pattern-matching of protein to DNA.[5][6] The Ensembl project was launched in 1999 in response to the imminent completion of the Human Genome Project, with the initial goals of automatically annotate the human genome, integrate this annotation with available biological data and make all this knowledge publicly available.[2]
In the Ensembl project, sequence data are fed into the gene annotation system (a collection of software "pipelines" written in Perl) which creates a set of predicted gene locations and saves them in a MySQL database for subsequent analysis and display. Ensembl makes these data freely accessible to the world research community. All the data and code produced by the Ensembl project is available to download,[7] and there is also a publicly accessible database server allowing remote access. In addition, the Ensembl website provides computer-generated visual displays of much of the data.
Over time the project has expanded to include additional species (including key
protists, focusing on providing taxonomic and evolutionary context to genes, whilst the original project continues to focus on vertebrates.[8][9]
As of 2020, Ensembl supported over 50 000 genomes across both Ensembl and Ensembl Genomes databases, adding some new innovative features such as Rapid Release, a new website designed to make genome annotation data available more quickly to users, and COVID-19, a new website to access to SARS-CoV-2 reference genome.
Central to the Ensembl concept is the ability to automatically generate graphical views of the alignment of genes and other genomic data against a reference genome. These are shown as data tracks, and individual tracks can be turned on and off, allowing the user to customise the display to suit their research interests. The interface also enables the user to zoom in to a region or move along the genome in either direction.
Other displays show data at varying levels of resolution, from whole
trees of similar genes (homologues) across a range of species. The graphics are complemented by tabular displays, and in many cases data can be exported directly from the page in a variety of standard file formats such as FASTA
.
Externally produced data can also be added to the display by uploading a suitable file in one of the supported formats, such as
Graphics are generated using a suite of custom Perl modules based on GD, the standard Perl graphics display library.
Alternative access methods
In addition to its website, Ensembl provides a REST
scripts to be written to retrieve data of interest. The same API is used internally by the web interface to display the data. It is divided in sections like the core API, the compara API (for comparative genomics
data), the variation API (for accessing SNPs, SNVs, CNVs..), and the functional genomics API (to access regulatory data).
The Ensembl website provides extensive information on how to install and use the API.
This software can be used to access the public MySQL database, avoiding the need to download enormous datasets. The users could even choose to retrieve data from the MySQL with direct SQL queries, but this requires an extensive knowledge of the current database schema.
Large datasets can be retrieved using the BioMart data-mining tool. It provides a web interface for downloading datasets using complex queries.
Last, there is an FTP server which can be used to download entire MySQL databases as well some selected data sets in other formats.
Current species
The annotated genomes include most fully sequenced vertebrates and selected model organisms. All of them are eukaryotes, there are no prokaryotes. As of 2022, there are 271 species registered, this includes:[11]
All data part of the Ensembl project is open access and all software is open source, being freely available to the scientific community, under a CC BY 4.0 license. Currently, Ensembl database website is mirrored at four different locations worldwide to improve the service.
