The Ensembl genome database project

By Tim J. P. Hubbard, Daniel Barker, Ewan Birney, G. Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas A. Down and 25 more. Nucleic Acids Res., 2002

1,641 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/fded6f9cefb06c1da7acddd5b9b89b1eabb08b7d

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Citations in the corpus

The Universal Protein Resource (UniProt) (2004, background): “UniRef100 is based on all UniProt Knowledgebase records, as well as UniParc records that represent sequences deemed over-represented in the Knowledgebase, DDBJ/EMBL/ GenBank Whole Genome Shotgun coding sequence translations, Ensembl protein translations from various organisms, as well as IPI data.”
UniProt: the Universal Protein knowledgebase (2004, background): “It contains publicly available protein sequences from many different sources, including Swiss-Prot, TrEMBL, PIR-PSD, EMBL (3), Ensembl (4), IPI (http://www.”
Comparative assessment of large-scale data sets of protein–protein interactions (2002, background): “Whole genomes can be screened for three types of interaction evidence: (1) in prokaryotic genomes, interacting proteins are often encoded by conserved operons(13,14,20); (2) interacting proteins have a tendency to be either present or absent together from fully sequenced genomes(21,22), that is, to ”
Apollo: a sequence annotation editor (2002, methodology): “were published. Both the Berkeley Drosophila Genome Project (BDGP) working with Celera Genomics and other researchers, and the Ensembl [ 26 ] project working on the human genome provided the community with annotations in a very short time.”
The Bioperl toolkit: Perl modules for the life sciences. (2002, methodology): “Bioperl is capable of parsing the output from a variety of programs including BLAST [both NCBI and WUBLAST ( Gish 2002 ) versions], HMMer (Eddy 2001), ClustalW (Thompson et al. 1994), T-Coffee (Notredame et al. 2000), Phylip (Felsenstein 1983), many EM-BOSS (Rice et al. 2000) programs, Genscan (Burg”
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003, background): “org/ in December 2002 (human release 9.30 and mosquito release 9.1; Hubbard et al. 2002).”
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations (2004, background): “These include GeneQuiz (1), GeneAtlas (2), Ensembl (3), PEDANT (4), Genotator (5), MAGPIE (6) and GAIA (7).”
DAVID: Database for Annotation, Visualization, and Integrated Discovery (2003, methodology): “A number of public efforts are currently focusing on the annotation and curation of gene-specific functional data, including LocusLink, Protein Information Resource (PIR), GeneCards, Proteome, Kyoto Encyclopedia of Genes and Genomes (KEGG), Ensembl, and Swiss-Prot to name but a few [2-8].”
The UCSC Genome Browser database: 2015 update (2014, methodology): “Ensembl genes.”
igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV) (2020, methodology): “…such views have been provided in genome browsers, including large client-server systems such as the UCSC Genome Browser [1] and the Ensembl Genome Browser [2], rich client web applications such as JBrowse [3], and desktop applications such as the Integrative Genomics Viewer (IGV) [4,5].”
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. (2003, methodology): “of the set are available at http //www.ebi.ac.uk/proteome/ SPTREnsembl.html.”
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data (2003, background): “Chromosome localization information, with direct links to NCBIs MapView, Ensembl (9), and UCSC genome browsers (10).”
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR (2015, methodology): “Please note that the gene definition refers to different gene build annotation systems, including RefGene from the National Center for Biotechnology Information (NCBI) 55 , UCSC Known Gene from UCSC 56 , ENSEMBL gene from the ENSEMBL project 57 and GENCODE gene from the GENCODE consortium 58 .”
GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations (2013, background): “Moreover, they come with varying documentation, they are frequently modified or updated, and they are housed in both centralized repositories [10,11] and on individual laboratory websites.”
Ensembl 2009 (2008, background): “The case of Ensembl is no different: the data contained in its databases is presented in different ways through a number of different ‘views’, which have been progressively added as project has developed, starting with relatively straightforward views summarizing information about a given gene, or d”
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes (2010, methodology): “Polymorphisms in genomic DNA, cDNA and amino acid sequences were also assigned a standardized description following recommendations made by the Human Genome Variation Society (13), a standard adopted by other SNP databases including dbSNP (14) and Ensembl (15).”