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BioMart

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Written inJava
Operating systemUnix-like
Available inEnglish
TypeFederated database system
LicenseLGPL
Websiteuseast.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]

Integration with Ensembl

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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

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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

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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]

References

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  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. ^ a b 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. ^ a b 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. ^ a b 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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