Ensembl variation resources

By Yuan Chen, Fiona Cunningham, Daniel Rios, William M. McLaren, James A. Smith, Bethan Pritchard, Giulietta Spudich, Simon Brent, Eugene Kulesha, P. Marín-García and 3 more. BMC Genomics, 2010

307 citations recorded by the source corpus.

BackgroundThe maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics.DescriptionThe Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl.ConclusionsVariation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/986b8a8962e4e660891f9f5118eaf836730718af

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Citations in the corpus

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants (2011, background): “The UCSC Genome Browser (14) and ENSEMBL Genome Browser (15,16) both allow genomic regions to be annotated with the results of cutting-edge genomic data, including chromatin state segmentations, ENCODE data, 1000 Genomes variants, evolutionary constraint, LD calculations and NHGRI catalog variants.”
Ensembl 2018 (2017, methodology): “Data from large variation discovery projects such as HapMap (7) and the 1000 Genome Project (8) were incorporated into our variation storage and annotation resources (9).”
Ensembl 2012 (2011, background): “Eighteen of our most popular species also include dedicated variation resources (5) derived from dbSNP (6), DGVa (7) and other sources.”
Ensembl 2013 (2012, methodology): “We create variation resources for 17 species by importing and merging data from many different sources through our pipeline (22).”
The Ensembl Regulatory Build (2015, background): “The Ensembl framework, which currently holds a consistent relation database of gene transcripts [41], variants [42], and now regulatory elements will be a natural home for this key component of cell biology.”
The Ensembl Variant Effect Predictor (2016, methodology): “Table 5: Regulatory element-related fields reported by VEP Frequency, phenotype and citation annotation The VEP searches the Ensembl Variation databases, which contain a large catalogue of freely available germ line and somatic variation data in vertebrates (Chen et al. 2010; Rios et al. 2010).”
Ensembl 2011 (2010, methodology): “A full description of our process for creating the Ensembl variation databases as well as a detailed description of each of the Ensembl variation displays was recently published (16).”
Ensembl 2017 (2016, unknown): “When a new genome assembly is included in Ensembl, we integrate diverse data to produce a collection of Ensembl resources for gene annotation (6), genome variation (7), gene regulation (8) and comparative genomics (9).”
Ensembl BioMarts: a hub for data retrieval across taxonomic space (2011, background): “For example, Ensembl variation data resources include those in dbSNP (2) as well as variation data created by the project in the context of genome analysis (3).”
Ensembl 2019 (2018, methodology): “Specifically, we improved the integration of Ensembl’s variation data (5) with the European Variant Archive (EVA; https://www.ebi.ac.uk/eva/) by configuring the Ensembl website to use EVA genotype data directly using Tabix indexed VCF files (16).”