EnsMart: a generic system for fast and flexible access to biological data.

By Arek Kasprzyk, Damian Keefe, D. Smedley, D. London, William Spooner, Craig Melsopp, M. Hammond, P. Rocca-Serra, Tony Cox, Ewan Birney. Genome Research, 2003

466 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f88c68975c9fbaf1bf35004558d5228d95121ab8

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Citations in the corpus

BioMart Central Portal—unified access to biological data (2009, background): “The Distributed Annotation System (DAS) (3) as well as BioMart (4) are functional examples of such frameworks.”
FlyMine: an integrated database for Drosophila and Anopheles genomics (2007, methodology): “Finally, like FlyMine, some systems integrate all the data into one place a data warehouse (for example, GUS [20], BioMart [21], Biozon [22], BioWarehouse [23], GIMS [24], Atlas [25] and Ondex [26]).”
Network-based global inference of human disease genes (2008, methodology): “The gene–phenotype associations are deﬁned in OMIM and are automatically extracted from BioMART (previously known as En-sMart ; Kasprzyk et al , 2004).”
The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, background): “Since its conception as a data-mining interface for the Human Genome Project (13) BioMart has rapidly grown to become an international collaboration involving a large number of different groups and organizations both in academia and in industry (14).”
Ensembl 2008 (2007, methodology): “Comparative genomics data and the supporting data for the Ensembl BioMart datamining tool (6) are provided in multi-species databases.”
Ensembl 2009 (2008, methodology): “– It allows its datasets to be dynamically federated with external datasets for data mining using the BioMart system (5).”
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis (2007, methodology): “A similar conclusion was obtained when we conducted comparisons to SOURCE [4], RESOURCER [5], IDcon-verter [6], BioMart [7], and UCSC Gene Sorter [8] with the same gene list [26] (see Additional File 7 for detailed results).”
Comparative Genomics (2007, unknown): “Comparative genomics tracks showing results of whole-genome alignments are available at the UCSC Genome Browser and Ensembl.”
State of the nation in data integration for bioinformatics (2008, methodology): “In 2007 BioMART [15] altered its interface four times, breaking any client software that used it.”
The Ensembl automatic gene annotation system. (2004, methodology): “For the human genome we link the Ensembl predictions to the eVoc expression vocabulary (Kelso et al. 2003).”
Analysis of cell-based RNAi screens (2006, methodology): “For the example dataset, the vignette 'End-to-end analysis of cell-based screens: from raw intensity readings to the annotated hit list' of the cellHTS package demonstrates how to obtain a comprehensive set of annotations for the targets of the Drosophila RNAi library using the biomaRt package [25],”
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments (2007, methodology): “1) Genomes for 31 organisms, respective namespace mappings, orthology matches, and GO annotations are all retrieved from the Ensembl database (18) via the BioMart (19) interface.”
Ensembl 2007 (2006, methodology): “For cases where researchers are working with sets of items, such as a particular class of genes, Ensembl provides data mining tools via the BioMart system (7).”
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data (2010, methodology): “The identified binding sites are usually converted to a format, such as BED or Wiggle (WIG), that can be uploaded to the UCSC Genome Browser, an open-access, web-based, up-to-date source for genome sequence data integrated with a large collection of related annotations [11].”
Human MicroRNA Targets (2004, methodology): “To facilitate surveys of target function and analysis of functional enrichment, InterPro domain assignments (Mulder et al. 2003) and GO (molecular function hierarchy) mappings (Ashburner and Lewis 2002) for all human genes were obtained using EnsMart.”
WebGestalt: an integrated system for exploring gene sets in various biological contexts (2005, background): “org/Multi/martview), in which the users can perform a genome information search and retrieval for sets of genes in human and several other eukaryotic species (3).”
The Vertebrate Genome Annotation (Vega) database (2004, background): “It is possible to use EnsMart (18), available at Ensembl (http://www.ensembl.org/ Multi/martview), to query a recent version of the gene structures from the Vega human database (which are displayed on the Ensembl website in ContigView).”