BioMart – biological queries made easy

By D. Smedley, Syed Haider, B. Ballester, Richard C. G. Holland, D. London, Gudmundur A. Thorisson, Arek Kasprzyk. BMC Genomics, 2009

1,019 citations recorded by the source corpus.

BackgroundBiologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. Frequently, more than one data source is required and for high-throughput analysis, cutting and pasting results between websites is certainly very time consuming. Therefore, many groups rely on local bioinformatics support to process queries by accessing the resource's programmatic interfaces if they exist. This is not an efficient solution in terms of cost and time. Instead, it would be better if the biologist only had to learn one generic interface. BioMart provides such a solution.ResultsBioMart enables scientists to perform advanced querying of biological data sources through a single web interface. The power of the system comes from integrated querying of data sources regardless of their geographical locations. Once these queries have been defined, they may be automated with its "scripting at the click of a button" functionality. BioMart's capabilities are extended by integration with several widely used software packages such as BioConductor, DAS, Galaxy, Cytoscape, Taverna. In this paper, we describe all aspects of BioMart from a user's perspective and demonstrate how it can be used to solve real biological use cases such as SNP selection for candidate gene screening or annotation of microarray results.ConclusionBioMart is an easy to use, generic and scalable system and therefore, has become an integral part of large data resources including Ensembl, UniProt, HapMap, Wormbase, Gramene, Dictybase, PRIDE, MSD and Reactome. BioMart is freely accessible to use at http://www.biomart.org.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f4f37ea065e38fc08bfd0fa591d9039968f9c281

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Citations in the corpus

Ensembl BioMarts: a hub for data retrieval across taxonomic space (2011, methodology): “The Ensembl BioMarts are comprised of seven databases (three hidden and four visible).”
The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, methodology): “Many other real usage examples are documented in our previous paper (10)”
Ensembl 2014 (2013, methodology): “The more established BioMart data-mining tool (43) provides users with a variety of ways of accessing the Ensembl data quickly and with relative ease.”
Ensembl 2012 (2011, background): “Data can also be accessed through the Ensembl BioMart (11,12).”
Concise Polygenic Models for Cancer-Specific Identification of Drug-Sensitive Tumors from Their Multi-Omics Profiles (2020, methodology): “The instructions also specify which input data files are used and hence have to be downloaded from https://www.cancerrxgene.org/ XGB models along with their predictive accuracies and OMC feature sets are specified in Supplementary File 1, Correspondence between Ensembl identifiers and HGNC gene name”
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine (2015, background): “Biomart [95] “BioMart enables scientists to perform advanced querying of biological data sources through a single web interface.”
WormBase 2016: expanding to enable helminth genomic research (2015, methodology): “We also provide a separate data mining platform for the WormBase ParaSite portal, using the BioMart technology (38).”
Ensembl 2011 (2010, methodology): “…we encourage incorporation of our code base and data into third party resources as well as the programmatic use of our results in external analysis pipelines that interact with these results using the Ensembl API (8), Ensembl tools such as the SNP Effect Predictor (9) and the Ensembl BioMart (10).”
Ensembl variation resources (2010, methodology): “Thousands of researchers from around the world access Ensembl data every day through the various portals provided by the project including the web interface at http://www.ensembl. org[15], the Ensembl API [16], and Ensembl BioMart [17].”
UniProt Knowledgebase: a hub of integrated protein data (2011, background): “BioMart (39) is an open-source data management system that allows for integrated querying of biological data resources regardless of their geographical”
BioMart Central Portal—unified access to biological data (2009, background): “A detailed description of usage and query formulation is explained in (11) and the project docs available at www.”
Ensembl’s 10th year (2009, background): “The Ensembl BioMart provides access to most of our data resources in a way that facilitates the creation of complex database queries in a relatively simple manner (16).”
Computational tools for prioritizing candidate genes: boosting disease gene discovery (2012, methodology): “Some data sets are easily retrievable over the Web in a well-structured format — for example, data that are retrievable through the Ensembl BioMart 125 — whereas in other cases format might be subject to change over time, or identifiers might become obsolete.”
Phytozome: a comparative platform for green plant genomics (2011, methodology): ““Get Data" provides access to the BioMart data query tool for this family, while the family page display can be customized on the “Display options” tab.”
BioMart: driving a paradigm change in biological data management (2011, background): “…to quickly deploy a website hosting any type of data, user-friendly graphical user interface, several programmatic interfaces and support for third party tools contributed to its success and adoption by many different types of projects around the world as their data management platform (14).”