) View Publication

Ensembl 2012.

Flicek P et al.
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

Ensembl 2013.

Flicek P et al.
Nucleic Acids Res 2012

View Paper (PubMed) View Publication

The Ensembl analysis pipeline.

Potter SC,Clarke L,Curwen V,Keenan S,Mongin E,Searle SM,Stabenau A,Storey R,Clamp M
Genome Res 2004

View Paper (PubMed) View Publication

The Ensembl automatic gene annotation system.

Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M
Genome Res 2004

View Paper (PubMed) View Publication

Ensembl 2019.

Cunningham F et al.
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

Ensembl 2020.

Yates AD, et al
Nucleic Acids Res 2019

View Paper (PubMed) View Publication

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