Difference between revisions of "Benchmark Extension"

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(Scientific Databases)
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The schema we collect at 05 Sep. 2008 are 46 and are available here: [http://yellowstone.cs.ucla.edu/schema-evolution/documents/BioSQL-schema.zip]
 
The schema we collect at 05 Sep. 2008 are 46 and are available here: [http://yellowstone.cs.ucla.edu/schema-evolution/documents/BioSQL-schema.zip]
  
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=== GUS ===
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The Genomics Unified Schema (GUS) is an extensive relational database schema and associated application framework designed to store, integrate, analyze and present functional genomics data. The GUS schema supports a wide range of data types including genomics, gene expression, transcript assemblies, proteomics and others. It emphasizes standards-based ontologies and strong-typing.
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The GUS Application Framework offers an object-relational layer and a Plugin API used to rapidly create robust data loading programs for diverse data sources. The GUS distribution includes plugins for standard data sources. The GUS Web Development Kit (WDK) is a rich environment for efficiently designing sophisticated query-based websites with little programming required.
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Their about page: http://www.gusdb.org/about.php
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The SVN: https://www.cbil.upenn.edu/svn/gus/
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=== NCBO ===
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The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form.
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In this Context they use relational DB backend.
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The SVN: http://smi-protege.stanford.edu/repos/cbio/ncbo/trunk/conf/ncbo_tables.sql
  
 
=== Genomic DB Survey ===  
 
=== Genomic DB Survey ===  
 
Another relevant source is [http://siloe.deis.unical.it/biodbSurvey/] where Erika De Francesco and Simona Rombo provide a survey of almost 80 genomic databases.
 
Another relevant source is [http://siloe.deis.unical.it/biodbSurvey/] where Erika De Francesco and Simona Rombo provide a survey of almost 80 genomic databases.

Revision as of 21:09, 15 October 2008

This section report the temporary results of an ongoing effort aimed at extending the existing dataset. The data available must be considered raw material to be used "as is".

Contents

CMS and Wiki

MediaWiki Schema Evolution

This is an update of the schema history to the current 05/23/2008

The SVN revision of the SQL script of the MediaWiki schema is available at:

The following .tar.gz file:

contains a dump of all the revisions (194) of the schema and few simple scripts that can be used for:

  • re-download an updated set of schemas from the SVN repository
  • batch install all the schema versions in a MySQL system
  • batch remove all the schema versions from a MySQL system
  • compute a simple set of statistics


Joomla! 1.5 Schema Evolution

Joomla! is an award-winning Content Management System (CMS) that will help you build websites and other powerful online applications. Best of all, Joomla! is an open source solution that is freely available to everybody.

The SVN revision of the SQL script of the Joomla! 1.5 schema is available at:

The following .tar.gz file:

contains a dump of all the revisions (46) of the schema and few simple scripts that can be used for:

  • re-download an updated set of schemas from the SVN repository
  • batch install all the schema versions in a MySQL system
  • batch remove all the schema versions from a MySQL system
  • (todo) compute a simple set of statistics

TikiWiki Schema Evolution

TikiWiki (Tiki) is your Groupware/CMS (Content Management System) solution. Tiki has the features you need:

  • Wikis (like Wikipedia)
  • Forums (like phpBB)
  • Blogs (like WordPress)
  • Articles (like Digg)
  • Image Gallery (like Flickr)
  • Map Server (like Google Maps)
  • Link Directory (like DMOZ)
  • Multilingual (like Babel Fish)
  • Bug tracker (like Bugzilla)
  • Free source software (LGPL)

The SVN revision of the SQL script of the TikiWiki schema is available at:

The following .tar.gz file:

contains a dump of all the revisions (152) of the schema and few simple scripts that can be used for:

  • re-download an updated set of schemas from the SVN repository
  • batch install all the schema versions in a MySQL system
  • batch remove all the schema versions from a MySQL system
  • (todo) compute a simple set of statistics

XOOPS Dynamic Web CMS

XOOPS is a dynamic web content management system written in PHP for the MySQL database. Its object orientation makes it an ideal tool for developing small or large community websites, intra company and corporate portals, weblogs and much more.

Popularity: 6,559,127 download from sourceforge at 05/22/2008

The SVN revision of the SQL script of the TikiWiki schema is available at:

The following .tar.gz file:

contains a dump of all the revisions (14) of the schema and few simple scripts that can be used for:

  • re-download an updated set of schemas from the SVN repository
  • batch install all the schema versions in a MySQL system
  • batch remove all the schema versions from a MySQL system
  • (todo) compute a simple set of statistics

Coppermine Photo Gallery:

Coppermine is an easily set-up, fast, feature-rich photo gallery script with mySQL database, user management, private galleries, automatic thumbnail creation, ecard feature and a template system for easy customization to match the rest of a site.

Popularity: 4,681,872 download from sourceforge at 05/22/2008

The SVN revision of the SQL script of the TikiWiki schema is available at:

https://coppermine.svn.sourceforge.net/svnroot/coppermine/trunk/cpg1.5.x/sql/schema.sql

The following .tar.gz file:

contains a dump of all the revisions (69) of the schema and few simple scripts that can be used for:

  • re-download an updated set of schemas from the SVN repository
  • batch install all the schema versions in a MySQL system
  • batch remove all the schema versions from a MySQL system
  • (todo) compute a simple set of statistics

TYPO3 Content Management Framework

TYPO3 is an enterprise class Web CMS written in PHP/MySQL. It's designed to be extended with custom written backend modules and frontend libraries for special functionality. It has very powerful integration of image manipulation.

Popularity: 3,277,323 download from sourceforge at 05/22/2008

The SVN revision of the SQL script of the TikiWiki schema is available at:

https://typo3.svn.sourceforge.net/svnroot/typo3/TYPO3core/trunk/t3lib/stddb/tables.sql

The following .tar.gz file:

contains a dump of all the revisions (39) of the schema and few simple scripts that can be used for:

  • re-download an updated set of schemas from the SVN repository
  • batch install all the schema versions in a MySQL system
  • batch remove all the schema versions from a MySQL system
  • (todo) compute a simple set of statistics

Scientific Databases

GrainGene

The GrainGenes 2.0 is a DB for Triticeae and Avena, releasing the current schema of the DB Backend available at: http://wheat.pw.usda.gov/ggmigration/gg_schema_mysql/

An on-line interface to formulate SQL queries to the DB: http://wheat.pw.usda.gov/cgi-bin/graingenes/sql.cgi?pre=0

UCSC Genome Bioinformatics

The UCSC database is a MySQL based project. http://genome.ucsc.edu/

BioSQL

BioSQL is a joint effort between the OBF projects (BioPerl, BioJava etc) to support a shared database schema for storing sequence data. In theory, you could load a GenBank file into the database with BioPerl, then using Biopython extract this from the database as a record object with featues - and get more or less the same thing as if you had loaded the GenBank file directly as a SeqRecord using SeqIO.

This is a promising source of data for our benchmark!

SVN: http://code.open-bio.org/svnweb/index.cgi/biosql/view/biosql-schema/trunk/sql/biosqldb-mysql.sql

The schema we collect at 05 Sep. 2008 are 46 and are available here: [1]

GUS

The Genomics Unified Schema (GUS) is an extensive relational database schema and associated application framework designed to store, integrate, analyze and present functional genomics data. The GUS schema supports a wide range of data types including genomics, gene expression, transcript assemblies, proteomics and others. It emphasizes standards-based ontologies and strong-typing.

The GUS Application Framework offers an object-relational layer and a Plugin API used to rapidly create robust data loading programs for diverse data sources. The GUS distribution includes plugins for standard data sources. The GUS Web Development Kit (WDK) is a rich environment for efficiently designing sophisticated query-based websites with little programming required.

Their about page: http://www.gusdb.org/about.php The SVN: https://www.cbil.upenn.edu/svn/gus/

NCBO

The National Center for Biomedical Ontology is a consortium of leading biologists, clinicians, informaticians, and ontologists who develop innovative technology and methods allowing scientists to create, disseminate, and manage biomedical information and knowledge in machine-processable form.

In this Context they use relational DB backend.

The SVN: http://smi-protege.stanford.edu/repos/cbio/ncbo/trunk/conf/ncbo_tables.sql

Genomic DB Survey

Another relevant source is [2] where Erika De Francesco and Simona Rombo provide a survey of almost 80 genomic databases.

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