Ensembl BioMarts: a hub for data retrieval across taxonomic space

By R. Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, G. Proctor, Giulietta Spudich, J. Almeida-King, D. Staines, P. Derwent, A. Kerhornou and 2 more. Database J. Biol. Databases Curation, 2011

1,401 citations recorded by the source corpus.

For a number of years the BioMart data warehousing system has proven to be a valuable resource for scientists seeking a fast and versatile means of accessing the growing volume of genomic data provided by the Ensembl project. The launch of the Ensembl Genomes project in 2009 complemented the Ensembl project by utilizing the same visualization, interactive and programming tools to provide users with a means for accessing genome data from a further five domains: protists, bacteria, metazoa, plants and fungi. The Ensembl and Ensembl Genomes BioMarts provide a point of access to the high-quality gene annotation, variation data, functional and regulatory annotation and evolutionary relationships from genomes spanning the taxonomic space. This article aims to give a comprehensive overview of the Ensembl and Ensembl Genomes BioMarts as well as some useful examples and a description of current data content and future objectives. Database URLs: http://www.ensembl.org/biomart/martview/; http://metazoa.ensembl.org/biomart/martview/; http://plants.ensembl.org/biomart/martview/; http://protists.ensembl.org/biomart/martview/; http://fungi.ensembl.org/biomart/martview/; http://bacteria.ensembl.org/biomart/martview/

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/962ad4fd765f196f494935080009621cc27acf77

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Citations in the corpus

A comprehensive map of molecular drug targets (2016, methodology): “…of Canis lupus familiaris (dog ), Sus scrofa ( pig ), Rattus norvegicus (rat) , Mus musculus (mouse), Danio rerio (zebrafish), Drosophila melanogaster (fruitfly), Caenorhabditis elegans (nematode) and Saccharomyces cerevisiae (yeast) were extracted from Ensembl Compara version 82 (REFS 57,58) .”
The stress granule transcriptome reveals principles of mRNA accumulation in stress granules (2017, neutral): “All length data (5 0 UTR, ORF, 3 0 UTR and total) was acquired using Ensemble’s Biomart tool (Aken et al., 2016; Kinsella et al., 2011).”
Ensembl 2016 (2015, methodology): “Our BioMart databases continue to be updated every release in order to provide the latest annotation and imported data (48).”
Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism (2018, positive): “Furthermore, all SNPs/SNVs for model genes were downloaded directly from dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) via the Ensembl BioMart interface 61 .”
BioMart: driving a paradigm change in biological data management (2011, methodology): “BioMart has successfully adapted data warehousing ideas such as data marts, dimensional modelling (4), and query optimization into the world of biological databases (5–13).”
Ensembl 2017 (2016, methodology): “We also develop and distribute a suite of databases, tools (10,11), APIs (12,13) and web interfaces (14) for generating, querying and distributing these data and in doing so”
WormBase 2016: expanding to enable helminth genomic research (2015, methodology): “For example, we have modified Ensembl code to provide a sequence search service and BioMart data mining platform (25) that allow the interrogation of all species, or large sub-groups of species (e.”
Ensembl 2020 (2019, methodology): “MANE Select tagged transcripts are visible on our transcript summary tables, integrated into our data mining platform BioMart (23) and available from Ensembl VEP.”
Ensembl 2014 (2013, methodology): “Themore established BioMart data-mining tool (43) provides users with a variety of ways of accessing the Ensembl data quickly and with relative ease.”