BioMart

Last updated
Written in Java
Operating system Unix-like
Available inEnglish
Type Federated database system
License LGPL
Website useast.ensembl.org/info/data/biomart/index.html

BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. Although the BioMart software is primarily used by the biomedical research community, it is designed in such a way that any type of data can be incorporated into the BioMart framework. The BioMart project originated at the European Bioinformatics Institute as a data management solution [1] for the Human Genome Project. [2] Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents. [3] [4] [5] [6]

Contents

Integration with Ensembl

BioMart is a powerful tool for researchers and bioinformaticians that allows a user to export data from Ensembl, this could include data such as gene ID’s, gene positions, associated variations, protein domains and sequences. BioMArt allows the data to be exported into convenient file types like FASTA, XLS, CSV, TSV, HTML. Researchers can use the exported data in a variety of applications, including genomic studies, gene expression analysis, and comparative genomics. BioMart's intuitive interface enables users to customize queries to access specific data sets or features of interest easily [7]

Software

BioMart is a freely available, open-source, federated database system that provides unified access to disparate, geographically distributed data sources. [8] BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects. BioMart contains several levels of query optimization to efficiently manage large data sets, and offers a diverse selection of graphical user interfaces and application programming interfaces to allow queries to be performed in whatever manner is most convenient for the user. BioMart's capabilities are extended by integration with several widely used software packages such as Bioconductor, [9] Galaxy, [10] Cytoscape, [11] and Taverna. [12]

Data sources and community

There are around 40 BioMart data sources including the Atlas of UTR Regulatory Activity (AURA), the COSMIC cancer database, Ensembl Genomes, HapMap, InterPro, Mouse Genome Informatics (MGI), Rfam and UniProt. Access is provided by institutions including the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute in the UK, Cold Spring Harbor Laboratory and the National Center for Biotechnology Information (NCBI) in the United States and French National Centre for Scientific Research (CNRS). [13] The BioMart Central Portal was established to provide a convenient single point of access to this growing pool of data sources. [3] [5] [6]

Related Research Articles

<span class="mw-page-title-main">Bioinformatics</span> Computational analysis of large, complex sets of biological data

Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.

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<span class="mw-page-title-main">Ensembl genome database project</span> Scientific project at the European Bioinformatics Institute

Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.

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The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.

<span class="mw-page-title-main">Apache Taverna</span>

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<span class="mw-page-title-main">Galaxy (computational biology)</span>

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<span class="mw-page-title-main">Gene set enrichment analysis</span> Bioinformatics method

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References

  1. ↑ Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C, et al. (January 2004). "EnsMart: a generic system for fast and flexible access to biological data". Genome Research. 14 (1): 160–169. doi:10.1101/gr.1645104. PMC   314293 . PMID   14707178.
  2. ↑ Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. Bibcode:2001Natur.409..860L. doi: 10.1038/35057062 . hdl: 2027.42/62798 . PMID   11237011.
  3. 1 2 Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, et al. (January 2009). "BioMart--biological queries made easy". BMC Genomics. 10: 22. doi: 10.1186/1471-2164-10-22 . PMC   2649164 . PMID   19144180.
  4. ↑ Kasprzyk A (2011). "BioMart: driving a paradigm change in biological data management". Database. 2011: bar049. doi:10.1093/database/bar049. PMC   3215098 . PMID   22083790.
  5. 1 2 Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A (July 2009). "BioMart Central Portal--unified access to biological data". Nucleic Acids Research. 37 (Web Server issue): W23–W27. doi:10.1093/nar/gkp265. PMC   2703988 . PMID   19420058.
  6. 1 2 Guberman JM, Ai J, Arnaiz O, Baran J, Blake A, Baldock R, et al. (2011). "BioMart Central Portal: an open database network for the biological community". Database. 2011: bar041. doi:10.1093/database/bar041. PMC   3263598 . PMID   21930507.
  7. ↑ An Introduction to BioMart . Retrieved 2024-04-18– via www.youtube.com.
  8. ↑ Zhang J, Haider S, Baran J, Cros A, Guberman JM, Hsu J, et al. (2011). "BioMart: a data federation framework for large collaborative projects". Database. 2011: bar038. doi:10.1093/database/bar038. PMC   3175789 . PMID   21930506.
  9. ↑ Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A, et al. (August 2005). "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis". Bioinformatics. 21 (16): 3439–3440. doi: 10.1093/bioinformatics/bti525 . PMID   16082012.
  10. ↑ Liu B, Madduri RK, Sotomayor B, Chard K, Lacinski L, Dave UJ, et al. (June 2014). "Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses". Journal of Biomedical Informatics. 49: 119–133. doi:10.1016/j.jbi.2014.01.005. PMC   4203338 . PMID   24462600.
  11. ↑ Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD (September 2010). "Cytoscape Web: an interactive web-based network browser". Bioinformatics. 26 (18): 2347–2348. doi:10.1093/bioinformatics/btq430. PMC   2935447 . PMID   20656902.
  12. ↑ Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, et al. (July 2013). "The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud". Nucleic Acids Research. 41 (Web Server issue): W557–W561. doi:10.1093/nar/gkt328. PMC   3692062 . PMID   23640334.
  13. ↑ "BioMart". www.biomart.org. Retrieved 14 July 2016.
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