Contents

• Home
• MetaBase Proposal
• Procrastination

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• Project Page
  Places for you to contribute
• Project FTP
  Main Repository of Content

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• MetaBase
  The implementation of the MetaBase proposal

Project Overview

Introduction

Objectives

• As a basic requirement, the MetaBase will contain a list of databases, URLs and short descriptions of the most commonly used biological databases available on the WWW.
• The MetaBase should be flexible, allowing many users to contribute, update and maintain the data.
• The MetaBase should be extensible, allowing for example, scientific papers to be linked to the databases through a variety of relationships.
• The MetaBase should be 'classifiable'. That is to say that it should not contain just one fixed database classification scheme, but many. Potentially any user could create his or her own classification of databases according to any criteria, and those classifications should be available to everyone.
• The MetaBase and its user management software should be built using PHP and MySQL for flexibility, allowing a continuous growth of the range and scope of databases and database information.
• Potentially the MetaBase could be used as a source of 'genuine' meta-data for integration projects.
• The MetaBase should link into the core requirements of the BioNeeds Group, providing an up to date source of biological database information, as well as tools for gathering database usage information from the biological community.
• The MetaBase should be published in a suitable open access journal.

A classification scheme

One biological datbase classification scheme

Primary database

A database which is compised of the results of basic scientific experiments. Like a primary witness, it is a basic (first hand) source of data.

Secondary database

A database including computationally derived information from the primary data. These databases apply processing in the form of various algorithms to produce 'secondary' data from the primary data. A secondary database my link several primary databases using hyperlinks, but no serious integration effort is involved.

Ternary database

An integrated database which combines primary and or secondary datbases into a derived 'classification' database.

Middle ware

The technology for producing a ternary database should not be confused with the database iteslf. This is confusing because many middleware technologies develope a ternary database to show off the technology 'in action', and it is hard to distinguish the two. One example of this is the ECOCYC database.

Beginning

Background

Other MetaBase ideas / existing technology / Database Databases and resources (in no particular order)...
• NAR-2005 Article. M Galperin. The Molecular Biology Database Collection. Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists the databases described in Nucleic Acids Research, together with other databases of value to the biologist. Database Summaries.
• Object Interaction Technologies (busines site). Bio Database: Enczclopedia of Biological Information Objects. Extensive database links within a content type classification scheme.
• Research Project-2004. J ChenBioDab A database of 25 bioinformatics databases.
• INFOBIOGEN (business site) DBcat A database of information about bioinformatics databases.
• ECCB-2003 Poster. D Laurent. A MetaBase of biological datasources for biologists and grid systems. European Conference on Computational Biology.
• VLDB-2004 Demonstration Paper. C Halascheck. Discovering and Ranking Semantic Associations offer a Large RDF MetaBase. Conference on Very Large Data Bases.

Hosting This project is hosted at Bioinformatics.Org and it is thanks to the open policy of BiO that projects like this can exist. The MetaBase is a project of the BioNeeds Group