| 词条 | BioMart |
| 释义 |
| name = BioMart | title = | logo = BioMartLogo.png | screenshot = BioMartQuickQueryScreenshot.gif | caption = BioMart QuickQuery Interface | collapsible = | author = | developer = | released = | discontinued = | latest release version = | latest release date = | latest preview version = | latest preview date = | programming language = Java | operating_system = Unix-like | platform = | size = | language = English | genre = Federated database system | license = LGPL | website = {{URL|http://biomart.org}} }}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] SoftwareBioMart is a freely available, open-source, federated database system that provides unified access to disparate, geographically distributed data sources.[7] 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,[8] Galaxy,[9] Cytoscape,[10] and Taverna.[11] ServicesThe BioMart community has set up a large number{{Quantify|date=July 2016}} of servers, which provide access to various types of research data. Using BioMart's data federation technology, the BioMart Central Portal[3][5][6] was established to provide a convenient single point of access to this growing pool of data sources. Data sources and communityThere 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).[12] References1. ^{{cite journal|display-authors=etal|vauthors=Kasprzyk A, Keefe D, Smedley D|year=2004|title=EnsMart: a generic system for fast and flexible access to biological data|url=|journal=Genome Res.|volume=14|issue=1|pages=160–9|doi=10.1101/gr.1645104|pmc=314293|pmid=14707178}} 2. ^{{cite journal|display-authors=etal|vauthors=Lander ES, Linton LM, Birren B|year=2001|title=Initial sequencing and analysis of the human genome|url=https://deepblue.lib.umich.edu/bitstream/2027.42/62798/1/409860a0.pdf|journal=Nature|volume=409|issue=6822|pages=860–921|doi=10.1038/35057062|pmid=11237011}} 3. ^1 {{cite journal|display-authors=etal|vauthors=Smedley D, Haider S, Ballester B|year=2009|title=BioMart--biological queries made easy|url=|journal=BMC Genomics|volume=10|issue=|pages=22|doi=10.1186/1471-2164-10-22|pmc=2649164|pmid=19144180}} 4. ^{{cite journal|author=Kasprzyk A|year=2011|title=BioMart: driving a paradigm change in biological data management|url=|journal=Database (Oxford)|volume=2011|issue=|pages=bar049|doi=10.1093/database/bar049|pmc=3215098|pmid=22083790}} 5. ^1 {{cite journal|vauthors=Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A|year=2009|title=BioMart Central Portal--unified access to biological data|url=|journal=Nucleic Acids Res.|volume=37|issue=Web Server issue|pages=W23–7|doi=10.1093/nar/gkp265|pmc=2703988|pmid=19420058}} 6. ^1 {{cite journal|display-authors=etal|vauthors=Guberman JM, Ai J, Arnaiz O|year=2011|title=BioMart Central Portal: an open database network for the biological community|url=|journal=Database (Oxford)|volume=2011|issue=|pages=bar041|doi=10.1093/database/bar041|pmc=3263598|pmid=21930507}} 7. ^{{cite journal|display-authors=etal|vauthors=Zhang J, Haider S, Baran J|year=2011|title=BioMart: a data federation framework for large collaborative projects|url=|journal=Database (Oxford)|volume=2011|issue=|pages=bar038|doi=10.1093/database/bar038|pmc=3175789|pmid=21930506}} 8. ^{{cite journal|display-authors=etal|vauthors=Durinck S, Moreau Y, Kasprzyk A, Davis S, De Moor B, Brazma A|year=2005|title=BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis.|url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=16082012|journal=Bioinformatics|volume=21|issue=16|pages=3439–40|doi=10.1093/bioinformatics/bti525|pmc=|pmid=16082012}} 9. ^{{cite journal|display-authors=etal|vauthors=Liu B, Madduri RK, Sotomayor B|year=2014|title=Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses|journal=J Biomed Inform|volume=49|issue=|pages=119–33|doi=10.1016/j.jbi.2014.01.005|pmc=4203338|pmid=24462600}} 10. ^{{cite journal|vauthors=Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD|year=2010|title=Cytoscape Web: an interactive web-based network browser|url=|journal=Bioinformatics|volume=26|issue=18|pages=2347–8|doi=10.1093/bioinformatics/btq430|pmc=2935447|pmid=20656902}} 11. ^{{cite journal|vauthors=Wolstencroft K, Haines R, Fellows D, et al.|year=2013|title=The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud|url=|journal=Nucleic Acids Res.|volume=41|issue=Web Server issue|pages=W557–61|doi=10.1093/nar/gkt328|pmc=3692062|pmid=23640334}} 12. ^{{cite web|title=BioMart|url=http://www.biomart.org/community.html|website=www.biomart.org|accessdate=14 July 2016}} External links
4 : Bioinformatics software|Free software projects|Biological databases|Data warehousing products |
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