Difference between revisions of "BioMart"

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{{Tool data
<center>{{#icon: Biomart250.png|BioMart||http://www.biomart.org/}}</center>
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|name=BioMart
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|status=mature
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|dev=active
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|support=active
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|type=Community Annotation, Database schema, Database tools, Genome Annotation, Middleware, Tool Integration, Data federation software
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|platform=linux, unix, os x, windows, web
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|about=BioMart is a freely available, open source, federated database system that provides unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework.
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|open source=Yes
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|licence=[http://opensource.org/licenses/LGPL-3.0 LGPL]
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|input=Any data that can be stored in the relational database
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|output=APIs: REST/SOAP, JAVA, SPARQL
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|release date=2001/01/01
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|logo=Biomart250.png
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|papers=http://www.biomart.org/publications.html
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|dl tracking=We do not track downloads but the usage can be also tracked through http://www.biomart.org/community.html
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|gmod date=
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|survey link=
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|contact email=arek.kasprzyk@gmail.com
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|dev status=
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}}
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All BioMart documentation has now been moved to the [http://www.biomart.org/ BioMart website].
  
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[[File:Biomart250.png|center|link=http://www.biomart.org/|BioMart]]
  
{{ComponentBox|{{BioMartResourcesBoxItem}}|||||}}
 
  
[http://www.biomart.org/ BioMart] is a robust, query-oriented data integration system, based on distributed data warehousing ideas. The system can be applied to a single or multiple databases. It supports scalable large scale querying of individual databases as well as query-chaining between them. All datasources in the system comply with the BioMart data model - a simple, query optimised database schema. The system consists of database schema specification, administration tools for deploying and configuring mart-spec databases and data access software, which includes web and standalone interfaces.
 
  
  
==Demo & Screenshots==
 
  
The BioMart web interface at OICR can be found [http://www.biomart.org/biomart/martview here]. For Ensembl implemetation look [http://www.ensembl.org/biomart/martview here]. The screenshots of standalone interfaces and admin tools can be found [http://www.biomart.org/user-docs.pdf here]
 
 
 
==Requirements==
 
 
The requirements will differ dependent on which part of the BioMart suite you want to install. For more details look http://www.biomart.org/install-overview.html
 
 
 
==Documentation==
 
 
* [http://www.biomart.org/install.html BioMart Documentation]
 
* [[BioMart Tutorial]]
 
 
=== How to Load a [[Chado]] Database into BioMart ===
 
 
A [[:Image:How to load chado to biomart.pdf|detailed document]] (available in both [[Media:How to load chado to biomart.pdf|PDF]] and [[Media:How to load chado to biomart.doc|Microsoft Word]] formats) on how to load a [[Chado]] database into BioMart has been written by Aminah Olivia KELIET, Joëlle Amselem, Sandra DEROZIE, and Delphine Steinbach, all of [http://www.urgi.versailles.inra.fr INRA URGI].  This document contains step by step instructions on how to load data from a Chado database into BioMart.  Contact Aminah Olivia KELIET <[mailto:aminah-olivia.keliet@versailles.inra.fr aminah-olivia.keliet@versailles.inra.fr]> if you have specific questions.
 
 
''Note: the eventual plan is to wikify this document.''
 
 
=== Presentations ===
 
 
* [[:Image:Jan2009BioMart.pdf|BioMart]], by Arek Kasprzyk at the [[January 2009 GMOD Meeting#BioMart|January 2009 GMOD Meeting]].
 
* [[:Image:Kasprzyk-050516.ppt‎|BioMart and Chado]], by Arek Kasprzyk at [[May 2005 GMOD Meeting]].
 
* [[:Image:Kasprzyk_040526.ppt‎|BioMart: A Federated Query Architecture]], by Arek Kasprzyk at the [[April 2004 GMOD Meeting]].
 
 
== Mailing Lists ==
 
 
{{MailingListsFor|BioMart}}
 
 
==Downloads==
 
 
The download/installation instructions can be found http://www.biomart.org/install-overview.html
 
  
 
[[Category:BioMart]]
 
[[Category:BioMart]]
 
[[Category:Database Tools]]
 
[[Category:Database Tools]]
 
[[Category:GMOD Components]]
 
[[Category:GMOD Components]]
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{{SemanticLink
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|linkurl=http://www.biomart.org/download.html
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|linktype=download
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}}
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{{SemanticLink
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|linkurl=http://www.biomart.org/
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|linktype=website
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}}
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{{SemanticLink
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|linkurl=http://www.biomart.org/community.html
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|linktitle=BioMart user community
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|linktype=wild URL
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|linkdesc=Links to BioMart installations in the wild
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}}
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{{InteroperableComponent
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|relationship=provides data for
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|object=GBrowse
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}}

Latest revision as of 22:26, 15 October 2013

All BioMart documentation has now been moved to the BioMart website.

BioMart
Facts about "BioMart"RDF feed
Available on platformlinux +, unix +, os x +, windows + and web +
Has URLhttp://www.biomart.org/download.html +, http://www.biomart.org/ + and http://www.biomart.org/community.html +
Has descriptionBioMart is a freely available, open sourceBioMart is a freely available, open source, federated database system that provides unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework.e incorporated into the BioMart framework. + and Links to BioMart installations in the wild +
Has development statusactive +
Has input formatAny data that can be stored in the relational database +
Has licenceLGPL +
Has logoBiomart250.png +
Has output formatAPIs: REST/SOAP +, JAVA + and SPARQL +
Has software maturity statusmature +
Has support statusactive +
Has titleBioMart user community +
Has topicBioMart +
Interaction typeprovides data for +
InteractorBioMart +
Interacts withGBrowse +
Is open sourceYes +
Link typedownload +, website + and wild URL +
Release date1 January 2001 +
Tool functionality or classificationCommunity Annotation +, Database schema +, Database tools +, Genome Annotation +, Middleware +, Tool Integration + and Data federation software +
Has subobjectThis property is a special property in this wiki.BioMart#http://www.biomart.org/download.html +, BioMart#http://www.biomart.org/ +, BioMart#http://www.biomart.org/community.html + and BioMart +