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BioMart

Topic: Software

 From HandWiki - Reading time: 4 min

BioMart
BioMart QuickQuery Interface
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

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]

References

  1. ↑ "EnsMart: a generic system for fast and flexible access to biological data". Genome Research 14 (1): 160–169. January 2004. doi:10.1101/gr.1645104. PMID 14707178. 
  2. ↑ "Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. February 2001. doi:10.1038/35057062. PMID 11237011. Bibcode: 2001Natur.409..860L. 
  3. ↑ 3.0 3.1 "BioMart--biological queries made easy". BMC Genomics 10: 22. January 2009. doi:10.1186/1471-2164-10-22. PMID 19144180. 
  4. ↑ "BioMart: driving a paradigm change in biological data management". Database 2011. 2011. doi:10.1093/database/bar049. PMID 22083790. 
  5. ↑ 5.0 5.1 "BioMart Central Portal--unified access to biological data". Nucleic Acids Research 37 (Web Server issue): W23–W27. July 2009. doi:10.1093/nar/gkp265. PMID 19420058. 
  6. ↑ 6.0 6.1 "BioMart Central Portal: an open database network for the biological community". Database 2011. 2011. doi:10.1093/database/bar041. PMID 21930507. 
  7. ↑ An Introduction to BioMart. Retrieved 2024-04-18 – via www.youtube.com.
  8. ↑ "BioMart: a data federation framework for large collaborative projects". Database 2011. 2011. doi:10.1093/database/bar038. PMID 21930506. 
  9. ↑ "BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis". Bioinformatics 21 (16): 3439–3440. August 2005. doi:10.1093/bioinformatics/bti525. PMID 16082012. 
  10. ↑ "Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses". Journal of Biomedical Informatics 49: 119–133. June 2014. doi:10.1016/j.jbi.2014.01.005. PMID 24462600. 
  11. ↑ "Cytoscape Web: an interactive web-based network browser". Bioinformatics 26 (18): 2347–2348. September 2010. doi:10.1093/bioinformatics/btq430. PMID 20656902. 
  12. ↑ "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. July 2013. doi:10.1093/nar/gkt328. PMID 23640334. 
  13. ↑ "BioMart". http://www.biomart.org/community.html. 



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