Ensembl
Homepage http://www.ensembl.org/
Countries that developed this resource European Union , United Kingdom
Created in 1999
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How to cite this record FAIRsharing.org: Ensembl; Ensembl; DOI: https://doi.org/10.25504/FAIRsharing.fx0mw7; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Dec 14 2019 2:31 a.m.
Record updated: Aug. 6, 2018, 9:43 a.m. by The FAIRsharing Team.
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Applies to: Database softwareData Access
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The Ensembl genome database project.
Hubbard T,Barker D,Birney E,Cameron G,Chen Y,Clark L,Cox T,Cuff J,Curwen V,Down T,Durbin R,Eyras E,Gilbert J,Hammond M,Huminiecki L,Kasprzyk A,Lehvaslaiho H,Lijnzaad P,Melsopp C,Mongin E,Pettett R,Pocock M,Potter S,Rust A,Schmidt E,Searle S,Slater G,Smith J,Spooner W,Stabenau A,Stalker J,Stupka E,Ureta-Vidal A,Vastrik I,Clamp M
Nucleic Acids Res 2001
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
The Ensembl Variant Effect Predictor.
McLaren W,Gil L,Hunt SE,Riat HS,Ritchie GR,Thormann A,Flicek P,Cunningham F
Genome Biol 2016
Incorporating RNA-seq data into the zebrafish Ensembl genebuild.
Collins JE,White S,Searle SM,Stemple DL
Genome Res 2012
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
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
The Ensembl core software libraries.
Stabenau A,McVicker G,Melsopp C,Proctor G,Clamp M,Birney E
Genome Res 2004
GENCODE: the reference human genome annotation for The ENCODE Project.
Harrow J,Frankish A,Gonzalez JM,Tapanari E,Diekhans M,Kokocinski F,Aken BL,Barrell D,Zadissa A,Searle S,Barnes I,Bignell A,Boychenko V,Hunt T,Kay M,Mukherjee G,Rajan J,Despacio-Reyes G,Saunders G,Steward C,Harte R,Lin M,Howald C,Tanzer A,Derrien T,Chrast J,Walters N,Balasubramanian S,Pei B,Tress M,Rodriguez JM,Ezkurdia I,van Baren J,Brent M,Haussler D,Kellis M,Valencia A,Reymond A,Gerstein M,Guigo R,Hubbard TJ
Genome Res 2012
Disease and phenotype data at Ensembl.
Spudich GM,Fernandez-Suarez XM
Curr Protoc Hum Genet 2011
Genome information resources - developments at Ensembl.
Hammond MP,Birney E
Trends Genet 2004
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
Ensembl 2007.
Hubbard TJ,Aken BL,Beal K,Ballester B,Caccamo M,Chen Y,Clarke L,Coates G,Cunningham F,Cutts T,Down T,Dyer SC,Fitzgerald S,Fernandez-Banet J,Graf S,Haider S,Hammond M,Herrero J,Holland R,Howe K,Howe K,Johnson N,Kahari A,Keefe D,Kokocinski F,Kulesha E,Lawson D,Longden I,Melsopp C,Megy K,Meidl P,Ouverdin B,Parker A,Prlic A,Rice S,Rios D,Schuster M,Sealy I,Severin J,Slater G,Smedley D,Spudich G,Trevanion S,Vilella A,Vogel J,White S,Wood M,Cox T,Curwen V,Durbin R,Fernandez-Suarez XM,Flicek P,Kasprzyk A,Proctor G,Searle S,Smith J,Ureta-Vidal A,Birney E
Nucleic Acids Res 2006
Ensembl 2006.
Birney E,Andrews D,Caccamo M,Chen Y,Clarke L,Coates G,Cox T,Cunningham F,Curwen V,Cutts T,Down T,Durbin R,Fernandez-Suarez XM,Flicek P,Graf S,Hammond M,Herrero J,Howe K,Iyer V,Jekosch K,Kahari A,Kasprzyk A,Keefe D,Kokocinski F,Kulesha E,London D,Longden I,Melsopp C,Meidl P,Overduin B,Parker A,Proctor G,Prlic A,Rae M,Rios D,Redmond S,Schuster M,Sealy I,Searle S,Severin J,Slater G,Smedley D,Smith J,Stabenau A,Stalker J,Trevanion S,Ureta-Vidal A,Vogel J,White S,Woodwark C,Hubbard TJ
Nucleic Acids Res 2005
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
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
Ensembl 2014.
Flicek P,Amode MR,Barrell D,Beal K,Billis K,Brent S,Carvalho-Silva D,Clapham P,Coates G,Fitzgerald S,Gil L,Giron CG,Gordon L,Hourlier T,Hunt S,Johnson N,Juettemann T,Kahari AK,Keenan S,Kulesha E,Martin FJ,Maurel T,McLaren WM,Murphy DN,Nag R,Overduin B,Pignatelli M,Pritchard B,Pritchard E,Riat HS,Ruffier M,Sheppard D,Taylor K,Thormann A,Trevanion SJ,Vullo A,Wilder SP,Wilson M,Zadissa A,Aken BL,Birney E,Cunningham F,Harrow J,Herrero J,Hubbard TJ,Kinsella R,Muffato M,Parker A,Spudich G,Yates A,Zerbino DR,Searle SM
Nucleic Acids Res 2013
Ensembl 2006.
Birney E,Andrews D,Caccamo M,Chen Y,Clarke L,Coates G,Cox T,Cunningham F,Curwen V,Cutts T,Down T,Durbin R,Fernandez-Suarez XM,Flicek P,Graf S,Hammond M,Herrero J,Howe K,Iyer V,Jekosch K,Kahari A,Kasprzyk A,Keefe D,Kokocinski F,Kulesha E,London D,Longden I,Melsopp C,Meidl P,Overduin B,Parker A,Proctor G,Prlic A,Rae M,Rios D,Redmond S,Schuster M,Sealy I,Searle S,Severin J,Slater G,Smedley D,Smith J,Stabenau A,Stalker J,Trevanion S,Ureta-Vidal A,Vogel J,White S,Woodwark C,Hubbard TJ
Nucleic Acids Res 2005
ncRNA orthologies in the vertebrate lineage.
Pignatelli M,Vilella AJ,Muffato M,Gordon L,White S,Flicek P,Herrero J
Database (Oxford) 2016
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
The Ensembl computing architecture.
Cuff JA,Coates GM,Cutts TJ,Rae M
Genome Res 2004
Ensembl 2005.
Hubbard T,Andrews D,Caccamo M,Cameron G,Chen Y,Clamp M,Clarke L,Coates G,Cox T,Cunningham F,Curwen V,Cutts T,Down T,Durbin R,Fernandez-Suarez XM,Gilbert J,Hammond M,Herrero J,Hotz H,Howe K,Iyer V,Jekosch K,Kahari A,Kasprzyk A,Keefe D,Keenan S,Kokocinsci F,London D,Longden I,McVicker G,Melsopp C,Meidl P,Potter S,Proctor G,Rae M,Rios D,Schuster M,Searle S,Severin J,Slater G,Smedley D,Smith J,Spooner W,Stabenau A,Stalker J,Storey R,Trevanion S,Ureta-Vidal A,Vogel J,White S,Woodwark C,Birney E
Nucleic Acids Res 2004
ESTGenes: alternative splicing from ESTs in Ensembl.
Eyras E,Caccamo M,Curwen V,Clamp M
Genome Res 2004
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
Ensembl 2017.
Aken BL,Achuthan P,Akanni W,Amode MR,Bernsdorff F,Bhai J,Billis K,Carvalho-Silva D,Cummins C,Clapham P,Gil L,Giron CG,Gordon L,Hourlier T,Hunt SE,Janacek SH,Juettemann T,Keenan S,Laird MR,Lavidas I,Maurel T,McLaren W,Moore B,Murphy DN,Nag R,Newman V,Nuhn M,Ong CK,Parker A,Patricio M,Riat HS,Sheppard D,Sparrow H,Taylor K,Thormann A,Vullo A,Walts B,Wilder SP,Zadissa A,Kostadima M,Martin FJ,Muffato M,Perry E,Ruffier M,Staines DM,Trevanion SJ,Cunningham F,Yates A,Zerbino DR,Flicek P
Nucleic Acids Res 2016
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
Ensembl 2016.
Yates A,Akanni W,Amode MR,Barrell D,Billis K,Carvalho-Silva D,Cummins C,Clapham P,Fitzgerald S,Gil L,Giron CG,Gordon L,Hourlier T,Hunt SE,Janacek SH,Johnson N,Juettemann T,Keenan S,Lavidas I,Martin FJ,Maurel T,McLaren W,Murphy DN,Nag R,Nuhn M,Parker A,Patricio M,Pignatelli M,Rahtz M,Riat HS,Sheppard D,Taylor K,Thormann A,Vullo A,Wilder SP,Zadissa A,Birney E,Harrow J,Muffato M,Perry E,Ruffier M,Spudich G,Trevanion SJ,Cunningham F,Aken BL,Zerbino DR,Flicek P
Nucleic Acids Res 2015
Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B,Herrero J,Fitzgerald S,Beal K,Flicek P,Holmes I,Birney E
Genome Res 2008
The ensembl regulatory build.
Zerbino DR,Wilder SP,Johnson N,Juettemann T,Flicek PR
Genome Biol 2015
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
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
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
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
The ensembl regulatory build.
Zerbino DR,Wilder SP,Johnson N,Juettemann T,Flicek PR
Genome Biol 2015
Ensembl 2009.
Hubbard TJ,Aken BL,Ayling S,Ballester B,Beal K,Bragin E,Brent S,Chen Y,Clapham P,Clarke L,Coates G,Fairley S,Fitzgerald S,Fernandez-Banet J,Gordon L,Graf S,Haider S,Hammond M,Holland R,Howe K,Jenkinson A,Johnson N,Kahari A,Keefe D,Keenan S,Kinsella R,Kokocinski F,Kulesha E,Lawson D,Longden I,Megy K,Meidl P,Overduin B,Parker A,Pritchard B,Rios D,Schuster M,Slater G,Smedley D,Spooner W,Spudich G,Trevanion S,Vilella A,Vogel J,White S,Wilder S,Zadissa A,Birney E,Cunningham F,Curwen V,Durbin R,Fernandez-Suarez XM,Herrero J,Kasprzyk A,Proctor G,Smith J,Searle S,Flicek P
Nucleic Acids Res 2008
Touring Ensembl: a practical guide to genome browsing.
Spudich GM,Fernandez-Suarez XM
BMC Genomics 2010
Genome browsing with Ensembl: a practical overview.
Spudich G,Fernandez-Suarez XM,Birney E
Brief Funct Genomic Proteomic 2007
Ensembl 2008.
Flicek P,Aken BL,Beal K,Ballester B,Caccamo M,Chen Y,Clarke L,Coates G,Cunningham F,Cutts T,Down T,Dyer SC,Eyre T,Fitzgerald S,Fernandez-Banet J,Graf S,Haider S,Hammond M,Holland R,Howe KL,Howe K,Johnson N,Jenkinson A,Kahari A,Keefe D,Kokocinski F,Kulesha E,Lawson D,Longden I,Megy K,Meidl P,Overduin B,Parker A,Pritchard B,Prlic A,Rice S,Rios D,Schuster M,Sealy I,Slater G,Smedley D,Spudich G,Trevanion S,Vilella AJ,Vogel J,White S,Wood M,Birney E,Cox T,Curwen V,Durbin R,Fernandez-Suarez XM,Herrero J,Hubbard TJ,Kasprzyk A,Proctor G,Smith J,Ureta-Vidal A,Searle S
Nucleic Acids Res 2007
Ensembl's 10th year.
Flicek P,Aken BL,Ballester B,Beal K,Bragin E,Brent S,Chen Y,Clapham P,Coates G,Fairley S,Fitzgerald S,Fernandez-Banet J,Gordon L,Graf S,Haider S,Hammond M,Howe K,Jenkinson A,Johnson N,Kahari A,Keefe D,Keenan S,Kinsella R,Kokocinski F,Koscielny G,Kulesha E,Lawson D,Longden I,Massingham T,McLaren W,Megy K,Overduin B,Pritchard B,Rios D,Ruffier M,Schuster M,Slater G,Smedley D,Spudich G,Tang YA,Trevanion S,Vilella A,Vogel J,White S,Wilder SP,Zadissa A,Birney E,Cunningham F,Dunham I,Durbin R,Fernandez-Suarez XM,Herrero J,Hubbard TJ,Parker A,Proctor G,Smith J,Searle SM
Nucleic Acids Res 2009
Ensembl 2011.
Flicek P,Amode MR,Barrell D,Beal K,Brent S,Chen Y,Clapham P,Coates G,Fairley S,Fitzgerald S,Gordon L,Hendrix M,Hourlier T,Johnson N,Kahari A,Keefe D,Keenan S,Kinsella R,Kokocinski F,Kulesha E,Larsson P,Longden I,McLaren W,Overduin B,Pritchard B,Riat HS,Rios D,Ritchie GR,Ruffier M,Schuster M,Sobral D,Spudich G,Tang YA,Trevanion S,Vandrovcova J,Vilella AJ,White S,Wilder SP,Zadissa A,Zamora J,Aken BL,Birney E,Cunningham F,Dunham I,Durbin R,Fernandez-Suarez XM,Herrero J,Hubbard TJ,Parker A,Proctor G,Vogel J,Searle SM
Nucleic Acids Res 2010
Ensembl 2012.
Flicek P,Amode MR,Barrell D,Beal K,Brent S,Carvalho-Silva D,Clapham P,Coates G,Fairley S,Fitzgerald S,Gil L,Gordon L,Hendrix M,Hourlier T,Johnson N,Kahari AK,Keefe D,Keenan S,Kinsella R,Komorowska M,Koscielny G,Kulesha E,Larsson P,Longden I,McLaren W,Muffato M,Overduin B,Pignatelli M,Pritchard B,Riat HS,Ritchie GR,Ruffier M,Schuster M,Sobral D,Tang YA,Taylor K,Trevanion S,Vandrovcova J,White S,Wilson M,Wilder SP,Aken BL,Birney E,Cunningham F,Dunham I,Durbin R,Fernandez-Suarez XM,Harrow J,Herrero J,Hubbard TJ,Parker A,Proctor G,Spudich G,Vogel J,Yates A,Zadissa A,Searle SM
Nucleic Acids Res 2011
Ensembl 2013.
Flicek P,Ahmed I,Amode MR,Barrell D,Beal K,Brent S,Carvalho-Silva D,Clapham P,Coates G,Fairley S,Fitzgerald S,Gil L,Garcia-Giron C,Gordon L,Hourlier T,Hunt S,Juettemann T,Kahari AK,Keenan S,Komorowska M,Kulesha E,Longden I,Maurel T,McLaren WM,Muffato M,Nag R,Overduin B,Pignatelli M,Pritchard B,Pritchard E,Riat HS,Ritchie GR,Ruffier M,Schuster M,Sheppard D,Sobral D,Taylor K,Thormann A,Trevanion S,White S,Wilder SP,Aken BL,Birney E,Cunningham F,Dunham I,Harrow J,Herrero J,Hubbard TJ,Johnson N,Kinsella R,Parker A,Spudich G,Yates A,Zadissa A,Searle SM
Nucleic Acids Res 2012
Ensembl 2002: accommodating comparative genomics.
Clamp M,Andrews D,Barker D,Bevan P,Cameron G,Chen Y,Clark L,Cox T,Cuff J,Curwen V,Down T,Durbin R,Eyras E,Gilbert J,Hammond M,Hubbard T,Kasprzyk A,Keefe D,Lehvaslaiho H,Iyer V,Melsopp C,Mongin E,Pettett R,Potter S,Rust A,Schmidt E,Searle S,Slater G,Smith J,Spooner W,Stabenau A,Stalker J,Stupka E,Ureta-Vidal A,Vastrik I,Birney E
Nucleic Acids Res 2003
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
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
Ensembl 2002: accommodating comparative genomics.
Clamp M,Andrews D,Barker D,Bevan P,Cameron G,Chen Y,Clark L,Cox T,Cuff J,Curwen V,Down T,Durbin R,Eyras E,Gilbert J,Hammond M,Hubbard T,Kasprzyk A,Keefe D,Lehvaslaiho H,Iyer V,Melsopp C,Mongin E,Pettett R,Potter S,Rust A,Schmidt E,Searle S,Slater G,Smith J,Spooner W,Stabenau A,Stalker J,Stupka E,Ureta-Vidal A,Vastrik I,Birney E
Nucleic Acids Res 2003
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
The Ensembl automatic gene annotation system.
Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M
Genome Res 2004
Reporting Guidelines
No guidelines defined
Terminology Artifacts
Models and Formats
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
- MitoMiner
- NONCODE
- Gene3D
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- WikiPathways
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- PRoteomics IDEntifications database
- Reactome - a curated knowledgebase of biological pathways
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- IUPHAR/BPS Guide to PHARMACOLOGY
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Record Maintainer
This record is maintained by Ensembl
Funds
The Wellcome Trust, UK (Charitable foundation)
European Commission under FP7 Grant Agreement (Government body)
