Ensembl’s 10th year

By Paul Flicek, Bronwen L. Aken, B. Ballester, Kathryn M Beal, E. Bragin, Simon Brent, Yuan Chen, P. Clapham, Guy Coates, S. Fairley and 47 more. Nucleic Acids Res., 2009

318 citations recorded by the source corpus.

Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

OMA 2011: orthology inference among 1000 complete genomes (2010, background): “In the version of the human genome currently in OMA (Ensembl v.55), genes have up to 44 annotated splice variants.”
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011, methodology): “ENCODE gene and transcript annotations are updated bimonthly and are available through the UCSC ENCODE browser, distributed annotation servers (DAS;seehttp://genome.ucsc.edu/cgi-bin/das/ hg18/features?segment=21:33031597, 33041570;type=wgEncodeGencodeManualV3), and the Ensembl Browser [22].”
LOVD v.2.0: the next generation in gene variant databases (2011, methodology): “Finally, graphical displays of the variants in several genome browsers (Ensembl [Flicek et al., 2010], UCSC [Kent et al., 2002], NCBI Sequence Viewer (http:// www.ncbi.nlm.nih.gov/projects/sviewer/)) are provided.”
UniProt Knowledgebase: a hub of integrated protein data (2011, background): “Regular feedback is provided to Ensembl and VEGA if erroneous annotations from these sources are identified during the course of UniProtKB manual curation so that incorrect sequences may be updated or withdrawn.”
The UCSC genome browser and associated tools (2012, methodology): “Both NCBI [11] and the Ensembl project [12] developed visualization tools at the beginning of the Human Genome Project and others, such as GBrowse [7] appeared soon thereafter.”
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data (2011, methodology): “For PUM2, IGF2BP1 and QKI, the complete gene sequences for all protein coding genes were used as background set (UTRs, coding sequence and introns as identified in ENSEMBL release 57 [42]).”
Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor (unknown): “Even before the developments reported in this article, Ensembl (Flicek et al., 2010) could also be used to derive similar annotation by setting up a full local Ensembl database containing the variant information and running scripts from the Ensembl Variation database production pipeline.”
The UCSC Genome Browser database: update 2011 (2010, background): “These include the Consensus Coding Sequence (CCDS) (37) tracks, which were updated on the human and mouse genomes, the Mammalian Gene Collection (MGC) tracks (38) on the human, mouse, rat, cow and frog genomes, and the Ensembl Genes tracks (6), available on approximately 25 different organisms.”
Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping (2011, methodology): “The tool relies on BioPerl [32], the Ensembl Perl Core and Compara APIs [33,34] and the EBI-Intact PSI Common Query InterfaCe (PSICQUIC) enabled web service [35,36] for its operation.”
PHOSIDA 2011: the posttranslational modification database (2010, unknown): “In contrast to the previous version of PHOSIDA, we now use the phylogentic relationships of 36 eukaryotes provided by the Ensembl Compara database (34).”
A human functional protein interaction network and its application to cancer data analysis (2010, methodology): “The numbers of interactions from three model organisms have been mapped to human proteins based on Ensembl Compara [48] (see text for details). a Numbers of PPIs in the original species.”
Ensembl 2011 (2010, methodology): “This article provides an overview of some of the new data and features that have been added to Ensembl since our previous report (11) and provides details of changes to our integrated analysis procedures that are designed to maximize the value of new and emerging technologies such as RNA-seq and…”
Ensembl 2012 (2011, methodology): “As with previous updates (15,16), we can only describe a subset of the information provided.”
The case for cloud computing in genome informatics (2010, background): “Most users access the information either through websites created by the archival databases, or through value-added integrators of genomic data, such as Ensembl [7], the University of California at Santa Cruz (UCSC) Genome Browser [8], Galaxy [9], or one of the many model organism databases [10-13].”
Phospho.ELM: a database of phosphorylation sites—update 2011 (2010, background): “The user can query the database by keyword or sequence identiﬁer [from UniProt (26) or Ensembl (27)] to get information about single proteins/substrates, or by kinase name to retrieve all phosphorylated substrates of a particular kinase.”