Difference between revisions of "BioMart"
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[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. | [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. |
Revision as of 20:58, 5 October 2010
__NOTITLE__
- Mature release
- Active development
- Active support
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.
Contents
Demo & Screenshots
The BioMart web interface at OICR can be found here. For Ensembl implemetation look here. The screenshots of standalone interfaces and admin tools can be found 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
How to Load a Chado Database into BioMart
A detailed document (available in both PDF and 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 INRA URGI. This document contains step by step instructions on how to load data from a Chado database into BioMart. Contact Aminah Olivia KELIET <aminah-olivia.keliet@versailles.inra.fr> if you have specific questions.
Note: the eventual plan is to wikify this document.
Presentations
- BioMart, by Arek Kasprzyk at the January 2009 GMOD Meeting.
- BioMart and Chado, by Arek Kasprzyk at May 2005 GMOD Meeting.
- BioMart: A Federated Query Architecture, by Arek Kasprzyk at the April 2004 GMOD Meeting.
Mailing Lists
Mailing List Link | Description | Archive(s) | |
---|---|---|---|
BioMart | announce | BioMart announcements mailing list | Nabble (2010/06+) |
users | BioMart users, developers, code and installation | Nabble (2010/06+) |
Downloads
The download/installation instructions can be found http://www.biomart.org/install-overview.html