 | |
| Content | |
|---|---|
| Description | An integrative resource for genome-scale data from non-vertebrate species. |
| Data types captured | Genomic database |
| Organisms | pan |
| Contact | |
| Research center | European Bioinformatics Institute |
| Primary citation | Kersey & al. (2012),[1] Howe & al. (2020)[2] |
| Release date | 2009 |
| Access | |
| Website | https://ensemblgenomes.org/ |
| Download URL | ftp://ftp.ensemblgenomes.org/pub/current |
| Web service URL | https://rest.ensembl.org/ |
| Public SQL access | [email protected]:4157 |
| Miscellaneous | |
| License | Apache 2.0 |
| Data release frequency | 4 times per year |
| Version | Release 52 (December 2021) |
Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species.[1][2]
The project is run by the European Bioinformatics Institute, and was launched in 2009 using the Ensembl technology.[3] The main objective of the Ensembl Genomes database is to complement the main Ensembl database by introducing five additional web pages to include genome data for bacteria, fungi, invertebrate metazoa, plants, and protists.[4] For each of the domains, the Ensembl tools are available for manipulation, analysis and visualization of genome data. Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl REST interface, the Perl API, Biomart or online.[5]
Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public.[6] Ensembl and Ensembl Genomes software uses an Apache 2.0 license[7] license.
- ^ a b Kersey, P. J.; Staines, D. M.; Lawson, D.; Kulesha, E.; Derwent, P.; Humphrey, J. C.; Hughes, D. S. T.; Keenan, S.; Kerhornou, A.; Koscielny, G.; Langridge, N.; McDowall, M. D.; Megy, K.; Maheswari, U.; Nuhn, M.; Paulini, M.; Pedro, H.; Toneva, I.; Wilson, D.; Yates, A.; Birney, E. (2011). "Ensembl Genomes: An integrative resource for genome-scale data from non-vertebrate species". Nucleic Acids Research. 40 (Database issue): D91–D97. doi:10.1093/nar/gkr895. PMC 3245118. PMID 22067447.
- ^ a b Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambel L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt S, Jaiswal P, Janacek S, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P (January 2020). "Ensembl Genomes 2020—enabling non-vertebrate genomic research". Nucleic Acids Research. 48(D1) (D1): D689–D695. doi:10.1093/nar/gkz890. PMC 6943047. PMID 31598706.
- ^ Hubbard, T. J. P.; Aken, B. L.; 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. (2009). "Ensembl 2009". Nucleic Acids Research. 37 (Database issue): D690–D697. doi:10.1093/nar/gkn828. PMC 2686571. PMID 19033362.
- ^ "About Ensembl Genomes". Ensembl Genomes. Ensembl. Retrieved 2 September 2014.
- ^ "Ensembl Genomes MySQL". ensemblgenomes.org. Ensembl Genomes. Retrieved 11 September 2014.
- ^ Kinsella, Rhoda J.; Kähäri, Andreas; Syed, Haider; Zamora, Jorge; Proctor, Glenn; Spudich, Giulietta; Almeida-King, Jeff; Staines, Daniel; Derwent, Paul; Kerhournou, Arnaud; Kersey, Paul; Flicek, Paul (2011). "Ensembl BioMarts: a hub for data retrieval across taxonomic space". Database. 2011 (2011): 2. doi:10.1093/database/bar030. PMC 3170168. PMID 21785142.
- ^ "Software License". Ensembl. Retrieved 9 June 2020.